EzCatDB: T00002

DB codeT00002
CATH domainDomain 13.40.50.720Catalytic domain
Domain 21.10.1040.10Catalytic domain
Domain 31.20.5.320
E.C.1.1.1.44
CSA2pgd

CATH domainRelated DB codes (homologues)
1.10.1040.10D00007,D00012,D00603,T00227
3.40.50.720S00543,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,D00604,D00605,D00615,D00845,D00857,D00858,M00161,M00171,M00210,T00010,T00011,T00015,T00227,T00247,T00408,T00414,D00827,D00262,D00274,D00275,M00035,T00109

Enzyme Name
Swiss-protKEGG

P31072P00349
Protein name6-phosphogluconate dehydrogenase, decarboxylating6-phosphogluconate dehydrogenase, decarboxylatingphosphogluconate dehydrogenase (decarboxylating)
phosphogluconic acid dehydrogenase
6-phosphogluconic dehydrogenase
6-phosphogluconic carboxylase
6-phosphogluconate dehydrogenase (decarboxylating)
6-phospho-D-gluconate dehydrogenase
SynonymsEC 1.1.1.44
EC 1.1.1.44

KEGG pathways
MAP codePathways
MAP00030Pentose phosphate pathway
MAP00480Glutathione metabolism

Swiss-prot:Accession NumberP31072P00349
Entry name6PGD_TRYBB6PGD_SHEEP
Activity6-phospho-D-gluconate + NADP(+) = D-ribulose 5-phosphate + CO(2) + NADPH.6-phospho-D-gluconate + NADP(+) = D-ribulose 5-phosphate + CO(2) + NADPH.
SubunitHomodimer.Homodimer.
Subcellular location

Cofactor



SubstratesProducts
KEGG-idC00003C00006C00345C00004C00005C00199C00011C00080
CompoundNAD+NADP+6-Phospho-D-gluconateNADHNADPHD-Ribulose 5-phosphateCO2H+
Typeamide group,amine group,nucleotideamide group,amine group,nucleotidecarbohydrate,carboxyl group,phosphate group/phosphate ionamide group,amine group,nucleotideamide group,amine group,nucleotidecarbohydrate,phosphate group/phosphate ionothersothers
1pgjA01UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1pgjB01UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1pgdA01UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1pgnA01UnboundAnalogue:NBPUnboundUnboundUnboundUnboundUnbound
1pgoA01UnboundUnboundUnboundBound:NDPUnboundUnboundUnbound
1pgpA01UnboundUnboundUnboundUnboundUnboundUnboundUnbound
2pgdA01UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1pgjA02UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1pgjB02UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1pgdA02UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1pgnA02UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1pgoA02UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1pgpA02UnboundUnboundBound:6PGUnboundUnboundUnboundUnbound
2pgdA02UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1pgjA03UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1pgjB03UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1pgdA03UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1pgnA03UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1pgoA03UnboundUnboundUnboundUnboundUnboundUnboundUnbound
1pgpA03UnboundUnboundUnboundUnboundUnboundUnboundUnbound
2pgdA03UnboundUnboundUnboundUnboundUnboundUnboundUnbound

Active-site residues
resource
PDB;1pgd & literature [14], [16], [18], [21], [24]
pdbCatalytic residues
1pgjA01
1pgjB01
1pgdA01
1pgnA01
1pgoA01
1pgpA01
2pgdA01
1pgjA02LYS 185;ASN 189;GLU 192
1pgjB02LYS 185;ASN 189;GLU 192
1pgdA02LYS 183;ASN 187;GLU 190
1pgnA02LYS 183;ASN 187;GLU 190
1pgoA02LYS 183;ASN 187;GLU 190
1pgpA02LYS 183;ASN 187;GLU 190
2pgdA02LYS 183;ASN 187;GLU 190
1pgjA03
1pgjB03
1pgdA03
1pgnA03
1pgoA03
1pgpA03
2pgdA03

