DB code: S00224

CATH domain 3.20.20.70 : TIM Barrel Catalytic domain
E.C. 5.1.3.1
CSA 1rpx
M-CSA 1rpx
MACiE M0270

CATH domain Related DB codes (homologues)
3.20.20.70 : TIM Barrel S00215 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

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Pfam RefSeq
Q43843 Ribulose-phosphate 3-epimerase, chloroplastic
EC 5.1.3.1
Pentose-5-phosphate 3-epimerase
PPE
R5P3E
RPE
PF00834 (Ribul_P_3_epim)
[Graphical View]
Q9SE42 Ribulose-phosphate 3-epimerase, cytoplasmic isoform
EC 5.1.3.1
Ribulose-5-phosphate-epimerase
Cyt-RPEase
RPEcyt
Pentose-5-phosphate 3-epimerase
PPE
PF00834 (Ribul_P_3_epim)
[Graphical View]
NP_001063604.2 (Protein)
NM_001070139.2 (DNA/RNA sequence)
P74061 Ribulose-phosphate 3-epimerase
EC 5.1.3.1
Pentose-5-phosphate 3-epimerase
PPE
R5P3E
PF00834 (Ribul_P_3_epim)
[Graphical View]
NP_441457.1 (Protein)
NC_000911.1 (DNA/RNA sequence)
YP_005651515.1 (Protein)
NC_017277.1 (DNA/RNA sequence)
YP_007451339.1 (Protein)
NC_020286.1 (DNA/RNA sequence)

KEGG enzyme name
ribulose-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

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
Q43843 RPE_SOLTU D-ribulose 5-phosphate = D-xylulose 5- phosphate. Homohexamer. Plastid, chloroplast thylakoid membrane.
Q9SE42 RPE1_ORYSJ D-ribulose 5-phosphate = D-xylulose 5- phosphate. Homodimer. Cytoplasm. Binds 1 zinc ion per subunit.
P74061 RPE_SYNY3 D-ribulose 5-phosphate = D-xylulose 5- phosphate.

KEGG Pathways
Map code Pathways E.C.
MAP00030 Pentose phosphate pathway
MAP00040 Pentose and glucuronate interconversions
MAP00710 Carbon fixation in photosynthetic organisms

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00038 C00199 C00231
E.C.
Compound Zinc D-Ribulose 5-phosphate D-Xylulose 5-phosphate
Type heavy metal carbohydrate,phosphate group/phosphate ion carbohydrate,phosphate group/phosphate ion
ChEBI 29105
17363
16332
PubChem 32051
439184
439190
1rpxA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1rpxB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1rpxC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1h1yA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1h1yB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1h1zA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound
1h1zB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound
1tqjA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1tqjB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1tqjC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1tqjD Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1tqjE Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound
1tqjF Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
literature [5], [8], [10]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1rpxA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 16;ASP 43;MET 45;MET 76;MET 147;ASP 185 HIS 41;ASP 43;HIS 74;ASP 185
1rpxB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 16;ASP 43;MET 45;MET 76;MET 147;ASP 185 HIS 41;ASP 43;HIS 74;ASP 185
1rpxC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 16;ASP 43;MET 45;MET 76;MET 147;ASP 185 HIS 41;ASP 43;HIS 74;ASP 185
1h1yA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 11;ASP 38;MET 40;MET 71;MET 144;ASP 178 HIS 36;ASP 38;HIS 69;ASP 178
1h1yB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 11;ASP 38;MET 40;MET 71;MET 144;ASP 178 HIS 36;ASP 38;HIS 69;ASP 178
1h1zA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 11;ASP 38;MET 40;MET 71;MET 144;ASP 178 HIS 36;ASP 38;HIS 69;ASP 178
1h1zB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 11;ASP 38;MET 40;MET 71;MET 144;ASP 178 HIS 36;ASP 38;HIS 69;ASP 178
1tqjA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 10;ASP 37;MET 39;MET 70;MET 141;ASP 179 HIS 35;ASP 37;HIS 68;ASP 179
1tqjB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 10;ASP 37;MET 39;MET 70;MET 141;ASP 179 HIS 35;ASP 37;HIS 68;ASP 179
1tqjC Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 10;ASP 37;MET 39;MET 70;MET 141;ASP 179 HIS 35;ASP 37;HIS 68;ASP 179
1tqjD Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 10;ASP 37;MET 39;MET 70;MET 141;ASP 179 HIS 35;ASP 37;HIS 68;ASP 179
1tqjE Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 10;ASP 37;MET 39;MET 70;MET 141;ASP 179 HIS 35;ASP 37;HIS 68;ASP 179
1tqjF Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 10;ASP 37;MET 39;MET 70;MET 141;ASP 179 HIS 35;ASP 37;HIS 68;ASP 179

