EzCatDB: S00224

DB codeS00224
CATH domainDomain 13.20.20.70Catalytic domain
E.C.5.1.3.1
CSA1rpx
MACiEM0270

CATH domainRelated DB codes (homologues)
3.20.20.70S00215,S00217,S00218,S00219,S00532,S00198,S00220,S00745,S00537,S00538,S00539,S00826,S00841,S00235,S00239,S00240,S00243,S00244,S00199,S00200,S00201,S00221,S00222,S00847,S00225,S00226,D00014,D00029,M00141,T00015,T00239,D00664,D00665,D00804,D00863,T00089

Enzyme Name
Swiss-protKEGG

Q43843Q9SE42P74061
Protein nameRibulose-phosphate 3-epimerase, chloroplasticRibulose-phosphate 3-epimerase, cytoplasmic isoformRibulose-phosphate 3-epimeraseribulose-phosphate 3-epimerase
phosphoribulose epimerase
erythrose-4-phosphate isomerase
phosphoketopentose 3-epimerase
xylulose phosphate 3-epimerase
phosphoketopentose epimerase
ribulose 5-phosphate 3-epimerase
D-ribulose phosphate-3-epimerase
D-ribulose 5-phosphate epimerase
D-ribulose-5-P 3-epimerase
D-xylulose-5-phosphate 3-epimerase
pentose-5-phosphate 3-epimerase
SynonymsEC 5.1.3.1
Pentose-5-phosphate 3-epimerase
PPE
R5P3E
RPE
EC 5.1.3.1
Ribulose-5-phosphate-epimerase
Cyt-RPEase
RPEcyt
Pentose-5-phosphate 3-epimerase
PPE
EC 5.1.3.1
Pentose-5-phosphate 3-epimerase
PPE
R5P3E

KEGG pathways
MAP codePathways
MAP00030Pentose phosphate pathway
MAP00040Pentose and glucuronate interconversions
MAP00710Carbon fixation in photosynthetic organisms

Swiss-prot:Accession NumberQ43843Q9SE42P74061
Entry nameRPE_SOLTURPE1_ORYSJRPE_SYNY3
ActivityD-ribulose 5-phosphate = D-xylulose 5- phosphate.D-ribulose 5-phosphate = D-xylulose 5- phosphate.D-ribulose 5-phosphate = D-xylulose 5- phosphate.
SubunitHomohexamer.Homodimer.
Subcellular locationPlastid, chloroplast thylakoid membrane.Cytoplasm.
Cofactor
Binds 1 zinc ion per subunit.


CofactorsSubstratesProducts
KEGG-idC00038C00199C00231
CompoundZincD-Ribulose 5-phosphateD-Xylulose 5-phosphate
Typeheavy metalcarbohydrate,phosphate group/phosphate ioncarbohydrate,phosphate group/phosphate ion
1rpxAUnboundUnboundUnbound
1rpxBUnboundUnboundUnbound
1rpxCUnboundUnboundUnbound
1h1yAUnboundUnboundUnbound
1h1yBUnboundUnboundUnbound
1h1zABound:_ZNUnboundUnbound
1h1zBBound:_ZNUnboundUnbound
1tqjAUnboundUnboundUnbound
1tqjBUnboundUnboundUnbound
1tqjCUnboundUnboundUnbound
1tqjDUnboundUnboundUnbound
1tqjEUnboundUnboundUnbound
1tqjFUnboundUnboundUnbound

Active-site residues
resource
literature [5], [8], [10]
pdbCatalytic residuesCofactor-binding residues
1rpxASER 16;ASP 43;MET 45;MET 76;MET 147;ASP 185
HIS 41;ASP 43;HIS 74;ASP 185
1rpxBSER 16;ASP 43;MET 45;MET 76;MET 147;ASP 185
HIS 41;ASP 43;HIS 74;ASP 185
1rpxCSER 16;ASP 43;MET 45;MET 76;MET 147;ASP 185
HIS 41;ASP 43;HIS 74;ASP 185
1h1yASER 11;ASP 38;MET 40;MET 71;MET 144;ASP 178
HIS 36;ASP 38;HIS 69;ASP 178
1h1yBSER 11;ASP 38;MET 40;MET 71;MET 144;ASP 178
HIS 36;ASP 38;HIS 69;ASP 178
1h1zASER 11;ASP 38;MET 40;MET 71;MET 144;ASP 178
HIS 36;ASP 38;HIS 69;ASP 178
1h1zBSER 11;ASP 38;MET 40;MET 71;MET 144;ASP 178
HIS 36;ASP 38;HIS 69;ASP 178
1tqjASER 10;ASP 37;MET 39;MET 70;MET 141;ASP 179
HIS 35;ASP 37;HIS 68;ASP 179
1tqjBSER 10;ASP 37;MET 39;MET 70;MET 141;ASP 179
HIS 35;ASP 37;HIS 68;ASP 179
1tqjCSER 10;ASP 37;MET 39;MET 70;MET 141;ASP 179
HIS 35;ASP 37;HIS 68;ASP 179
1tqjDSER 10;ASP 37;MET 39;MET 70;MET 141;ASP 179
HIS 35;ASP 37;HIS 68;ASP 179
1tqjESER 10;ASP 37;MET 39;MET 70;MET 141;ASP 179
HIS 35;ASP 37;HIS 68;ASP 179
1tqjFSER 10;ASP 37;MET 39;MET 70;MET 141;ASP 179
HIS 35;ASP 37;HIS 68;ASP 179