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[14]Fig.14, p.661-665
[17]SCHEME 1, Fig. 5, p.219-222
[18]p.265-266
[21]Scheme 1, p.15697
[22]Fig.1
[24]p.11237
[30]p.1210-1211
[31]Fig.1, Fig.2, p.3427
[33]Fig.2, p.2644-2647

references
[1]
PubMed ID4773872
JournalEur J Biochem
Year1973
Volume38
Pages229-38
AuthorsSilverberg M, Dalziel K
TitleCrystalline 6-phosphogluconate dehydrogenase from sheep liver.
[2]
PubMed ID4772689
JournalFEBS Lett
Year1973
Volume38
Pages49-52
AuthorsPearse BM, Harris JJ
Title6-Phosphogluconate dehydrogenase from Bacillus stearothermophilus.
[3]
PubMed ID236441
JournalMethods Enzymol
Year1975
Volume41
Pages214-20
AuthorsSilverberg M, Dalziel K
Title6-Phospho-D-gluconate dehydrogenase from sheep liver.
[4]
PubMed ID875016
JournalJ Mol Biol
Year1977
Volume112
Pages183-97
AuthorsAdams MJ, Helliwell JR, Bugg CE
TitleSturucture of 6-phosphogluconate dehydrogenase from sheep liver at 6 A resolution.
[5]
PubMed ID38116
JournalEur J Biochem
Year1979
Volume98
Pages121-30
AuthorsAbdallah MA, Adams MJ, Archibald IG, Biellmann JF, Helliwell JR, Jenkins SE
TitleBinding of coenzyme and substrate and coenzyme analogues to 6-phosphogluconate dehydrogenase from sheep liver. An X-ray study at 0.6 nm resolution.
[6]
PubMed ID7194116
JournalBiochim Biophys Acta
Year1981
Volume657
Pages232-42
AuthorsMinchiotti L, Ronchi S, Rippa M
TitleAmino acid sequence around the pyridoxal 5'-phosphate binding sites of 6-phosphogluconate dehydrogenase.
[7]
CommentsX-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS)
Medline ID84057760
PubMed ID6641716
JournalEMBO J
Year1983
Volume2
Pages1009-14
AuthorsAdams MJ, Archibald IG, Bugg CE, Carne A, Gover S, Helliwell JR, Pickersgill RW, White SW
TitleThe three dimensional structure of sheep liver 6-phosphogluconate dehydrogenase at 2.6 A resolution.
Related Swiss-protP00349
[8]
PubMed ID3699023
JournalEur J Biochem
Year1986
Volume156
Pages555-67
AuthorsTopham CM, Matthews B, Dalziel K
TitleKinetic studies of 6-phosphogluconate dehydrogenase from sheep liver.
[9]
PubMed ID3581436
JournalCell Biochem Funct
Year1987
Volume5
Pages79-95
AuthorsRosemeyer MA
TitleThe biochemistry of glucose-6-phosphate dehydrogenase, 6-phosphogluconate dehydrogenase and glutathione reductase.
[10]
PubMed ID2167091
JournalBiochem Int
Year1990
Volume21
Pages85-95
AuthorsUmazume K, Nishida M, Sakurai H, Yoshimura Y, Kawada J
TitleVariations in manganese effect on 6-phosphogluconate dehydrogenases from the thyroid and liver of the mouse and an evidence for non-interchangeability of manganese and magnesium.
[11]
CommentsX-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS)
Medline ID92172317
PubMed ID1793548
JournalActa Crystallogr B
Year1991
Volume47
Pages817-20
AuthorsAdams MJ, Gover S, Leaback R, Phillips C, Somers DO
TitleThe structure of 6-phosphogluconate dehydrogenase refined at 2.5 A resolution.
Related PDB1pgd,2pgd
Related Swiss-protP00349
[12]
PubMed ID1645186
JournalBiochemistry
Year1991
Volume30
Pages4970-7
AuthorsKnight WB, Sem DS, Smith K, Miziorko HM, Rendina AR, Cleland WW
TitlePhosphorylated thiosugars: synthesis, properties, and reactivity in enzymatic reactions.
[13]
PubMed ID1827991
JournalBiochemistry
Year1991
