|
UniProtKB:Accession Number | P18188 | P12944 | P21852 | P18187 | P12943 | P21853 |
---|
Entry name | PHNL_DESFR | PHNL_DESGI | PHNL_DESVM | PHNS_DESFR | PHNS_DESGI | PHNS_DESVM |
---|
Activity | 2 H(2) + ferricytochrome c3 = 4 H(+) + ferrocytochrome c3. | 2 H(2) + ferricytochrome c3 = 4 H(+) + ferrocytochrome c3. | 2 H(2) + ferricytochrome c3 = 4 H(+) + ferrocytochrome c3. | 2 H(2) + ferricytochrome c3 = 4 H(+) + ferrocytochrome c3. | 2 H(2) + ferricytochrome c3 = 4 H(+) + ferrocytochrome c3. | 2 H(2) + ferricytochrome c3 = 4 H(+) + ferrocytochrome c3. |
---|
Subunit | Heterodimer of a large and a small subunit. | Heterodimer of a large and a small subunit. | Heterodimer of a large and a small subunit. | Heterodimer of a large and a small subunit. | Heterodimer of a large and a small subunit. | Heterodimer of a large and a small subunit. |
---|
Subcellular location | Periplasm. | Periplasm. | Periplasm. | Periplasm. | Periplasm. | Periplasm. |
---|
Cofactor | Binds 1 nickel ion per subunit. | Binds 1 nickel ion per subunit. | Nickel.,Iron. | Binds 2 4Fe-4S clusters.,Binds 1 3Fe-4S cluster. | Binds 2 4Fe-4S clusters.,Binds 1 3Fe-4S cluster. | Binds 2 4Fe-4S clusters.,Binds 1 3Fe-4S cluster. |
---|
Compound table: links to PDB-related databases & PoSSuM |
---|
| Cofactors | Substrates | Products | intermediates |
---|
KEGG-id | L00024 | L00027 | L00028 | C00282 | C02682 | C00080 | C02684 |
|
|
---|
Compound | [4Fe-4S] | [3Fe-4S] | Ni--Fe(CN)2(CO) | H2 | ferricytochrome c3 | H+ | ferrocytochrome c3 | Transition-state | Transition-state |
---|
Type | heavy metal,sulfide group | heavy metal,sulfide group | heavy metal,others | others | aromatic ring (with nitrogen atoms),carbohydrate,heavy metal,peptide/protein,sulfide group | others | aromatic ring (with nitrogen atoms),carbohydrate,heavy metal,peptide/protein,sulfide group |
|
|
---|
ChEBI | 33725
| 47402
|
| 18276
|
| 15378
|
|
|
|
---|
PubChem |
|
|
| 58838673 783
|
| 1038
|
|
|
|
---|
| | | | | | | | | | | | | | | | |
---|
1frfL |  |  |  |  |  |  |  | Unbound | Unbound | Analogue:_NI-Fe | Unbound | Unbound | | Unbound | | |
---|
1yqwQ |  |  |  |  |  |  |  | Unbound | Unbound | Bound:_NI-FCO | Unbound | Unbound | | Unbound | Transition-state-bound:PER(Ni-SU status) | |
---|
1yqwR |  |  |  |  |  |  |  | Unbound | Unbound | Bound:_NI-FCO | Unbound | Unbound | | Unbound | Transition-state-bound:PER(Ni-SU status) | |
---|
1yqwS |  |  |  |  |  |  |  | Unbound | Unbound | Bound:_NI-FCO | Unbound | Unbound | | Unbound | Transition-state-bound:PER(Ni-SU status) | |
---|
1yrqH |  |  |  |  |  |  |  | Unbound | Unbound | Bound:_NI-FCO | Unbound | Unbound | | Unbound | | |
---|
1yrqI |  |  |  |  |  |  |  | Unbound | Unbound | Bound:_NI-FCO | Unbound | Unbound | | Unbound | | |
---|
1yrqJ |  |  |  |  |  |  |  | Unbound | Unbound | Bound:_NI-FCO | Unbound | Unbound | | Unbound | | |
---|
1yrqK |  |  |  |  |  |  |  | Unbound | Unbound | Bound:_NI-FCO | Unbound | Unbound | | Unbound | | |
---|
1yrqM |  |  |  |  |  |  |  | Unbound | Unbound | Bound:_NI-FCO | Unbound | Unbound | | Unbound | | |
---|
1yrqN |  |  |  |  |  |  |  | Unbound | Unbound | Bound:_NI-FCO | Unbound | Unbound | | Unbound | | |
---|
1frvB |  |  |  |  |  |  |  | Unbound | Unbound | Analogue:_NI-FEL | Unbound | Unbound | | Unbound | | |
---|
1frvD |  |  |  |  |  |  |  | Unbound | Unbound | Analogue:_NI-FEL | Unbound | Unbound | | Unbound | | |
---|
1yq9H |  |  |  |  |  |  |  | Unbound | Unbound | Bound:_NI-FCO | Unbound | Unbound | | Unbound | Transition-state-bound:PER(Ni-A status) | |
---|
1yq9I |  |  |  |  |  |  |  | Unbound | Unbound | Bound:_NI-FCO | Unbound | Unbound | | Unbound | Transition-state-bound:PER(Ni-A status) | |
---|
2frvB |  |  |  |  |  |  |  | Unbound | Unbound | Bound:_NI-FCO | Unbound | Unbound | | Unbound | | Transition-state-bound:__O(Ni-B state) |
---|
2frvD |  |  |  |  |  |  |  | Unbound | Unbound | Bound:_NI-FCO | Unbound | Unbound | | Unbound | | Transition-state-bound:__O(Ni-B state) |
---|
2frvF |  |  |  |  |  |  |  | Unbound | Unbound | Bound:_NI-FCO | Unbound | Unbound | | Unbound | | Transition-state-bound:__O(Ni-B state) |
---|
2frvH |  |  |  |  |  |  |  | Unbound | Unbound | Bound:_NI-FCO | Unbound | Unbound | | Unbound | | Transition-state-bound:__O(Ni-B state) |
