DB code: T00239

RLCP classification 8.131.42001.6 : Isomerization
8.113.42001.5 : Isomerization
CATH domain 3.40.50.1260 : Rossmann fold Catalytic domain
3.40.50.1270 : Rossmann fold Catalytic domain
3.20.20.70 : TIM Barrel Catalytic domain
E.C. 2.7.2.3 5.3.1.1
CSA
M-CSA
MACiE

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 S00224 S00225 S00226 D00014 D00029 M00141 T00015 D00664 D00665 D00804 D00863 T00089

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Includes RefSeq Pfam
P36204 Bifunctional PGK/TIM
None Phosphoglycerate kinase
EC 2.7.2.3
Triosephosphate isomerase
(TIM)
EC 5.3.1.1
Triose-phosphate isomerase
NP_228498.1 (Protein)
NC_000853.1 (DNA/RNA sequence)
PF00162 (PGK)
PF00121 (TIM)
[Graphical View]

KEGG enzyme name
phosphoglycerate kinase
(EC 2.7.2.3 )
PGK
(EC 2.7.2.3 )
3-PGK
(EC 2.7.2.3 )
ATP-3-phospho-D-glycerate-1-phosphotransferase
(EC 2.7.2.3 )
ATP:D-3-phosphoglycerate 1-phosphotransferase
(EC 2.7.2.3 )
3-phosphoglycerate kinase
(EC 2.7.2.3 )
3-phosphoglycerate phosphokinase
(EC 2.7.2.3 )
3-phosphoglyceric acid kinase
(EC 2.7.2.3 )
3-phosphoglyceric acid phosphokinase
(EC 2.7.2.3 )
3-phosphoglyceric kinase
(EC 2.7.2.3 )
glycerate 3-phosphate kinase
(EC 2.7.2.3 )
glycerophosphate kinase
(EC 2.7.2.3 )
phosphoglyceric acid kinase
(EC 2.7.2.3 )
phosphoglyceric kinase
(EC 2.7.2.3 )
phosphoglycerokinase
(EC 2.7.2.3 )
triose-phosphate isomerase
(EC 5.3.1.1 )
phosphotriose isomerase
(EC 5.3.1.1 )
triose phosphoisomerase
(EC 5.3.1.1 )
triose phosphate mutase
(EC 5.3.1.1 )
D-glyceraldehyde-3-phosphate ketol-isomerase
(EC 5.3.1.1 )

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P36204 PGKT_THEMA ATP + 3-phospho-D-glycerate = ADP + 3-phospho- D-glyceroyl phosphate. D-glyceraldehyde 3-phosphate = glycerone phosphate. Monomer (PGK) and homotetramer (PGK-TIM). Cytoplasm.

KEGG Pathways
Map code Pathways E.C.
MAP00010 Glycolysis / Gluconeogenesis 2.7.2.3 5.3.1.1
MAP00031 Inositol metabolism 5.3.1.1
MAP00051 Fructose and mannose metabolism 5.3.1.1
MAP00710 Carbon fixation in photosynthetic organisms 2.7.2.3 5.3.1.1

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00305 C00002 C00197 C00118 C00008 C00236 C00111 I00178
E.C. 2.7.2.3
2.7.2.3
2.7.2.3
5.3.1.1
2.7.2.3
2.7.2.3
5.3.1.1
5.3.1.1
Compound Magnesium ATP 3-Phospho-D-glycerate D-Glyceraldehyde 3-phosphate ADP 3-Phospho-D-glyceroyl phosphate Glycerone phosphate Enediol form of glycerone phosphate
Type divalent metal (Ca2+, Mg2+) amine group,nucleotide carbohydrate,carboxyl group,phosphate group/phosphate ion carbohydrate,phosphate group/phosphate ion amine group,nucleotide carbohydrate,phosphate group/phosphate ion carbohydrate,phosphate group/phosphate ion
ChEBI 18420
15422
17794
29052
16761
16001
16108
PubChem 888
5957
439183
439168
6022
439191
668
1vpeA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Bound:3PG Unbound Unbound Unbound Unbound Unbound
1vpeA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_MG Analogue:ANP Unbound Unbound Unbound Unbound Unbound Unbound
1b9bA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1b9bB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
Swiss-prot;P36204, literature [3], [4], [6], [7]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1vpeA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 36
1vpeA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 201;ASN 317 ASP 355 GLY 354;GLY 377
1b9bA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 10;LYS 12;HIS 96;GLU 168
1b9bB Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASN 510;LYS 512;HIS 596;GLU 668