Volume30
Pages4978-84
AuthorsSem DS, Cleland WW
TitlePhosphorylated aminosugars: synthesis, properties, and reactivity in enzymatic reactions.
[14]
CommentsX-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS)
Medline ID95006333
PubMed ID7922042
JournalStructure
Year1994
Volume2
Pages651-68
AuthorsAdams MJ, Ellis GH, Gover S, Naylor CE, Phillips C
TitleCrystallographic study of coenzyme, coenzyme analogue and substrate binding in 6-phosphogluconate dehydrogenase: implications for NADP specificity and the enzyme mechanism.
Related PDB1pgn,1pgo,1pgp
Related Swiss-protP00349
[15]
CommentsX-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS)
JournalActa Crystallogr D Biol Crystallogr
Year1995
Volume51
Pages290-304
AuthorsPhillips C, Gover S, Adams MJ
TitleStructure of 6-phosphogluconate dehydrogenase refined at 2 angstroms resolution.
Related Swiss-protP00349
[16]
PubMed ID8589652
JournalBiochem Mol Biol Int
Year1995
Volume37
Pages785-93
AuthorsHanau S, Bertelli M, Dallocchio F, Rippa M
TitleBromopyruvate for the affinity labelling of a single cysteine residue near the carboxylate binding site of lamb liver 6-phosphogluconate dehydrogenase.
[17]
PubMed ID8954568
JournalArch Biochem Biophys
Year1996
Volume336
Pages215-23
AuthorsPrice NE, Cook PF
TitleKinetic and chemical mechanisms of the sheep liver 6-phosphogluconate dehydrogenase.
[18]
PubMed ID8766712
JournalFEBS Lett
Year1996
Volume389
Pages263-7
AuthorsHawes JW, Harper ET, Crabb DW, Harris RA
TitleStructural and mechanistic similarities of 6-phosphogluconate and 3-hydroxyisobutyrate dehydrogenases reveal a new enzyme family, the 3-hydroxyacid dehydrogenases.
[19]
PubMed ID8856059
JournalEur J Biochem
Year1996
Volume240
Pages592-9
AuthorsHanau S, Rippa M, Bertelli M, Dallocchio F, Barrett MP
Title6-Phosphogluconate dehydrogenase from Trypanosoma brucei. Kinetic analysis and inhibition by trypanocidal drugs.
[20]
PubMed ID9315293
JournalBiochem Mol Biol Int
Year1997
Volume43
Pages153-60
AuthorsGiovannini PP, Rippa M, Dallocchio F, Tetaud M, Barrett MP, Hanau S
TitleThe cross-linking by o-phthalaldehyde of two amino acid residues at the active site of 6-phosphogluconate dehydrogenase.
[21]
PubMed ID9843373
JournalBiochemistry
Year1998
Volume37
Pages15691-7
AuthorsKarsten WE, Chooback L, Cook PF
TitleGlutamate 190 is a general acid catalyst in the 6-phosphogluconate-dehydrogenase-catalyzed reaction.
[22]
PubMed ID9920387
JournalBiochim Biophys Acta
Year1998
Volume1429
Pages83-92
AuthorsRippa M, Giovannini PP, Barrett MP, Dallocchio F, Hanau S
Title6-Phosphogluconate dehydrogenase: the mechanism of action investigated by a comparison of the enzyme from different species.
[23]
CommentsX-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS)
Medline ID98411456
PubMed ID9737929
JournalJ Mol Biol
Year1998
Volume282
Pages667-81
AuthorsPhillips C, Dohnalek J, Gover S, Barrett MP, Adams MJ
TitleA 2.8 A resolution structure of 6-phosphogluconate dehydrogenase from the protozoan parasite Trypanosoma brucei: comparison with the sheep enzyme accounts for differences in activity with coenzyme and substrate analogues.
Related PDB1pgj
Related Swiss-protP31072
[24]
PubMed ID10471272
JournalBiochemistry