---|
2frvJ |  |  |  |  |  |  |  | Unbound | Unbound | Bound:_NI-FCO | Unbound | Unbound | | Unbound | | Transition-state-bound:__O(Ni-B state) |
---|
2frvL |  |  |  |  |  |  |  | Unbound | Unbound | Bound:_NI-FCO | Unbound | Unbound | | Unbound | | Transition-state-bound:__O(Ni-B state) |
---|
1h2aL |  |  |  |  |  |  |  | Unbound | Unbound | Analogue:NFE | Unbound | Unbound | | Unbound | | |
---|
1h2rL |  |  |  |  |  |  |  | Unbound | Unbound | Analogue:NFE | Unbound | Unbound | | Unbound | | |
---|
1ubhL |  |  |  |  |  |  |  | Unbound | Unbound | Analogue:FNE-CMO | Unbound | Unbound | | Unbound | | |
---|
1ubjL |  |  |  |  |  |  |  | Unbound | Unbound | Analogue:FNE-CMO | Unbound | Unbound | | Unbound | | |
---|
1ubkL |  |  |  |  |  |  |  | Unbound | Unbound | Analogue:FNE-CMO | Unbound | Unbound | | Unbound | | |
---|
1ublL |  |  |  |  |  |  |  | Unbound | Unbound | Analogue:FNE-CMO | Unbound | Unbound | | Unbound | | |
---|
1ubmL |  |  |  |  |  |  |  | Unbound | Unbound | Analogue:FNE | Unbound | Unbound | | Unbound | | |
---|
1uboL |  |  |  |  |  |  |  | Unbound | Unbound | Analogue:FNE-CMO | Unbound | Unbound | | Unbound | | |
---|
1ubrL |  |  |  |  |  |  |  | Unbound | Unbound | Analogue:FNE-CMO | Unbound | Unbound | | Unbound | | |
---|
1ubtL |  |  |  |  |  |  |  | Unbound | Unbound | Analogue:FNE | Unbound | Unbound | | Unbound | | |
---|
1ubuL |  |  |  |  |  |  |  | Unbound | Unbound | Analogue:FNE | Unbound | Unbound | | Unbound | | |
---|
1wuhL |  |  |  |  |  |  |  | Unbound | Unbound | Analogue:NFC | Unbound | Unbound | | Unbound | Transition-state-bound:NFC(Ni-A status) | |
---|
1wuiL |  |  |  |  |  |  |  | Unbound | Unbound | Analogue:NFC | Unbound | Unbound | | Unbound | Transition-state-bound:NFC(Ni-A status) | |
---|
1wujL |  |  |  |  |  |  |  | Unbound | Unbound | Analogue:NFO | Unbound | Unbound | | Unbound | | Transition-state-bound:NFO(Ni-B status) |
---|
1wukL |  |  |  |  |  |  |  | Unbound | Unbound | Analogue:NFO | Unbound | Unbound | | Unbound | | Transition-state-bound:NFO(oxidized status) |
---|
1wulL |  |  |  |  |  |  |  | Unbound | Unbound | Bound:NFR | Unbound | Unbound | | Unbound | | |
---|
1frfS01 |  |  |  |  |  |  |  | Bound:SF4 | Unbound | Unbound | Unbound | Unbound | | Unbound | | |
---|
1yqwA01 |  |  |  |  |  |  |  | Bound:SF4 | Unbound | Unbound | Unbound | Unbound | | Unbound | | |
---|
1yqwB01 |  |  |  |  |  |  |  | Bound:SF4 | Unbound | Unbound | Unbound | Unbound | | Unbound | | |
---|
1yqwC01 |  |  |  |  |  |  |  | Bound:SF4 | Unbound | Unbound | Unbound | Unbound | | Unbound | | |
---|
1yrqA01 |  |  |  |  |  |  |  | Bound:SF4 | Unbound | Unbound | Unbound | Unbound | | Unbound | | |
---|
1yrqB01 |  |  |  |  |  |  |  | Bound:SF4 | Unbound | Unbound | Unbound | Unbound | | Unbound | | |
---|
1yrqC01 |  |  |  |  |  |  |  | Bound:SF4 | Unbound | Unbound | Unbound | Unbound | | Unbound | | |
---|
1yrqD01 |  |  |  |  |  |  |  | Bound:SF4 | Unbound | Unbound | Unbound | Unbound | | Unbound | | |
---|
1yrqF01 |  |  |  |  |  |  |  | Bound:SF4 | Unbound | Unbound | Unbound | Unbound | | Unbound | | |
---|
1yrqG01 |  |  |  |  |  |  |  | Bound:SF4 | Unbound | Unbound | Unbound | Unbound | | Unbound | | |
---|
1frvA01 |  |  |  |  |  |  |  | Bound:SF4 | Unbound | Unbound | Unbound | Unbound | | Unbound | | |
---|
1frvC01 |  |  |  |  |  |  |  | Bound:SF4 | Unbound | Unbound | Unbound | Unbound | | Unbound | | |
---|
1yq9A01 |  |  |  |  |  |  |  | Bound:SF4 | Unbound | Unbound | Unbound | Unbound | | Unbound | | |
---|
1yq9B01 |  |  |  |  |  |  |  | Bound:SF4 | Unbound | Unbound | Unbound | Unbound | | Unbound | | |
---|
2frvA01 |  |  |  |  |  |  |  | Bound:SF4 | Unbound | Unbound | Unbound | Unbound | | Unbound | | |
---|
2frvC01 |  |  |  |  |  |  |  | Bound:SF4 | Unbound | Unbound | Unbound | Unbound | | Unbound | | |
---|
2frvE01 |  |  |  |  |  |  |  | Bound:SF4 | Unbound | Unbound | Unbound | Unbound | | Unbound | | |
---|
2frvG01 |  |  |  |  |  |  |  | Bound:SF4 | Unbound | Unbound | Unbound | Unbound | | Unbound | | |
---|
2frvI01 |  |  |  |  |  |  |  | Bound:SF4 | Unbound | Unbound | Unbound | Unbound | | Unbound | | |
---|
2frvS01 |  |  |  |  |  |  |  | Bound:SF4 | Unbound | Unbound | Unbound | Unbound | | Unbound | | |
---|
