DB code: D00604

RLCP classification 8.131.1241100.8201 : Isomerization
8.113.1441400.8202 : Isomerization
9.5010.536200.8010 : Hydride transfer
CATH domain 3.40.50.720 : Rossmann fold Catalytic domain
3.90.25.10 : UDP-galactose 4-epimerase; domain 1 Catalytic domain
E.C. 1.1.1.271
CSA 1e7q
M-CSA 1e7q
MACiE M0227

CATH domain Related DB codes (homologues)
3.40.50.720 : Rossmann fold S00543 S00551 S00552 S00553 S00602 S00604 S00605 S00608 S00610 S00625 S00319 S00328 S00329 S00330 S00331 S00332 D00456 D00457 D00458 S00324 S00320 S00325 S00326 S00327 D00459 S00335 S00336 S00334 T00219 S00339 D00513 D00001 D00002 D00003 D00005 D00007 D00008 D00010 D00012 D00017 D00018 D00023 D00027 D00028 D00031 D00032 D00033 D00034 D00035 D00037 D00048 D00071 D00476 D00481 D00482 D00490 D00492 D00494 D00545 D00601 D00603 D00605 D00615 D00845 D00857 D00858 M00161 M00171 M00210 T00002 T00010 T00011 T00015 T00227 T00247 T00408 T00414 D00827 D00262 D00274 D00275 M00035 T00109
3.90.25.10 : UDP-galactose 4-epimerase; domain 1 D00513 D00601 D00262 D00274 D00275

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P32055 GDP-L-fucose synthetase
EC 1.1.1.271
GDP-4-keto-6-deoxy-D-mannose-3,5-epimerase-4-reductase
NP_416556.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_490294.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PF01370 (Epimerase)
[Graphical View]

KEGG enzyme name
GDP-L-fucose synthase
GDP-4-keto-6-deoxy-D-mannose-3,5-epimerase-4-reductase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P32055 FCL_ECOLI GDP-L-fucose + NADP(+) = GDP-4-dehydro-6-deoxy-D-mannose + NADPH. Homodimer. Cytoplasm.

KEGG Pathways
Map code Pathways E.C.
MAP00051 Fructose and mannose metabolism
MAP00520 Amino sugar and nucleotide sugar metabolism

Compound table
Substrates Products Intermediates
KEGG-id C01222 C00005 C00080 C00325 C00006 I00097 I00098 I00099 I00100
E.C.
Compound GDP-4-dehydro-6-deoxy-D-mannose NADPH H+ GDP-L-fucose NADP+ GDP-6-deoxy-3,4-ene-mannose GDP-6-deoxy-4-dehydro-altrose GDP-6-deoxy-4,5-ene-altrose GDP-6-deoxy-4-dehydro-L-galactose
Type amide group,amine group,carbohydrate,nucleotide amide group,amine group,nucleotide others amide group,amine group,carbohydrate,nucleotide amide group,amine group,nucleotide
ChEBI 16955
16474
15378
13332
18009
PubChem 439446
5884
1038
10918995
5886
1bsvA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:NDP Unbound Unbound Unbound Unbound Unbound Unbound
1bwsA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:NDP Unbound Unbound Unbound Unbound Unbound Unbound
1e6uA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Bound:NAP Unbound Unbound Unbound Unbound
1e7qA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Bound:NAP Unbound Unbound Unbound Unbound
1e7rA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Bound:NAP Unbound Unbound Unbound Unbound
1e7sA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Bound:NAP Unbound Unbound Unbound Unbound
1fxsA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Bound:NAP Unbound Unbound Unbound Unbound
1gfsA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1bsvA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1bwsA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1e6uA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1e7qA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1e7rA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1e7sA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1fxsA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1gfsA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [5], [7], [9], [13], [14]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1bsvA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 107;CYS 109;TYR 136;LYS 140
1bwsA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 107;CYS 109;TYR 136;LYS 140
1e6uA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 107;CYS 109;TYR 136;LYS 140
1e7qA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ;CYS 109;TYR 136;LYS 140 mutant S107A
1e7rA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 107;CYS 109;;LYS 140 mutant Y136E
1e7sA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 107;CYS 109;TYR 136; mutant K140R
1fxsA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 107;CYS 109;TYR 136;LYS 140
1gfsA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 107;CYS 109;TYR 136;LYS 140
1bsvA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 179
1bwsA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 179
1e6uA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 179
1e7qA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 179
1e7rA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 179
1e7sA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 179
1fxsA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 179
1gfsA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 179

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[5]
Fig.7, p.1607-1608
[7]
p.84-87
[9]
p.1658-1659
[13]
Scheme 12, p.9833-9834
[14]
Fig.8, p.17598-17599

