EzCatDB: D00544
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DB codeD00544
RLCP classification9.1050.440000.8011 : Hydride transfer
9.5010.536200.8011 : Hydride transfer
CATH domainDomain 13.40.50.720 : Rossmann foldCatalytic domain
Domain 23.90.25.10 : UDP-galactose 4-epimerase; domain 1
E.C.5.1.3.2


Enzyme Name
UniProtKBKEGG

Q81K34
Protein name
UDP-glucose 4-epimerase
UDP-galactose 4-epimerase
uridine diphosphoglucose epimerase
galactowaldenase
UDPG-4-epimerase
uridine diphosphate galactose 4-epimerase
uridine diphospho-galactose-4-epimerase
UDP-glucose epimerase
UDP-galactose 4-epimerase
4-epimerase
UDPG-4-epimerase
uridine diphosphoglucose 4-epimerase
uridine diphosphate glucose 4-epimerase
UDP-D-galactose 4-epimerase
SynonymsUDP-glucose 4-epimerase
EC 5.1.3.2
RefSeqNP_847665.1 (Protein)
NC_003997.3 (DNA/RNA sequence)
YP_022172.1 (Protein)
NC_007530.2 (DNA/RNA sequence)
YP_031353.1 (Protein)
NC_005945.1 (DNA/RNA sequence)
PfamPF01370 (Epimerase)
PF13950 (Epimerase_Csub)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00052Galactose metabolism
MAP00520Nucleotide sugars metabolism

UniProtKB:Accession NumberQ81K34
Entry nameQ81K34_BACAN
Activity
Subunit
Subcellular location
Cofactor

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProductsintermediates
KEGG-idC00003C00029C00052I00016
CompoundNAD+UDP-glucoseUDP-galactoseUDP-4-ketohexopyranose
Typeamide group,amine group,nucleotideamide group,carbohydrate,nucleotideamide group,carbohydrate,nucleotide
ChEBI15846
46229


PubChem5893
8629
23724458

            
2c20A01Bound:NADUnboundUnbound 
2c20B01Bound:NADUnboundUnbound 
2c20C01Bound:NADUnboundUnbound 
2c20D01Bound:NADUnboundUnbound 
2c20E01Bound:NADUnboundUnbound 
2c20F01Bound:NADUnboundUnbound 
2c20A02UnboundUnboundUnbound 
2c20B02UnboundUnboundUnbound 
2c20C02UnboundUnboundUnbound 
2c20D02UnboundUnboundUnbound 
2c20E02UnboundUnboundUnbound 
2c20F02UnboundUnboundUnbound 

Active-site residues
resource
literature [22], [31], [35]
pdbCatalytic residues
         
2c20A01THR 118;TYR 142;LYS 146
2c20B01THR 118;TYR 142;LYS 146
2c20C01THR 118;TYR 142;LYS 146
2c20D01THR 118;TYR 142;LYS 146
2c20E01THR 118;TYR 142;LYS 146
2c20F01THR 118;TYR 142;LYS 146
2c20A02 
2c20B02 
2c20C02 
2c20D02 
2c20E02 
2c20F02 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[3]Fig.2, p.135-136
[6]Fig.2, p.373
[7]p.13227-13230
[8]p.13235-13236
[11]p.5139-5143
[12]Fig.10, p.2156-2159
[13]Scheme 1, Scheme 2, Scheme 3, p.10682-10683
[14]p.10694-10695
[15]Scheme 1, p.6294-6295, p.6302-6303
[18]Scheme 1, p.11474-11477
[20]Scheme 1, p.5697-5700
[22]Scheme 1, Fig.4, p.6703-6705
[23]Scheme 1, p.9187-9188
[24]Scheme 1, Fig.6, p.11284-11286
[29]p.250
[30]Scheme 1
[31]p.177-179
[32]Fig.2, p.13371
[33]Scheme 2, p.3065-3066
[35]p.832-833