1h2aS01 |  |  |  |  |  |  |  | Bound:SF4 | Unbound | Unbound | Unbound | Unbound | | Unbound | | |
---|
1h2rS01 |  |  |  |  |  |  |  | Bound:SF4 | Unbound | Unbound | Unbound | Unbound | | Unbound | | |
---|
1ubhS01 |  |  |  |  |  |  |  | Bound:SF4 | Unbound | Unbound | Unbound | Unbound | | Unbound | | |
---|
1ubjS01 |  |  |  |  |  |  |  | Bound:SF4 | Unbound | Unbound | Unbound | Unbound | | Unbound | | |
---|
1ubkS01 |  |  |  |  |  |  |  | Bound:SF4 | Unbound | Unbound | Unbound | Unbound | | Unbound | | |
---|
1ublS01 |  |  |  |  |  |  |  | Bound:SF4 | Unbound | Unbound | Unbound | Unbound | | Unbound | | |
---|
1ubmS01 |  |  |  |  |  |  |  | Bound:SF4 | Unbound | Unbound | Unbound | Unbound | | Unbound | | |
---|
1uboS01 |  |  |  |  |  |  |  | Bound:SF4 | Unbound | Unbound | Unbound | Unbound | | Unbound | | |
---|
1ubrS01 |  |  |  |  |  |  |  | Bound:SF4 | Unbound | Unbound | Unbound | Unbound | | Unbound | | |
---|
1ubtS01 |  |  |  |  |  |  |  | Bound:SF4 | Unbound | Unbound | Unbound | Unbound | | Unbound | | |
---|
1ubuS01 |  |  |  |  |  |  |  | Bound:SF4 | Unbound | Unbound | Unbound | Unbound | | Unbound | | |
---|
1wuhS01 |  |  |  |  |  |  |  | Bound:SF4 | Unbound | Unbound | Unbound | Unbound | | Unbound | | |
---|
1wuiS01 |  |  |  |  |  |  |  | Bound:SF4 | Unbound | Unbound | Unbound | Unbound | | Unbound | | |
---|
1wujS01 |  |  |  |  |  |  |  | Bound:SF4 | Unbound | Unbound | Unbound | Unbound | | Unbound | | |
---|
1wukS01 |  |  |  |  |  |  |  | Bound:SF4 | Unbound | Unbound | Unbound | Unbound | | Unbound | | |
---|
1wulS01 |  |  |  |  |  |  |  | Bound:SF4 | Unbound | Unbound | Unbound | Unbound | | Unbound | | |
---|
1frfS02 |  |  |  |  |  |  |  | Bound:SF4 | Bound:F3S | Unbound | Unbound | Unbound | | Unbound | | |
---|
1yqwA02 |  |  |  |  |  |  |  | Bound:SF4 | Bound:F3S | Unbound | Unbound | Unbound | | Unbound | | |
---|
1yqwB02 |  |  |  |  |  |  |  | Bound:SF4 | Bound:F3S | Unbound | Unbound | Unbound | | Unbound | | |
---|
1yqwC02 |  |  |  |  |  |  |  | Bound:SF4 | Bound:F3S | Unbound | Unbound | Unbound | | Unbound | | |
---|
1yrqA02 |  |  |  |  |  |  |  | Bound:SF4 | Bound:F3S | Unbound | Unbound | Unbound | | Unbound | | |
---|
1yrqB02 |  |  |  |  |  |  |  | Bound:SF4 | Bound:F3S | Unbound | Unbound | Unbound | | Unbound | | |
---|
1yrqC02 |  |  |  |  |  |  |  | Bound:SF4 | Bound:F3S | Unbound | Unbound | Unbound | | Unbound | | |
---|
1yrqD02 |  |  |  |  |  |  |  | Bound:SF4 | Bound:F3S | Unbound | Unbound | Unbound | | Unbound | | |
---|
1yrqF02 |  |  |  |  |  |  |  | Bound:SF4 | Bound:F3S | Unbound | Unbound | Unbound | | Unbound | | |
---|
1yrqG02 |  |  |  |  |  |  |  | Bound:SF4 | Bound:F3S | Unbound | Unbound | Unbound | | Unbound | | |
---|
1frvA02 |  |  |  |  |  |  |  | Bound:SF4 | Bound:F3S | Unbound | Unbound | Unbound | | Unbound | | |
---|
1frvC02 |  |  |  |  |  |  |  | Bound:SF4 | Bound:F3S | Unbound | Unbound | Unbound | | Unbound | | |
---|
1yq9A02 |  |  |  |  |  |  |  | Bound:SF4 | Bound:F3S | Unbound | Unbound | Unbound | | Unbound | | |
---|
1yq9B02 |  |  |  |  |  |  |  | Bound:SF4 | Bound:F3S | Unbound | Unbound | Unbound | | Unbound | | |
---|
2frvA02 |  |  |  |  |  |  |  | Bound:SF4 | Bound:F3S | Unbound | Unbound | Unbound | | Unbound | | |
---|
2frvC02 |  |  |  |  |  |  |  | Bound:SF4 | Bound:F3S | Unbound | Unbound | Unbound | | Unbound | | |
---|
2frvE02 |  |  |  |  |  |  |  | Bound:SF4 | Bound:F3S | Unbound | Unbound | Unbound | | Unbound | | |
---|
2frvG02 |  |  |  |  |  |  |  | Bound:SF4 | Bound:F3S | Unbound | Unbound | Unbound | | Unbound | | |
---|
2frvI02 |  |  |  |  |  |  |  | Bound:SF4 | Bound:F3S | Unbound | Unbound | Unbound | | Unbound | | |
---|
2frvS02 |  |  |  |  |  |  |  | Bound:SF4 | Bound:F3S | Unbound | Unbound | Unbound | | Unbound | | |
---|
1h2aS02 |  |  |  |  |  |  |  | Bound:SF4 | Bound:F3S | Unbound | Unbound | Unbound | | Unbound | | |
---|
1h2rS02 |  |  |  |  |  |  |  | Bound:SF4 | Bound:F3S | Unbound | Unbound | Unbound | | Unbound | | |
---|
1ubhS02 |  |  |  |  |  |  |  | Bound:SF4 | Bound:F3S | Unbound | Unbound | Unbound | | Unbound | | |
---|
1ubjS02 |  |  |  |  |  |  |  | Bound:SF4 | Bound:F3S | Unbound | Unbound | Unbound | | Unbound | | |
---|
1ubkS02 |  |  |  |  |  |  |  | Bound:SF4 | Bound:F3S | Unbound | Unbound | Unbound | | Unbound | | |