References
[1]
Resource
Comments
Medline ID
PubMed ID 7742302
Journal Biochemistry
Year 1995
Volume 34
Pages 6003-13
Authors Jornvall H, Persson B, Krook M, Atrian S, Gonzalez-Duarte R, Jeffery J, Ghosh D
Title Short-chain dehydrogenases/reductases (SDR).
Related PDB
Related UniProtKB
[2]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) IN COMPLEX WITH NADPH.
Medline ID
PubMed ID 8805511
Journal Structure
Year 1996
Volume 4
Pages 33-45
Authors Tanaka N, Nonaka T, Nakanishi M, Deyashiki Y, Hara A, Mitsui Y
Title Crystal structure of the ternary complex of mouse lung carbonyl reductase at 1.8 A resolution: the structural origin of coenzyme specificity in the short-chain dehydrogenase/reductase family.
Related PDB 1cyd
Related UniProtKB P08074
[3]
Resource
Comments X-RAY CRYSTALLOGRAPHY
Medline ID
PubMed ID 9271498
Journal Biochemistry
Year 1997
Volume 36
Pages 10675-84
Authors Liu Y, Thoden JB, Kim J, Berger E, Gulick AM, Ruzicka FJ, Holden HM, Frey PA
Title Mechanistic roles of tyrosine 149 and serine 124 in UDP-galactose 4-epimerase from Escherichia coli.
Related PDB 1kvu
Related UniProtKB
[4]
Resource
Comments X-RAY CRYSTALLOGRAPHY
Medline ID
PubMed ID 9817848
Journal Structure
Year 1998
Volume 6
Pages 1453-65
Authors Rizzi M, Tonetti M, Vigevani P, Sturla L, Bisso A, Flora AD, Bordo D, Bolognesi M
Title GDP-4-keto-6-deoxy-D-mannose epimerase/reductase from Escherichia coli, a key enzyme in the biosynthesis of GDP-L-fucose, displays the structural characteristics of the RED protein homology superfamily.
Related PDB 1bws
Related UniProtKB
[5]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS)
Medline ID
PubMed ID 9862812
Journal Structure
Year 1998
Volume 6
Pages 1601-12
Authors Somers WS, Stahl ML, Sullivan FX
Title GDP-fucose synthetase from Escherichia coli: structure of a unique member of the short-chain dehydrogenase/reductase family that catalyzes two distinct reactions at the same active site.
Related PDB 1bsv 1fxs 1gfs
Related UniProtKB P32055
[6]
Resource
Comments
Medline ID
PubMed ID 10480878
Journal J Biol Chem
Year 1999
Volume 274
Pages 26743-50
Authors Menon S, Stahl M, Kumar R, Xu GY, Sullivan F
Title Stereochemical course and steady state mechanism of the reaction catalyzed by the GDP-fucose synthetase from Escherichia coli.
Related PDB
Related UniProtKB
[7]
Resource
Comments X-RAY CRYSTALLOGRAPHY
Medline ID
PubMed ID 11021971
Journal J Mol Biol
Year 2000
Volume 303
Pages 77-91
Authors Rosano C, Bisso A, Izzo G, Tonetti M, Sturla L, De Flora A, Bolognesi M
Title Probing the catalytic mechanism of GDP-4-keto-6-deoxy-d-mannose Epimerase/Reductase by kinetic and crystallographic characterization of site-specific mutants.
Related PDB 1e6u 1e7q 1e7r 1e7s
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 10896473
Journal Structure
Year 2000
Volume 8
Pages 453-62
Authors Deacon AM, Ni YS, Coleman WG Jr, Ealick SE
Title The crystal structure of ADP-L-glycero-D-mannoheptose 6-epimerase: catalysis with a twist.
Related PDB 1eq2
Related UniProtKB P67910
[9]
Resource
Comments
Medline ID
PubMed ID 11706991
Journal Cell Mol Life Sci
Year 2001
Volume 58
Pages 1650-65
Authors Allard ST, Giraud MF, Naismith JH
Title Epimerases: structure, function and mechanism.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 15023057
Journal Biochemistry
Year 2004
Volume 43
Pages 3057-67
Authors Vogan EM, Bellamacina C, He X, Liu HW, Ringe D, Petsko GA
Title Crystal structure at 1.8 A resolution of CDP-D-glucose 4,6-dehydratase from Yersinia pseudotuberculosis.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 15823050
Journal Biochemistry
Year 2005
Volume 44
Pages 5907-15
Authors Morrison JP, Read JA, Coleman WG Jr, Tanner ME
Title Dismutase activity of ADP-L-glycero-D-manno-heptose 6-epimerase: evidence for a direct oxidation/reduction mechanism.
Related PDB
Related UniProtKB
[12]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.4 ANGSTROMS) OF 1-377 IN COMPLEX WITH NAD AND SUBSTRATES, SUBUNIT, MUTAGENESIS OF CYS-145; TYR-174; LYS-178; LYS-217 AND ARG-306.
Medline ID
PubMed ID 16366586
Journal J Am Chem Soc
Year 2005
Volume 127
Pages 18309-20
Authors Major LL, Wolucka BA, Naismith JH
Title Structure and function of GDP-mannose-3',5'-epimerase: an enzyme which performs three chemical reactions at the same active site.
Related PDB 2c5A 2c5e 2c54 2c59
Related UniProtKB Q93VR3
[13]
Resource
Comments
Medline ID
PubMed ID 19058170
Journal Angew Chem Int Ed Engl
Year 2008
Volume 47
Pages 9814-59
Authors Thibodeaux CJ, Melancon CE 3rd, Liu HW
Title Natural-product sugar biosynthesis and enzymatic glycodiversification.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 19053199
Journal J Am Chem Soc
Year 2008
Volume 130
Pages 17593-602
Authors Lau ST, Tanner ME
Title Mechanism and active site residues of GDP-fucose synthase.
Related PDB
Related UniProtKB