Year1999
Volume38
Pages11231-8
AuthorsZhang L, Chooback L, Cook PF
TitleLysine 183 is the general base in the 6-phosphogluconate dehydrogenase-catalyzed reaction.
[25]
PubMed ID9931298
JournalBiochem J
Year1999
Volume338
Pages55-60
AuthorsTetaud E, Hanau S, Wells JM, Le Page RW, Adams MJ, Arkison S, Barrett MP
Title6-Phosphogluconate dehydrogenase from Lactococcus lactis: a role for arginine residues in binding substrate and coenzyme.
[26]
PubMed ID10848959
JournalEur J Biochem
Year2000
Volume267
Pages3442-52
AuthorsMoritz B, Striegel K, De Graaf AA, Sahm H
TitleKinetic properties of the glucose-6-phosphate and 6-phosphogluconate dehydrogenases from Corynebacterium glutamicum and their application for predicting pentose phosphate pathway flux in vivo.
[27]
PubMed ID11430979
JournalPhytochemistry
Year2001
Volume57
Pages1061-8
AuthorsMagel EA, Hillinger C, Wagner T, Holl W
TitleOxidative pentose phosphate pathway and pyridine nucleotides in relation to heartwood formation in Robinia pseudoacacia L.
[28]
PubMed ID11394739
JournalJ Comput Aided Mol Des
Year2001
Volume15
Pages465-75
AuthorsBertelli M, El-Bastawissy E, Knaggs MH, Barrett MP, Hanau S, Gilbert IH
TitleSelective inhibition of 6-phosphogluconate dehydrogenase from Trypanosoma brucei.
[29]
PubMed ID12818683
JournalBioorg Med Chem
Year2003
Volume11
Pages3205-14
AuthorsDardonville C, Rinaldi E, Hanau S, Barrett MP, Brun R, Gilbert IH
TitleSynthesis and biological evaluation of substrate-based inhibitors of 6-phosphogluconate dehydrogenase as potential drugs against African trypanosomiasis.
[30]
PubMed ID12628648
JournalBioorg Med Chem
Year2003
Volume11
Pages1207-14
AuthorsPasti C, Rinaldi E, Cervellati C, Dallocchio F, Hardre R, Salmon L, Hanau S
TitleSugar derivatives as new 6-phosphogluconate dehydrogenase inhibitors selective for the parasite Trypanosoma brucei.
[31]
PubMed ID15189039
JournalJ Med Chem
Year2004
Volume47
Pages3427-37
AuthorsDardonville C, Rinaldi E, Barrett MP, Brun R, Gilbert IH, Hanau S
TitleSelective inhibition of Trypanosoma brucei 6-phosphogluconate dehydrogenase by high-energy intermediate and transition-state analogues.
[32]
PubMed ID14698432
JournalMol Biochem Parasitol
Year2004
Volume133
Pages197-207
AuthorsEsteve MI, Cazzulo JJ
TitleThe 6-phosphogluconate dehydrogenase from Trypanosoma cruzi: the absence of two inter-subunit salt bridges as a reason for enzyme instability.
[33]
PubMed ID15544466
JournalCurr Med Chem
Year2004
Volume11
Pages2639-50
AuthorsHanau S, Rinaldi E, Dallocchio F, Gilbert IH, Dardonville C, Adams MJ, Gover S, Barrett MP
Title6-phosphogluconate dehydrogenase: a target for drugs in African trypanosomes.

comments
This enzyme is composed of three domains (or regions). The CATH classifications of the C-terminal domain of the enzymes from sheep and Trypanosoma were different from each other, but their structures (2pgd & 1pgd, respectively) could be superimposed perfectly. So, these structures were clustered together in this entry.

createdupdated
2004-02-032009-02-26
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 2010)
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)

© Computational Biology Research Center, AIST, 2004 All Rights Reserved.