---|
1ublS02 |  |  |  |  |  |  |  | Bound:SF4 | Bound:F3S | Unbound | Unbound | Unbound | | Unbound | | |
---|
1ubmS02 |  |  |  |  |  |  |  | Bound:SF4 | Bound:F3S | Unbound | Unbound | Unbound | | Unbound | | |
---|
1uboS02 |  |  |  |  |  |  |  | Bound:SF4 | Bound:F3S | Unbound | Unbound | Unbound | | Unbound | | |
---|
1ubrS02 |  |  |  |  |  |  |  | Bound:SF4 | Bound:F3S | Unbound | Unbound | Unbound | | Unbound | | |
---|
1ubtS02 |  |  |  |  |  |  |  | Bound:SF4 | Bound:F3S | Unbound | Unbound | Unbound | | Unbound | | |
---|
1ubuS02 |  |  |  |  |  |  |  | Bound:SF4 | Bound:F3S | Unbound | Unbound | Unbound | | Unbound | | |
---|
1wuhS02 |  |  |  |  |  |  |  | Bound:SF4 | Bound:F3S | Unbound | Unbound | Unbound | | Unbound | | |
---|
1wuiS02 |  |  |  |  |  |  |  | Bound:SF4 | Bound:F3S | Unbound | Unbound | Unbound | | Unbound | | |
---|
1wujS02 |  |  |  |  |  |  |  | Bound:SF4 | Bound:F3S | Unbound | Unbound | Unbound | | Unbound | | |
---|
1wukS02 |  |  |  |  |  |  |  | Bound:SF4 | Bound:F3S | Unbound | Unbound | Unbound | | Unbound | | |
---|
1wulS02 |  |  |  |  |  |  |  | Bound:SF4 | Bound:F3S | Unbound | Unbound | Unbound | | Unbound | | |
---|
References for Catalytic Mechanism | References | Sections | No. of steps in catalysis |
---|
[7] | p.987-988 |
| [9] | Fig.5, Fig.9, Fig.10, p.14346-14348 |
| [10] | p.825-828 |
| [12] | Fig.5, p.582-585 |
| [14] | Fig.7, p.12995-12996 |
| [16] | Fig.4, p.7850-7854 |
| [17] | Fig.2, p.664-665 |
| [20] | p.1675-1677 |
| [21] | p.399-400 |
| [22] | p.11628-11630 |
| [23] | p.298 |
| [24] | p.3336-3337 |
| [25] | Fig.3, p.553-554 |
| [31] | Scheme 1, Fig.2, p.6202-6203 |
| [32] | Scheme 1, p.5840 | 2 | [33] | Table 1, p.469-472 |
| [34] | p.457-458 |
| [35] | p.71-73, p.77-80 |
| [36] | p.156-157, p.158-159 |
| [37] | Fig.4, p.4432-4434 |
| [38] | Fig.7, p.11634-11635 |
| [42] | Fig.8, p.92 |
| [44] | Fig.2, p.134-138 |
| [45] | p.10511-10513 |
| [47] | Fig.1, p.641-642 |
| [48] | Fig3., Fig.4, p.872-875 |
| [50] | Fig.6, p.246-248 |
| [51] | Fig.3, p.1637-1640 |
|
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Title | Characterization of the nickel-iron periplasmic hydrogenase from Desulfovibrio fructosovorans. |
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Related UniProtKB | P18187,P18188 |
---|
[4] |
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PubMed ID | 1316088 |
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Journal | Anal Chem |
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Year | 1992 |
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Volume | 64 |
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Journal | FEMS Microbiol Rev |
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Year | 1992 |
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Volume | 8 |
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Title | Structure-function relationships among the nickel-containing hydrogenases. |
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Pages | 302-8 |
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---|
Title | Characterization of D. desulfuricans (ATCC 27774) [NiFe] hydrogenase EPR and redox properties of the native and the dihydrogen reacted states. |
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Journal | Eur J Biochem |
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Year | 1993 |
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Volume | 217 |
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Pages | 981-9 |
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---|
Title | Voltammetric studies of the catalytic electron-transfer process between the Desulfovibrio gigas hydrogenase and small proteins isolated from the same genus. |
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[8] |
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PubMed ID | 8501043 |
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Journal | J Bacteriol |
---|
Year | 1993 |
---|
Volume | 175 |
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Pages | 3388-93 |
---|
Authors | Rousset M, Dermoun Z, Wall JD, Belaich JP |
---|
Title | Analysis of the periplasmic [NiFe] hydrogenase transcription unit from Desulfovibrio fructosovorans. |
---|
[9] |