Comments
This enzyme is a distant homologue of the short-chain dehydrogenase/reductase (SDR) superfamily, which includes Drosophia alcohol dehydrogenase (S00319 in EzCatDB). This enzyme has got a catalytic triad composed of conserved residues, Ser, Tyr, and Lys. This enzyme is more closely related to dTDP-glucose 4,6-dehydratase (EC 4.2.1.46; D00262 in EzCatDB) and UDP-glucose 4-epimerase (EC 5.1.3.2; D00274 in EzCatDB).
This enzyme catalyzes three reactions, two epimerizations and a reduction. According to the literature [6] and [7], although this enzyme can catalyze the epimerization reaction without NADP or NADPH, these coenzymes can assist the reaction. According to the literature, Tyr136 and Lys140 seems to be involved in the epimerization, along with Cys109 and His179. As in the reduction reaction by the SDR family, Lys140 may modulate the activity of Tyr136 through the 2'-OH of NADP(H).
According to the literature [14], Cys109 acts as a general base to deprotonate C3' atom of the substrate in the first epimerization, and C5' atom of the intermediate in the second epimerization, whereas His179 serves as a general acid to protonate the C3' atom from the opposite side in the first epimerization, and the the C5' atom in the second epimerization. For the same residues to play the role as either general base or acid in the two consecutive reaction steps, there must be a proton shuttle mechanism to and from the active site during the lifetime of the GDP-6-deoxy-4-dehydro-altrose intermediate, in order to recover the protonation state of these catalytic residues. However, such proton shuttle system has not be found so far. (Ser107/Tyr136 can be involved in the proton shuttle, though.)
Taken together, this enzyme catalyze the following reactions.
(A) Isomerization from GDP-4-dehydro-6-deoxy-D-mannose to GDP-6-deoxy-3,4-ene-mannose (I00097):
(A0) Lys140 modulates the activity (or pKa) of Tyr136 via 2'-hydroxyl group of NADPH.
(A1) Cys109 acts as a general base to deprotonate C3' atom of the substrate, leading to the negative charge formation at the carbonyl oxygen at C4' position, to produce the intermediate (I00097). Here, Tyr136 may stabilize the negative charge on the O4'.
(B) Isomerization from GDP-6-deoxy-3,4-ene-mannose to GDP-6-deoxy-4-dehydro-altrose (I00098):
(B0) Lys140 modulates the activity (or pKa) of Tyr136 via 2'-hydroxyl group of NADPH. Tyr136 may stabilize the negative charge on the O4'.
(B1) His179 acts as a general acid to protonate the C3' atom of the intermediate (I00097). Simultaneously, the negative charge on the O4 decreases, leading to the formation of the second intermediate (I00098).
##Here, the protonation states of Cys109 and His179 must be recovered somehow.
(C) Isomerization from GDP-6-deoxy-4-dehydro-altrose to GDP-6-deoxy-4,5-ene-altrose (I00099):
(C0) Lys140 modulates the activity (or pKa) of Tyr136 via 2'-hydroxyl group of NADPH.
(C1) Cys109 acts as a general base to deprotonate C5' atom of the second intermediate (I00098), leading to the negative charge formation at the carbonyl oxygen at C4' position, to produce the third intermediate (I00099). Here, Tyr136 may stabilize the negative charge on the O4'.
(D) Isomerization from GDP-6-deoxy-4,5-ene-altrose to GDP-6-deoxy-4-dehydro-L-galactose (I00100):
(D0) Lys140 modulates the activity (or pKa) of Tyr136 via 2'-hydroxyl group of NADPH. Tyr136 may stabilize the negative charge on the O4'.
(D1) His179 acts as a general acid to protonate the C5' atom of the third intermediate (I00099). Simultaneously, the negative charge on the O4 decreases, leading to the formation of the fourth intermediate (I00100).
(E) Hydride transfer from NADPH to C5' atom of GDP-6-deoxy-4-dehydro-L-galactose:
(E0) Lys140 modulates the activity (or pKa) of Tyr136 via 2'-hydroxyl group of NADPH, along with the N1 atom of the nicotinamide group in NADPH, whereas Ser107 modulates the pKa of carbonyl oxygen of the intermediate (I00100).
(E1) Tyr136 acts as a general acid to protonate the carbonyl oxygen of the substrate. Meanwhile, the hydride transfer occurs from the C4 atom of the nicotinamide to the carbonyl carbon of the intermediate (I00100).

Created Updated
2010-08-06 2011-08-10