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[4]Fig.1, p.2134-2136
[5]Fig.1, Fig.9, p.769
[7]Fig.1, p.262-263
[8]Fig.9, p.132-133
[9]Scheme 3
[10]p.1689-1690

references
[1]
PubMed ID3987693
JournalEur J Biochem
Year1985
Volume148
Pages345-51
AuthorsTerada T, Mukae H, Ohashi K, Hosomi S, Mizoguchi T, Uehara K
TitleCharacterization of an enzyme which catalyzes isomerization and epimerization of D-erythrose 4-phosphate.
[2]
PubMed ID1939111
JournalJ Biol Chem
Year1991
Volume266
Pages20610-8
AuthorsVolk R, Bacher A
TitleBiosynthesis of riboflavin. Studies on the mechanism of L-3,4-dihydroxy-2-butanone 4-phosphate synthase.
[3]
PubMed ID9733539
JournalPlant Physiol
Year1998
Volume118
Pages199-207
AuthorsChen YR, Hartman FC, Lu TY, Larimer FW
TitleD-Ribulose-5-phosphate 3-epimerase: cloning and heterologous expression of the spinach gene, and purification and characterization of the recombinant enzyme.
[4]
PubMed ID9890975
JournalJ Biol Chem
Year1999
Volume274
Pages2132-6
AuthorsChen YR, Larimer FW, Serpersu EH, Hartman FC
TitleIdentification of a catalytic aspartyl residue of D-ribulose 5-phosphate 3-epimerase by site-directed mutagenesis.
[5]
CommentsX-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
Medline ID99208761
PubMed ID10191144
JournalJ Mol Biol
Year1999
Volume287
Pages761-71
AuthorsKopp J, Kopriva S, Suss KH, Schulz GE
TitleStructure and mechanism of the amphibolic enzyme D-ribulose-5-phosphate 3-epimerase from potato chloroplasts.
Related PDB1rpx
Related Swiss-protQ43843
[6]
PubMed ID10625676
JournalJ Biol Chem
Year2000
Volume275
Pages1294-9
AuthorsKopriva S, Koprivova A, Suss KH
TitleIdentification, cloning, and properties of cytosolic D-ribulose-5-phosphate 3-epimerase from higher plants.
[7]
PubMed ID12137277
JournalNat Prod Rep
Year2002
Volume19
Pages261-77
AuthorsSamuel J, Tanner ME
TitleMechanistic aspects of enzymatic carbohydrate epimerization.
[8]
CommentsX-RAY CRYSTALLOGRAPHY (1.87 ANGSTROMS) IN COMPLEX WITH ZINC.
PubMed ID12547196
JournalJ Mol Biol
Year2003
Volume326
Pages127-35
AuthorsJelakovic S, Kopriva S, Suss KH, Schulz GE
TitleStructure and catalytic mechanism of the cytosolic D-ribulose-5-phosphate 3-epimerase from rice.
Related PDB1h1y,1h1z
Related Swiss-protQ9SE42
[9]
PubMed ID15023082
JournalAcc Chem Res
Year2004
Volume37
Pages149-58
AuthorsWise EL, Rayment I
TitleUnderstanding the importance of protein structure to nature's routes for divergent evolution in TIM barrel enzymes.
[10]
PubMed ID15333955
JournalActa Crystallogr D Biol Crystallogr
Year2004
Volume60
Pages1687-90
AuthorsWise EL, Akana J, Gerlt JA, Rayment I
TitleStructure of D-ribulose 5-phosphate 3-epimerase from Synechocystis to 1.6 A resolution.
Related PDB1tqj

comments
Although zinc is included as cofactor, it is not clear whether it is involved in catalysis.
As the catalytic mechanism has been controversial, complex structure with substrate/product will be necessary to identify its catalytic mechanism.

createdupdated
2005-07-152009-02-26
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)

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