references
[1]
PubMed ID3061645
JournalCarbohydr Res
Year1988
Volume179
Pages289-99
AuthorsKaca W, de Jongh-Leuvenink J, Zahringer U, Rietschel ET, Brade H, Verhoef J, Sinnwell V
TitleIsolation and chemical analysis of 7-O-(2-amino-2-deoxy-alpha-D-glucopyranosyl)-L-glycero-D-manno-heptose as a constituent of the lipopolysaccharides of the UDP-galactose epimerase-less mutant J-5 of Escherichia coli and Vibrio cholerae.
[2]
PubMed ID2659075
JournalBiochemistry
Year1989
Volume28
Pages2645-54
AuthorsKonopka JM, Halkides CJ, Vanhooke JL, Gorenstein DG, Frey PA
TitleUDP-galactose 4-epimerase. Phosphorus-31 nuclear magnetic resonance analysis of NAD+ and NADH bound at the active site.
[3]
PubMed ID2008433
JournalProteins
Year1991
Volume9
Pages135-42
AuthorsBauer AJ, Rayment I, Frey PA, Holden HM
TitleThe isolation, purification, and preliminary crystallographic characterization of UDP-galactose-4-epimerase from Escherichia coli.
[4]
PubMed ID1601848
JournalJ Biol Chem
Year1992
Volume267
Pages11714-20
AuthorsBhattacharjee H, Bhaduri A
TitleDistinct functional roles of two active site thiols in UDPglucose 4-epimerase from Kluyveromyces fragilis.
[5]
PubMed ID1297789
JournalJ Nutr Sci Vitaminol (Tokyo)
Year1992
VolumeSpec No
Pages461-4
AuthorsFrey PA, Bauer AJ, Vanhooke JL, Konopka JM, Rayment I, Holden HM
TitleChemical spectroscopic and crystallographic studies of UDP-galactose 4-epimerase from Escherichia coli.
[6]
CommentsX-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
Medline ID92253563
PubMed ID1579570
JournalProteins
Year1992
Volume12
Pages372-81
AuthorsBauer AJ, Rayment I, Frey PA, Holden HM
TitleThe molecular structure of UDP-galactose 4-epimerase from Escherichia coli determined at 2.5 A resolution.
Related PDB1udp
Related UniProtKBP09147
[7]
PubMed ID8241177
JournalBiochemistry
Year1993
Volume32
Pages13220-30
AuthorsBurke JR, Frey PA
TitleThe importance of binding energy in catalysis of hydride transfer by UDP-galactose 4-epimerase: a 13C and 15N NMR and kinetic study.
[8]
PubMed ID8241178
JournalBiochemistry
Year1993
Volume32
Pages13231-6
AuthorsSwanson BA, Frey PA
TitleIdentification of lysine 153 as a functionally important residue in UDP-galactose 4-epimerase from Escherichia coli.
[9]
PubMed ID8652544
JournalBiochemistry
Year1996
Volume35
Pages7615-20
AuthorsLiu Y, Vanhooke JL, Frey PA
TitleUDP-galactose 4-epimerase: NAD+ content and a charge-transfer band associated with the substrate-induced conformational transition.
[10]
CommentsX-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
Medline ID96180680
PubMed ID8611559
JournalBiochemistry
Year1996
Volume35
Pages2557-66
AuthorsThoden JB, Frey PA, Holden HM
TitleCrystal structures of the oxidized and reduced forms of UDP-galactose 4-epimerase isolated from Escherichia coli.
Related PDB1nah,1nai
Related UniProtKBP09147
[11]
CommentsX-ray crystallography
PubMed ID8611497
JournalBiochemistry
Year1996
Volume35
Pages5137-44
AuthorsThoden JB, Frey PA, Holden HM
TitleMolecular structure of the NADH/UDP-glucose abortive complex of UDP-galactose 4-epimerase from Escherichia coli: implications for the catalytic mechanism.
Related PDB1xel
[12]
CommentsX-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
Medline ID97084800
PubMed ID8931134
JournalProtein Sci
Year1996
Volume5
Pages2149-61
AuthorsThoden JB, Frey PA, Holden HM
TitleHigh-resolution X-ray structure of UDP-galactose 4-epimerase complexed with UDP-phenol.
Related PDB2udp
Related UniProtKBP09147
[13]
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
[14]
CommentsX-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF SER-124 MUTANTS.
Medline ID97419132
PubMed ID9271499
JournalBiochemistry
Year1997
Volume36
Pages10685-95