References for Catalytic Mechanism
References Sections No. 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]
Resource
Comments
Medline ID
PubMed ID 3987693
Journal Eur J Biochem
Year 1985
Volume 148
Pages 345-51
Authors Terada T, Mukae H, Ohashi K, Hosomi S, Mizoguchi T, Uehara K
Title Characterization of an enzyme which catalyzes isomerization and epimerization of D-erythrose 4-phosphate.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 1939111
Journal J Biol Chem
Year 1991
Volume 266
Pages 20610-8
Authors Volk R, Bacher A
Title Biosynthesis of riboflavin. Studies on the mechanism of L-3,4-dihydroxy-2-butanone 4-phosphate synthase.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 9733539
Journal Plant Physiol
Year 1998
Volume 118
Pages 199-207
Authors Chen YR, Hartman FC, Lu TY, Larimer FW
Title D-Ribulose-5-phosphate 3-epimerase: cloning and heterologous expression of the spinach gene, and purification and characterization of the recombinant enzyme.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 9890975
Journal J Biol Chem
Year 1999
Volume 274
Pages 2132-6
Authors Chen YR, Larimer FW, Serpersu EH, Hartman FC
Title Identification of a catalytic aspartyl residue of D-ribulose 5-phosphate 3-epimerase by site-directed mutagenesis.
Related PDB
Related UniProtKB
[5]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
Medline ID 99208761
PubMed ID 10191144
Journal J Mol Biol
Year 1999
Volume 287
Pages 761-71
Authors Kopp J, Kopriva S, Suss KH, Schulz GE
Title Structure and mechanism of the amphibolic enzyme D-ribulose-5-phosphate 3-epimerase from potato chloroplasts.
Related PDB 1rpx
Related UniProtKB Q43843
[6]
Resource
Comments
Medline ID
PubMed ID 10625676
Journal J Biol Chem
Year 2000
Volume 275
Pages 1294-9
Authors Kopriva S, Koprivova A, Suss KH
Title Identification, cloning, and properties of cytosolic D-ribulose-5-phosphate 3-epimerase from higher plants.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 12137277
Journal Nat Prod Rep
Year 2002
Volume 19
Pages 261-77
Authors Samuel J, Tanner ME
Title Mechanistic aspects of enzymatic carbohydrate epimerization.
Related PDB
Related UniProtKB
[8]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.87 ANGSTROMS) IN COMPLEX WITH ZINC.
Medline ID
PubMed ID 12547196
Journal J Mol Biol
Year 2003
Volume 326
Pages 127-35
Authors Jelakovic S, Kopriva S, Suss KH, Schulz GE
Title Structure and catalytic mechanism of the cytosolic D-ribulose-5-phosphate 3-epimerase from rice.
Related PDB 1h1y 1h1z
Related UniProtKB Q9SE42
[9]
Resource
Comments
Medline ID
PubMed ID 15023082
Journal Acc Chem Res
Year 2004
Volume 37
Pages 149-58
Authors Wise EL, Rayment I
Title Understanding the importance of protein structure to nature's routes for divergent evolution in TIM barrel enzymes.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 15333955
Journal Acta Crystallogr D Biol Crystallogr
Year 2004
Volume 60
Pages 1687-90
Authors Wise EL, Akana J, Gerlt JA, Rayment I
Title Structure of D-ribulose 5-phosphate 3-epimerase from Synechocystis to 1.6 A resolution.
Related PDB 1tqj
Related UniProtKB

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.

Created Updated
2005-07-15 2009-02-26