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PubMed ID | 7947844 |
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Journal | Biochemistry |
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Year | 1994 |
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Volume | 33 |
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Pages | 14339-50 |
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Authors | Roberts LM, Lindahl PA |
---|
Title | Analysis of oxidative titrations of Desulfovibrio gigas hydrogenase; implications for the catalytic mechanism. |
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[10] |
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PubMed ID | 8174562 |
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[11] |
---|
PubMed ID | 7718585 |
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Journal | Biochemistry |
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Year | 1995 |
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Pages | 4781-90 |
---|
Authors | Guigliarelli B, More C, Fournel A, Asso M, Hatchikian EC, Williams R, Cammack R, Bertrand P |
---|
Title | Structural organization of the Ni and (4Fe-4S) centers in the active form of Desulfovibrio gigas hydrogenase. Analysis of the magnetic interactions by electron paramagnetic resonance spectroscopy. |
---|
[12] |
---|
Comments | X-RAY CRYSTALLOGRAPHY (2.85 ANGSTROMS). |
---|
PubMed ID | 7854413 |
---|
Journal | Nature |
---|
Year | 1995 |
---|
Volume | 373 |
---|
Pages | 580-7 |
---|
Authors | Volbeda A, Charon MH, Piras C, Hatchikian EC, Frey M, Fontecilla-Camps JC |
---|
Title | Crystal structure of the nickel-iron hydrogenase from Desulfovibrio gigas. |
---|
Related PDB | 1frv |
---|
Related UniProtKB | P12943,P12944 |
---|
[13] |
---|
PubMed ID | 8973216 |
---|
Journal | Biochemistry |
---|
Year | 1996 |
---|
Volume | 35 |
---|
Pages | 16399-406 |
---|
Authors | Dole F, Medina M, More C, Cammack R, Bertrand P, Guigliarelli B |
---|
Title | Spin-spin interactions between the Ni site and the [4Fe-4S] centers as a probe of light-induced structural changes in active Desulfovibrio gigas hydrogenase. |
---|
[14] |
---|
Comments | X-ray crystallography |
---|
Journal | J Am Chem Soc |
---|
Year | 1996 |
---|
Volume | 118 |
---|
Pages | 12989-96 |
---|
Authors | Volbeda A, Garcin E, Piras C, de Lacey A L, Fernandez VM, Hatchikian EC, Frey M, Fontecilla-Camps JC |
---|
Title | Structure of the [NiFe] Hydrogenase Active Site: Evidence for Biologically Uncommon Fe Ligands. |
---|
Related PDB | 2frv |
---|
[15] |
---|
PubMed ID | 8605619 |
---|
Journal | Nat Struct Biol |
---|
Year | 1996 |
---|
Volume | 3 |
---|
Pages | 213-7 |
---|
Authors | Collman JP |
---|
Title | Coupling H2 to electron transfer. |
---|
[16] |
---|
PubMed ID | 9201928 |
---|
Journal | Biochemistry |
---|
Year | 1997 |
---|
Volume | 36 |
---|
Pages | 7847-54 |
---|
Authors | Dole F, Fournel A, Magro V, Hatchikian EC, Bertrand P, Guigliarelli B |
---|
Title | Nature and electronic structure of the Ni-X dinuclear center of Desulfovibrio gigas hydrogenase. Implications for the enzymatic mechanism. |
---|
[17] |
---|
PubMed ID | 9479448 |
---|
Journal | Biochimie |
---|
Year | 1997 |
---|
Volume | 79 |
---|
Pages | 661-6 |
---|
Authors | Fontecilla-Camps JC, Frey M, Garcin E, Hatchikian C, Montet Y, Piras C, Vernede X, Volbeda A |
---|
Title | Hydrogenase: a hydrogen-metabolizing enzyme. What do the crystal structures tell us about its mode of action? |
---|
[18] |
---|
PubMed ID | 9228943 |
---|
Journal | Nat Struct Biol |
---|
Year | 1997 |
---|
Volume | 4 |
---|
Pages | 523-6 |
---|
Authors | Montet Y, Amara P, Volbeda A, Vernede X, Hatchikian EC, Field MJ, Frey M, Fontecilla-Camps JC |
---|
Title | Gas access to the active site of Ni-Fe hydrogenases probed by X-ray crystallography and molecular dynamics. |
---|
[19] |
---|
PubMed ID | 8990114 |
---|
Journal | Nature |
---|
Year | 1997 |
---|
Volume | 385 |
---|
Pages | 126 |
---|
Authors | Happe RP, Roseboom W, Pierik AJ, Albracht SP, Bagley KA |
---|
Title | Biological activation of hydrogen. |
---|
[20] |
---|
Comments | X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 19-552. |
---|
PubMed ID | 9438867 |
---|
Journal | Structure |
---|
Year | 1997 |
---|
Volume | 5 |
---|
Pages | 1671-80 |