AuthorsThoden JB, Gulick AM, Holden HM
TitleMolecular structures of the S124A, S124T, and S124V site-directed mutants of UDP-galactose 4-epimerase from Escherichia coli.
Related PDB1kvq,1kvr,1kvs,1kvt
Related UniProtKBP09147
[15]
CommentsX-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS).
Medline ID97317070
PubMed ID9174344
JournalBiochemistry
Year1997
Volume36
Pages6294-304
AuthorsThoden JB, Hegeman AD, Wesenberg G, Chapeau MC, Frey PA, Holden HM
TitleStructural analysis of UDP-sugar binding to UDP-galactose 4-epimerase from Escherichia coli.
Related PDB1uda,1udb,1udc
Related UniProtKBP09147
[16]
PubMed ID9119006
JournalEur J Biochem
Year1997
Volume244
Pages407-13
AuthorsDutta S, Maiti NR, Bhattacharyya D
TitleReversible folding of UDP-galactose 4-epimerase from Escherichia coli.
[17]
PubMed ID9224707
JournalFEBS Lett
Year1997
Volume409
Pages449-51
AuthorsNayar S, Bhattacharyya D
TitleUDP-galactose 4-epimerase from Escherichia coli: existence of a catalytic monomer.
[18]
CommentsX-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF MUTANTS.
Medline ID98376428
PubMed ID9708982
JournalBiochemistry
Year1998
Volume37
Pages11469-77
AuthorsThoden JB, Holden HM
TitleDramatic differences in the binding of UDP-galactose and UDP-glucose to UDP-galactose 4-epimerase from Escherichia coli.
Related PDB1a9y,1a9z
Related UniProtKBP09147
[19]
PubMed ID10329648
JournalJ Biol Chem
Year1999
Volume274
Pages14573-8
AuthorsBhattacharyya U, Dhar G, Bhaduri A
TitleAn arginine residue is essential for stretching and binding of the substrate on UDP-glucose-4-epimerase from Escherichia coli. Use of a stacked and quenched uridine nucleotide fluorophore as probe.
[20]
CommentsX-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
Medline ID20263487
PubMed ID10801319
JournalBiochemistry
Year2000
Volume39
Pages5691-701
AuthorsThoden JB, Wohlers TM, Fridovich-Keil JL, Holden HM
TitleCrystallographic evidence for Tyr 157 functioning as the active site base in human UDP-galactose 4-epimerase.
Related PDB1ek5,1ek6
Related UniProtKBQ14376
[21]
PubMed ID11437350
JournalArch Biochem Biophys
Year2001
Volume391
Pages188-96
AuthorsBarat B, Bhattacharyya D
TitleUDP-galactose 4-epimerase from Escherichia coli: formation of catalytic site during reversible folding.
[22]
PubMed ID11380265
JournalBiochemistry
Year2001
Volume40
Pages6699-705
AuthorsBerger E, Arabshahi A, Wei Y, Schilling JF, Frey PA
TitleAcid-base catalysis by UDP-galactose 4-epimerase: correlations of kinetically measured acid dissociation constants with thermodynamic values for tyrosine 149.
[23]
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.
[24]
PubMed ID11551228
JournalBiochemistry
Year2001
Volume40
Pages11279-87
AuthorsWei Y, Lin J, Frey PA
Title13C NMR analysis of electrostatic interactions between NAD+ and active site residues of UDP-galactose 4-epimerase: implications for the activation induced by uridine nucleotides.
[25]
PubMed ID11726498
JournalEMBO J
Year2001
Volume20
Pages6619-26
AuthorsStammers DK, Ren J, Leslie K, Nichols CE, Lamb HK, Cocklin S, Dodds A, Hawkins AR
TitleThe structure of the negative transcriptional regulator NmrA reveals a structural superfamily which includes the short-chain dehydrogenase/reductases.
[26]
CommentsX-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) OF VARIANT EDG MET-94.
Medline ID21282994
PubMed ID11279193
JournalJ Biol Chem
Year2001
Volume276
Pages20617-23
AuthorsThoden JB, Wohlers TM, Fridovich-Keil JL, Holden HM
TitleMolecular basis for severe epimerase deficiency galactosemia. X-ray structure of the human V94m-substituted UDP-galactose 4-epimerase.
Related PDB1i3k,1i3l,1i3m,1i3n
Related UniProtKBQ14376
[27]
CommentsX-ray crystallography
PubMed ID11279032
JournalJ Biol Chem