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[4]
p.4431-4435

References
[1]
Resource
Comments
Medline ID
PubMed ID 9165089
Journal Biol Chem
Year 1997
Volume 378
Pages 327-9
Authors Auerbach G, Jacob U, Grattinger M, Schurig H, Jaenicke R
Title Crystallographic analysis of phosphoglycerate kinase from the hyperthermophilic bacterium Thermotoga maritima.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 9278147
Journal Biol Chem
Year 1997
Volume 378
Pages 679-85
Authors Beaucamp N, Schurig H, Jaenicke R
Title The PGK-TIM fusion protein from Thermotoga maritima and its constituent parts are intrinsically stable and fold independently.
Related PDB
Related UniProtKB
[3]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF PGK, AND REVISIONS.
Medline ID 98046096
PubMed ID 9384563
Journal Structure
Year 1997
Volume 5
Pages 1475-83
Authors Auerbach G, Huber R, Grattinger M, Zaiss K, Schurig H, Jaenicke R, Jacob U
Title Closed structure of phosphoglycerate kinase from Thermotoga maritima reveals the catalytic mechanism and determinants of thermal stability.
Related PDB 1vpe
Related UniProtKB P36204
[4]
Resource
Comments
Medline ID
PubMed ID 9521762
Journal Biochemistry
Year 1998
Volume 37
Pages 4429-36
Authors Bernstein BE, Hol WG
Title Crystal structures of substrates and products bound to the phosphoglycerate kinase active site reveal the catalytic mechanism.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID 99315861
PubMed ID 10383424
Journal J Biol Chem
Year 1999
Volume 274
Pages 19181-7
Authors Alvarez M, Wouters J, Maes D, Mainfroid V, Rentier-Delrue F, Wyns L, Depiereux E, Martial JA
Title Lys13 plays a crucial role in the functional adaptation of the thermophilic triose-phosphate isomerase from Bacillus stearothermophilus to high temperatures.
Related PDB
Related UniProtKB
[6]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.85 ANGSTROMS) OF TIM.
Medline ID 20058648
PubMed ID 10591103
Journal Proteins
Year 1999
Volume 37
Pages 441-53
Authors Maes D, Zeelen JP, Thanki N, Beaucamp N, Alvarez M, Thi MH, Backmann J, Martial JA, Wyns L, Jaenicke R, Wierenga RK
Title The crystal structure of triosephosphate isomerase (TIM) from Thermotoga maritima: a comparative thermostability structural analysis of ten different TIM structures.
Related PDB 1b9b
Related UniProtKB P36204
[7]
Resource
Comments
Medline ID
PubMed ID 11243785
Journal J Mol Biol
Year 2001
Volume 306
Pages 745-57
Authors Walden H, Bell GS, Russell RJ, Siebers B, Hensel R, Taylor GL
Title Tiny TIM: a small, tetrameric, hyperthermostable triosephosphate isomerase.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 11265486
Journal Methods Enzymol
Year 2001
Volume 331
Pages 90-104
Authors Crowhurst G, McHarg J, Littlechild JA
Title Phosphoglycerate kinases from bacteria and archaea.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 12102622
Journal Biochemistry
Year 2002
Volume 41
Pages 8796-806
Authors Kovari Z, Flachner B, Naray-Szabo G, Vas M
Title Crystallographic and thiol-reactivity studies on the complex of pig muscle phosphoglycerate kinase with ATP analogues: correlation between nucleotide binding mode and helix flexibility.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 14997553
Journal Proteins
Year 2004
Volume 55
Pages 198-209
Authors Kovari Z, Vas M
Title Protein conformer selection by sequence-dependent packing contacts in crystals of 3-phosphoglycerate kinase.
Related PDB
Related UniProtKB

Comments
This enzyme is composed of the N-terminal phosphoglycerate kinase (E.C. 2.7.2.3) domains, and the C-terminal triose-phosphate isomerase (E.C. 5.3.1.1) domain.
The N-terminal phosphoglycerate kinase domains (swiss-prot;P36204 residues 2-399) are homologous to those of the counterpart enzyme (D00125 in EzCatDB), whereas the C-terminal triose-phosphate isomerase domain (swiss-prot;P36204 residues 400-654) is homologous to that of its counterpart enzyme (S00225 in EzCatDB).
Since the catalytic residues are conserved in both the domains, the catalytic mechanisms must be the same as the counterpart enzymes (D00125 and S00225 in EzCatDB).
(A) Transfer of phosphoryl group from ATP to carboxyl oxygen (N-terminal domains):
(B) Isomerization; Shift of double-bond from carbonyl group to adjacent C=C (C-terminal domain):
(C) Isomerization; Shift of double-bond from C=C to carbonyl group (C-terminal domain):

Created Updated
2006-01-24 2014-07-08