---|
Authors | Higuchi Y, Yagi T, Yasuoka N |
---|
Title | Unusual ligand structure in Ni-Fe active center and an additional Mg site in hydrogenase revealed by high resolution X-ray structure analysis. |
---|
Related PDB | 1h2a |
---|
Related UniProtKB | P21852,P21853 |
---|
[21] |
---|
PubMed ID | 9765886 |
---|
Journal | Biochem Soc Trans |
---|
Year | 1998 |
---|
Volume | 26 |
---|
Pages | 396-401 |
---|
Authors | Garcin E, Montet Y, Volbeda A, Hatchikian C, Frey M, Fontecilla-Camps JC |
---|
Title | Structural bases for the catalytic mechanism of [NiFe] hydrogenases. |
---|
[22] |
---|
Comments | X-ray Diffraction |
---|
PubMed ID | 9751716 |
---|
Journal | Proc Natl Acad Sci U S A |
---|
Year | 1998 |
---|
Volume | 95 |
---|
Pages | 11625-30 |
---|
Authors | Rousset M, Montet Y, Guigliarelli B, Forget N, Asso M, Bertrand P, Fontecilla-Camps JC, Hatchikian EC |
---|
Title | [3Fe-4S] to [4Fe-4S] cluster conversion in Desulfovibrio fructosovorans [NiFe] hydrogenase by site-directed mutagenesis. |
---|
Related PDB | 1frf |
---|
[23] |
---|
PubMed ID | 10049702 |
---|
Journal | Biochem Biophys Res Commun |
---|
Year | 1999 |
---|
Volume | 255 |
---|
Pages | 295-9 |
---|
Authors | Higuchi Y, Yagi T |
---|
Title | Liberation of hydrogen sulfide during the catalytic action of Desulfovibrio hydrogenase under the atmosphere of hydrogen. |
---|
[24] |
---|
PubMed ID | 9920874 |
---|
Journal | J Biol Chem |
---|
Year | 1999 |
---|
Volume | 274 |
---|
Pages | 3331-7 |
---|
Authors | Pierik AJ, Roseboom W, Happe RP, Bagley KA, Albracht SP |
---|
Title | Carbon monoxide and cyanide as intrinsic ligands to iron in the active site of [NiFe]-hydrogenases. NiFe(CN)2CO, Biology's way to activate H2. |
---|
[25] |
---|
Comments | X-RAY CRYSTALLOGRAPHY (1.4 ANGSTROMS). |
---|
PubMed ID | 10378274 |
---|
Journal | Structure Fold Des |
---|
Year | 1999 |
---|
Volume | 7 |
---|
Pages | 549-56 |
---|
Authors | Higuchi Y, Ogata H, Miki K, Yasuoka N, Yagi T |
---|
Title | Removal of the bridging ligand atom at the Ni-Fe active site of [NiFe] hydrogenase upon reduction with H2, as revealed by X-ray structure analysis at 1.4 A resolution. |
---|
Related PDB | 1h2r |
---|
Related UniProtKB | P21852,P21853 |
---|
[26] |
---|
PubMed ID | 11128995 |
---|
Journal | J Biol Inorg Chem |
---|
Year | 2000 |
---|
Volume | 5 |
---|
Pages | 682-91 |
---|
Authors | Bertrand P, Dole F, Asso M, Guigliarelli B |
---|
Title | Is there a rate-limiting step in the catalytic cycle of Ni-Fe hydrogenases? |
---|
[27] |
---|
PubMed ID | 10766434 |
---|
Journal | J Biol Inorg Chem |
---|
Year | 2000 |
---|
Volume | 5 |
---|
Pages | 36-44 |
---|
Authors | Trofanchuk O, Stein M, Gessner C, Lendzian F, Higuchi Y, Lubitz W |
---|
Title | Single crystal EPR studies of the oxidized active site of [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F. |
---|
[28] |
---|
PubMed ID | 11001090 |
---|
Journal | J Inorg Biochem |
---|
Year | 2000 |
---|
Volume | 80 |
---|
Pages | 205-11 |
---|
Authors | Higuchi Y, Toujou F, Tsukamoto K, Yagi T |
---|
Title | The presence of a SO molecule in [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki as detected by mass spectrometry. |
---|
[29] |
---|
PubMed ID | 11170458 |
---|
Journal | Biochemistry |
---|
Year | 2001 |
---|
Volume | 40 |
---|
Pages | 1317-24 |
---|
Authors | Fritz G, Griesshaber D, Seth O, Kroneck PM |
---|
Title | Nonaheme cytochrome c, a new physiological electron acceptor for [Ni,Fe] hydrogenase in the sulfate-reducing bacterium Desulfovibrio desulfuricans Essex: primary sequence, molecular parameters, and redox properties.. |
---|
[30] |
---|
PubMed ID | 11195380 |
---|
Journal | Inorg Chem |
---|
Year | 2001 |
---|
Volume | 40 |
---|
Pages | 18-24 |
---|
Authors | Li S, Hall MB |
---|
Title | Modeling the active sites of metalloenzymes. 4. Predictions of the unready states of [NiFe] Desulfovibrio gigas hydrogenase from density functional theory. |
---|
[31] |
---|
PubMed ID | 11703120 |
---|
Journal | Inorg Chem |
---|
Year | 2001 |
---|
Volume | 40 |
---|
Pages | 6201-3 |
---|
Authors | Niu S, Hall MB |
---|
Title | Modeling the active sites in metalloenzymes 5. The heterolytic bond cleavage of H(2) in the [NiFe] hydrogenase of desulfovibrio gigas by a nucleophilic addition mechanism. |
