EzCatDB: D00601
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DB codeD00601
RLCP classification9.5010.536200.8011 : Hydride transfer
CATH domainDomain 13.40.50.720 : Rossmann foldCatalytic domain
Domain 23.90.25.10 : UDP-galactose 4-epimerase; domain 1
E.C.1.1.1.133

CATH domainRelated DB codes (homologues)
3.40.50.720 : Rossmann foldS00543,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,D00603,D00604,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 1D00513,D00604,D00262,D00274,D00275

Enzyme Name
UniProtKBKEGG

P26392Q9F7K7Q97GQ1Q96Z61
Protein namedTDP-4-dehydrorhamnose reductase


dTDP-4-dehydrorhamnose reductase
dTDP-4-keto-L-rhamnose reductase
Reductase, thymidine diphospho-4-ketorhamnose
dTDP-4-ketorhamnose reductase
TDP-4-keto-rhamnose reductase
Thymidine diphospho-4-ketorhamnose reductase
SynonymsEC 1.1.1.133
dTDP-4-keto-L-rhamnose reductase
dTDP-6-deoxy-L-mannose dehydrogenase
dTDP-L-rhamnose synthetase
DTDP-6-deoxy-L-mannose-dehydrogenase
DTDP-4-dehydrorhamnose reductase, rfbD ortholog
273aa long hypothetical dTDP-4-dehydrorhamnose reductase
RefSeqNP_461041.1 (Protein)
NC_003197.1 (DNA/RNA sequence)

NP_348931.1 (Protein)
NC_003030.1 (DNA/RNA sequence)
NP_377956.1 (Protein)
NC_003106.2 (DNA/RNA sequence)
PfamPF04321 (RmlD_sub_bind)
[Graphical view]
PF04321 (RmlD_sub_bind)
[Graphical view]
PF04321 (RmlD_sub_bind)
[Graphical view]
PF04321 (RmlD_sub_bind)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00521Streptomycin biosynthesis
MAP00523Polyketide sugar unit biosynthesis

UniProtKB:Accession NumberP26392Q9F7K7Q97GQ1Q96Z61
Entry nameRFBD_SALTYQ9F7K7_SALCHQ97GQ1_CLOABQ96Z61_SULTO
ActivitydTDP-6-deoxy-L-mannose + NADP(+) = dTDP-4-dehydro-6-deoxy-L-mannose + NADPH.


Subunit



Subcellular location



Cofactor




Compound table: links to PDB-related databases & PoSSuM

SubstratesProducts
KEGG-idC00688C00005C00080C03319C00006
CompounddTDP-4-dehydro-6-deoxy-L-mannoseNADPHH+dTDP-6-deoxy-L-mannoseNADP+
Typeamide group,carbohydrate,nucleotideamide group,amine group,nucleotideothersamide group,carbohydrate,nucleotideamide group,amine group,nucleotide
ChEBI45868
16474
15378
15774
18009
PubChem443211
5884
1038
121966
5886
             
1kbzA01UnboundUnbound UnboundUnbound
1kc1A01UnboundUnbound UnboundBound:NDP
1kc3A01UnboundBound:NDP Bound:TRHUnbound
1kc0A01UnboundUnbound UnboundBound:NDP
1n2sA01UnboundAnalogue:NAD UnboundUnbound
1vl0A01UnboundUnbound UnboundAnalogue:NAI
1vl0B01UnboundUnbound UnboundAnalogue:NAI
1vl0C01UnboundUnbound UnboundAnalogue:NAI
2ggsA01UnboundUnbound UnboundBound:NDP
2ggsB01UnboundUnbound UnboundBound:NDP
1kbzA02UnboundUnbound UnboundUnbound
1kc1A02UnboundUnbound UnboundUnbound
1kc3A02UnboundUnbound UnboundUnbound
1kc0A02UnboundUnbound UnboundUnbound
1n2sA02UnboundUnbound UnboundUnbound
1vl0A02UnboundUnbound UnboundUnbound
1vl0B02UnboundUnbound UnboundUnbound
1vl0C02UnboundUnbound UnboundUnbound
2ggsA02UnboundUnbound UnboundUnbound
2ggsB02UnboundUnbound UnboundUnbound

Active-site residues
resource
literature [4], [7]
pdbCatalytic residues
         
1kbzA01THR 104;TYR 128;LYS 132
1kc1A01THR 104;TYR 128;LYS 132
1kc3A01THR 104;TYR 128;LYS 132
1kc0A01THR 104;TYR 128;LYS 132
1n2sA01THR 104;TYR 128;LYS 132
1vl0A01THR 101;TYR 125;LYS 129
1vl0B01THR 101;TYR 125;LYS 129
1vl0C01THR 101;TYR 125;LYS 129
2ggsA01THR 107;TYR 130;LYS 134
2ggsB01THR 107;TYR 130;LYS 134
1kbzA02                       
1kc1A02                       
1kc3A02                       
1kc0A02                       
1n2sA02                       
1vl0A02                       
1vl0B02                       
1vl0C02                       
2ggsA02                       
2ggsB02                       