Year2001
Volume276
Pages15131-6
AuthorsThoden JB, Wohlers TM, Fridovich-Keil JL, Holden HM
TitleHuman UDP-galactose 4-epimerase. Accommodation of UDP-N-acetylglucosamine within the active site.
Related PDB1hzj
[28]
CommentsX-ray crystallography
PubMed ID12019271
JournalJ Biol Chem
Year2002
Volume277
Pages27528-34
AuthorsThoden JB, Henderson JM, Fridovich-Keil JL, Holden HM
TitleStructural analysis of the Y299C mutant of Escherichia coli UDP-galactose 4-epimerase. Teaching an old dog new tricks.
Related PDB1lrj,1lrk,1lrl
[29]
PubMed ID12604210
JournalChem Biol Interact
Year2003
Volume143-144
Pages247-53
AuthorsOppermann U, Filling C, Hult M, Shafqat N, Wu X, Lindh M, Shafqat J, Nordling E, Kallberg Y, Persson B, Jornvall H
TitleShort-chain dehydrogenases/reductases (SDR): the 2002 update.
[30]
PubMed ID12642575
JournalJ Biol Chem
Year2003
Volume278
Pages20874-81
AuthorsKoropatkin NM, Liu HW, Holden HM
TitleHigh resolution x-ray structure of tyvelose epimerase from Salmonella typhi.
[31]
CommentsX-ray crystallography
PubMed ID12615316
JournalMol Biochem Parasitol
Year2003
Volume126
Pages173-80
AuthorsShaw MP, Bond CS, Roper JR, Gourley DG, Ferguson MA, Hunter WN
TitleHigh-resolution crystal structure of Trypanosoma brucei UDP-galactose 4'-epimerase: a potential target for structure-based development of novel trypanocides.
Related PDB1gy8
[32]
PubMed ID15491143
JournalBiochemistry
Year2004
Volume43
Pages13370-9
AuthorsGatzeva-Topalova PZ, May AP, Sousa MC
TitleCrystal structure of Escherichia coli ArnA (PmrI) decarboxylase domain. A key enzyme for lipid A modification with 4-amino-4-deoxy-L-arabinose and polymyxin resistance.
[33]
PubMed ID15023057
JournalBiochemistry
Year2004
Volume43
Pages3057-67
AuthorsVogan EM, Bellamacina C, He X, Liu HW, Ringe D, Petsko GA
TitleCrystal structure at 1.8 A resolution of CDP-D-glucose 4,6-dehydratase from Yersinia pseudotuberculosis.
[34]
PubMed ID15175331
JournalJ Biol Chem
Year2004
Volume279
Pages32796-803
AuthorsSchulz JM, Watson AL, Sanders R, Ross KL, Thoden JB, Holden HM, Fridovich-Keil JL
TitleDeterminants of function and substrate specificity in human UDP-galactose 4'-epimerase.
[35]
PubMed ID16946458
JournalActa Crystallograph Sect F Struct Biol Cryst Commun
Year2006
Volume62
Pages829-34
AuthorsAlphey MS, Burton A, Urbaniak MD, Boons GJ, Ferguson MA, Hunter WN
TitleTrypanosoma brucei UDP-galactose-4'-epimerase in ternary complex with NAD+ and the substrate analogue UDP-4-deoxy-4-fluoro-alpha-D-galactose.
Related PDB2cnb

comments
This enzyme is a homologous enzyme to the counterpart enzymes from E. coli, trypanosoma and human (D00274 in EzCatDB).
This enzyme is a distant homologue of the short-chain dehydrogenase/reductase (SDR) superfamily, which includes Drosophia alcohol dehydrogenase (S00319 in EzCatDB). Those homologous enzymes have got a catalytic triad composed of conserved residues, Ser, Tyr, and Lys. At the position of the catalytic serine residue, this enzyme has got threonine residue, which seems to play the same role as the catalytic serine.
According to the literature [22], [31] and [35], this enzyme catalyzes the following reactions:
(A) Hydride transfer from C4' atom of substrate to NAD+, forming 4-keto intermediate and NADH.
This reaction mechanism must be the same as that by Drosophia alcohol dehydrogenase.
(X) Rotation or conformation change of the intermediate.
(B) Hydride transfer from NADH to C4' atom of the 4-ketose intermediate, recovering NAD+.
This reaction mechanism also must be the same as the reverse reaction by Drosophia alcohol dehydrogenase.

createdupdated
2011-07-042011-07-05


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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