---|
[32] |
---|
PubMed ID | 11403633 |
---|
Journal | J Am Chem Soc |
---|
Year | 2001 |
---|
Volume | 123 |
---|
Pages | 5839-40 |
---|
Authors | Stein M, van Lenthe E, Baerends EJ, Lubitz W |
---|
Title | Relativistic DFT calculations of the paramagnetic intermediates of [NiFe] hydrogenase. Implications for the enzymatic mechanism. |
---|
[33] |
---|
PubMed ID | 11372206 |
---|
Journal | J Biol Inorg Chem |
---|
Year | 2001 |
---|
Volume | 6 |
---|
Pages | 467-73 |
---|
Authors | Fan HJ, Hall MB |
---|
Title | Recent theoretical predictions of the active site for the observed forms in the catalytic cycle of Ni-Fe hydrogenase. |
---|
[34] |
---|
PubMed ID | 11372204 |
---|
Journal | J Biol Inorg Chem |
---|
Year | 2001 |
---|
Volume | 6 |
---|
Pages | 453-9 |
---|
Authors | Maroney MJ, Bryngelson PA |
---|
Title | Spectroscopic and model studies of the Ni-Fe hydrogenase reaction mechanism. |
---|
[35] |
---|
PubMed ID | 11191224 |
---|
Journal | J Biol Inorg Chem |
---|
Year | 2001 |
---|
Volume | 6 |
---|
Pages | 63-81 |
---|
Authors | Matias PM, Soares CM, Saraiva LM, Coelho R, Morais J, Le Gall J, Carrondo MA |
---|
Title | [NiFe] hydrogenase from Desulfovibrio desulfuricans ATCC 27774: gene sequencing, three-dimensional structure determination and refinement at 1.8 A and modelling studies of its interaction with the tetrahaem cytochrome c3. |
---|
[36] |
---|
PubMed ID | 11921392 |
---|
Journal | Chembiochem |
---|
Year | 2002 |
---|
Volume | 3 |
---|
Pages | 153-60 |
---|
Authors | Frey M |
---|
Title | Hydrogenases: hydrogen-activating enzymes. |
---|
[37] |
---|
PubMed ID | 12184759 |
---|
Journal | Inorg Chem |
---|
Year | 2002 |
---|
Volume | 41 |
---|
Pages | 4424-34 |
---|
Authors | Stadler C, de Lacey AL, Montet Y, Volbeda A, Fontecilla-Camps JC, Conesa JC, Fernandez VM |
---|
Title | Density functional calculations for modeling the active site of nickel-iron hydrogenases. 2. Predictions for the unready and ready States and the corresponding activation processes. |
---|
[38] |
---|
PubMed ID | 11782180 |
---|
Journal | J Am Chem Soc |
---|
Year | 2002 |
---|
Volume | 124 |
---|
Pages | 281-6 |
---|
Authors | Carepo M, Tierney DL, Brondino CD, Yang TC, Pamplona A, Telser J, Moura I, Moura JJ, Hoffman BM |
---|
Title | 17O ENDOR detection of a solvent-derived Ni-(OH(x))-Fe bridge that is lost upon activation of the hydrogenase from Desulfovibrio gigas. |
---|
[39] |
---|
Comments | X-ray Diffraction |
---|
PubMed ID | 12296727 |
---|
Journal | J Am Chem Soc |
---|
Year | 2002 |
---|
Volume | 124 |
---|
Pages | 11628-35 |
---|
Authors | Ogata H, Mizoguchi Y, Mizuno N, Miki K, Adachi S, Yasuoka N, Yagi T, Yamauchi O, Hirota S, Higuchi Y |
---|
Title | Structural studies of the carbon monoxide complex of [NiFe]hydrogenase from Desulfovibrio vulgaris Miyazaki F: suggestion for the initial activation site for dihydrogen. |
---|
Related PDB | 1ubh,1ubj,1ubk,1ubl,1ubm,1ubo,1ubr,1ubt |
---|
[40] |
---|
PubMed ID | 11935356 |
---|
Journal | J Biol Inorg Chem |
---|
Year | 2002 |
---|
Volume | 7 |
---|
Pages | 318-26 |
---|
Authors | De Lacey AL, Stadler C, Fernandez VM, Hatchikian EC, Fan HJ, Li S, Hall MB |
---|
Title | IR spectroelectrochemical study of the binding of carbon monoxide to the active site of Desulfovibrio fructosovorans Ni-Fe hydrogenase. |
---|
[41] |
---|
PubMed ID | 11862554 |
---|
Journal | J Biol Inorg Chem |
---|
Year | 2002 |
---|
Volume | 7 |
---|
Pages | 177-94 |
---|
Authors | Muller A, Tscherny I, Kappl R, Hatchikian C, Huttermann J, Cammack R |
---|
Title | Hydrogenases in the "active" state: determination of g-matrix axes and electron spin distribution at the active site by 1H ENDOR spectroscopy. |
---|
[42] |
---|
PubMed ID | 12515509 |
---|
Journal | J Am Chem Soc |
---|
Year | 2003 |
---|
Volume | 125 |
---|
Pages |
|
---|
Authors | Foerster S, Stein M, Brecht M, Ogata H, Higuchi Y, Lubitz W |
---|
Title | Single crystal EPR studies of the reduced active site of [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F. |
---|
[43] |
---|
PubMed ID | 12459907 |
---|
Journal | J Biol Inorg Chem |
---|
Year | 2003 |
---|
Volume | 8 |
---|
Pages | 129-34 |
---|
Authors | DeLacey AL, Fernandez VM, Rousset M, Cavazza C, Hatchikian EC |
---|