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[4]p.13101
[7]Fig.6, p.782-783
[8]Fig.4, p.648-650

references
[1]
PubMed ID7742302
JournalBiochemistry
Year1995
Volume34
Pages6003-13
AuthorsJornvall H, Persson B, Krook M, Atrian S, Gonzalez-Duarte R, Jeffery J, Ghosh D
TitleShort-chain dehydrogenases/reductases (SDR).
[2]
CommentsX-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS).
PubMed ID8805577
JournalStructure
Year1996
Volume4
Pages905-15
AuthorsBreton R, Housset D, Mazza C, Fontecilla-Camps JC
TitleThe structure of a complex of human 17beta-hydroxysteroid dehydrogenase with estradiol and NADP+ identifies two principal targets for the design of inhibitors.
Related PDB1fds,1fdt
Related UniProtKBP14061
[3]
CommentsX-RAY CRYSTALLOGRAPHY
PubMed ID9271498
JournalBiochemistry
Year1997
Volume36
Pages10675-84
AuthorsLiu Y, Thoden JB, Kim J, Berger E, Gulick AM, Ruzicka FJ, Holden HM, Frey PA
TitleMechanistic roles of tyrosine 149 and serine 124 in UDP-galactose 4-epimerase from Escherichia coli.
Related PDB1kvu
[4]
CommentsX-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) IN COMPLEX WITH NAD(+) AND UDP-GLUCOSE.
PubMed ID10557279
JournalProc Natl Acad Sci U S A
Year1999
Volume96
Pages13097-102
AuthorsMulichak AM, Theisen MJ, Essigmann B, Benning C, Garavito RM
TitleCrystal structure of SQD1, an enzyme involved in the biosynthesis of the plant sulfolipid headgroup donor UDP-sulfoquinovose.
Related PDB1qrr
Related UniProtKBO48917
[5]
PubMed ID11478886
JournalBiochemistry
Year2001
Volume40
Pages9187-95
AuthorsGerratana B, Cleland WW, Frey PA
TitleMechanistic roles of Thr134, Tyr160, and Lys 164 in the reaction catalyzed by dTDP-glucose 4,6-dehydratase.
[6]
CommentsX-RAY CRYSTALLOGRAPHY
PubMed ID11243820
JournalJ Mol Biol
Year2001
Volume307
Pages283-95
AuthorsAllard ST, Giraud MF, Whitfield C, Graninger M, Messner P, Naismith JH
TitleThe crystal structure of dTDP-D-Glucose 4,6-dehydratase (RmlB) from Salmonella enterica serovar Typhimurium, the second enzyme in the dTDP-l-rhamnose pathway.
Related PDB1g1a
[7]
CommentsX-RAY CRYSTALLOGRAPHY
PubMed ID12057193
JournalStructure
Year2002
Volume10
Pages773-86
AuthorsBlankenfeldt W, Kerr ID, Giraud MF, McMiken HJ, Leonard G, Whitfield C, Messner P, Graninger M, Naismith JH
TitleVariation on a theme of SDR. dTDP-6-deoxy-L- lyxo-4-hexulose reductase (RmlD) shows a new Mg2+-dependent dimerization mode.
Related PDB1kbz,1kc1,1kc3,1kc0,1n2s
[8]
PubMed ID15493979
JournalBiochem Soc Trans
Year2004
Volume32
Pages647-54
AuthorsNaismith JH
TitleChemical insights from structural studies of enzymes.

comments
This enzyme belongs to the Short-chain dehydrogenases/reductases (SDR) (literature [1] & [7]).
This enzyme is homologous to Estradiol 17-beta-dehydrogenase 1 (EC=1.1.1.62, S00327 in EzCatDB), UDP-glucose 4-epimerase (EC=5.1.3.2, D00274) and dTDP-glucose 4,6-dehydratase (EC=4.2.1.46, D00262).
Although this enzyme requires Mg2+ for full activity, Mg2+ is necessary for its dimerization rather than its catalysis (see [7]).
According to the literature [7] and [8], the reaction of this enzyme proceeds as follows:
(0) Lys132 (of 1kbz) modulates the activity (or pKa) of Tyr128 via 2'-hydroxyl group of NADPH, along with the N1 atom of the nicotinamide group in NAD, whereas Thr104 modulates the pKa of 4-carbonyl oxygen of the substrate.
(1) Tyr128 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 substrate.

createdupdated
2010-05-072011-06-01
Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
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