Title | Spectroscopic and kinetic characterization of active site mutants of Desulfovibrio fructosovoransNi-Fe hydrogenase. |
---|
[44] |
---|
PubMed ID | 15062773 |
---|
Journal | Curr Opin Chem Biol |
---|
Year | 2004 |
---|
Volume | 8 |
---|
Pages | 133-40 |
---|
Authors | Armstrong FA |
---|
Title | Hydrogenases: active site puzzles and progress. |
---|
[45] |
---|
PubMed ID | 14688251 |
---|
Journal | J Biol Chem |
---|
Year | 2004 |
---|
Volume | 279 |
---|
Pages | 10508-13 |
---|
Authors | Dementin S, Burlat B, De Lacey AL, Pardo A, Adryanczyk-Perrier G, Guigliarelli B, Fernandez VM, Rousset M |
---|
Title | A glutamate is the essential proton transfer gate during the catalytic cycle of the [NiFe] hydrogenase. |
---|
[46] |
---|
PubMed ID | 15365900 |
---|
Journal | J Biol Inorg Chem |
---|
Year | 2004 |
---|
Volume | 9 |
---|
Pages | 873-84 |
---|
Authors | Bruschi M, De Gioia L, Zampella G, Reiher M, Fantucci P, Stein M |
---|
Title | A theoretical study of spin states in Ni-S4 complexes and models of the [NiFe] hydrogenase active site. |
---|
[47] |
---|
PubMed ID | 15175937 |
---|
Journal | J Biol Inorg Chem |
---|
Year | 2004 |
---|
Volume | 9 |
---|
Pages | 636-42 |
---|
Authors | De Lacey AL, Pardo A, Fernandez VM, Dementin S, Adryanczyk-Perrier G, Hatchikian EC, Rousset M |
---|
Title | FTIR spectroelectrochemical study of the activation and inactivation processes of [NiFe] hydrogenases: effects of solvent isotope replacement and site-directed mutagenesis. |
---|
[48] |
---|
PubMed ID | 15134933 |
---|
Journal | J Inorg Biochem |
---|
Year | 2004 |
---|
Volume | 98 |
---|
Pages | 862-77 |
---|
Authors | Stein M, Lubitz W |
---|
Title | Relativistic DFT calculation of the reaction cycle intermediates of [NiFe] hydrogenase: a contribution to understanding the enzymatic mechanism. |
---|
[49] |
---|
PubMed ID | 15667250 |
---|
Journal | Biochem Soc Trans |
---|
Year | 2005 |
---|
Volume | 33 |
---|
Pages | 7-11 |
---|
Authors | van Gastel M, Fichtner C, Neese F, Lubitz W |
---|
Title | EPR experiments to elucidate the structure of the ready and unready states of the [NiFe] hydrogenase of Desulfovibrio vulgaris Miyazaki F. |
---|
[50] |
---|
PubMed ID | 15803334 |
---|
Journal | J Biol Inorg Chem |
---|
Year | 2005 |
---|
Volume | 10 |
---|
Pages | 239-49 |
---|
Authors | Volbeda A, Martin L, Cavazza C, Matho M, Faber BW, Roseboom W, Albracht SP, Garcin E, Rousset M, Fontecilla-Camps JC |
---|
Title | Structural differences between the ready and unready oxidized states of [NiFe] hydrogenases. |
---|
Related PDB | 1yq9,1yqw,1yrq |
---|
[51] |
---|
PubMed ID | 16271886 |
---|
Journal | Structure |
---|
Year | 2005 |
---|
Volume | 13 |
---|
Pages | 1635-42 |
---|
Authors | Ogata H, Hirota S, Nakahara A, Komori H, Shibata N, Kato T, Kano K, Higuchi Y |
---|
Title | Activation process of [NiFe] hydrogenase elucidated by high-resolution X-Ray analyses: conversion of the ready to the unready state. |
---|
Related PDB | 1wuh,1wui,1wuj,1wuk,1wul |
---|
comments | This enzyme catalyzes the following reactions: (A) Electron transfer from heme iron of cytochrome c3 to [4Fe-4S] cluster-2 located on the surface of small subunit: (A1) His184 (1frf) bound to Fe4-S4, is exposed to the surface of the S subunit. This residue might interact with cytochrome c3, for electron transfer (see [12]). (B) Electron transfer from [4Fe-4S] cluster-2 to [3Fe-4S] cluster: (B1) Indirect transfer from [4Fe-4S] cluster-2 to [3Fe-4S] cluster through Cys218 (bound to [4Fe-4S] cluster-2) and Cys245 (bound to [3Fe-4S]) (see [12]). (C) Electron transfer from [3Fe-4S] cluster to [4Fe-4S] cluster-1: (C1) Indirect transfer from [3Fe-4S] cluster to [4Fe-4S] cluster-1 through Cys248 (bound to [3Fe-4S]) and Cys147 (bound to [4Fe-4S] cluster-1) (see [12]). (D) Electron transfer from [4Fe-4S] cluster-1 to the Nickel-Iron cluster (reaction center): (D1) Indirect transfer from [4Fe-4S] cluster-1 to Nickel-Iron cluster through Cys17 (bound to [4Fe-4S] cluster-1) and Cys72 of Large subunit (bound to Nickel-Iron cluster) (see [12]). (E) Hydrogenation at the Nickel-Iron cluster (reaction center):
|
created | updated |
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2005-08-12 | 2009-02-26 |
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