EzCatDB: T00239
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DB codeT00239
RLCP classification8.131.42001.6 : Isomerization
8.113.42001.5 : Isomerization
CATH domainDomain 13.40.50.1260 : Rossmann foldCatalytic domain
Domain 23.40.50.1270 : Rossmann foldCatalytic domain
Domain 33.20.20.70 : TIM BarrelCatalytic domain
E.C.2.7.2.3,5.3.1.1

CATH domainRelated DB codes (homologues)
3.20.20.70 : TIM BarrelS00215,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

Enzyme Name
UniProtKBKEGG

P36204
Protein nameBifunctional PGK/TIMphosphoglycerate 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)

SynonymsNone
IncludesPhosphoglycerate kinase
   EC 2.7.2.3
Triosephosphate isomerase
(TIM)
   EC 5.3.1.1
Triose-phosphate isomerase
RefSeqNP_228498.1 (Protein)
NC_000853.1 (DNA/RNA sequence)
PfamPF00162 (PGK)
PF00121 (TIM)
[Graphical view]

KEGG pathways
MAP codePathwaysE.C.
MAP00010Glycolysis / Gluconeogenesis2.7.2.3,5.3.1.1
MAP00031Inositol metabolism5.3.1.1
MAP00051Fructose and mannose metabolism5.3.1.1
MAP00710Carbon fixation in photosynthetic organisms2.7.2.3,5.3.1.1

UniProtKB:Accession NumberP36204
Entry namePGKT_THEMA
ActivityATP + 3-phospho-D-glycerate = ADP + 3-phospho- D-glyceroyl phosphate.,D-glyceraldehyde 3-phosphate = glycerone phosphate.
SubunitMonomer (PGK) and homotetramer (PGK-TIM).
Subcellular locationCytoplasm.
Cofactor

Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProductsintermediates
KEGG-idC00305C00002C00197C00118C00008C00236C00111I00178
E.C.2.7.2.32.7.2.32.7.2.35.3.1.12.7.2.32.7.2.35.3.1.15.3.1.1
CompoundMagnesiumATP3-Phospho-D-glycerateD-Glyceraldehyde 3-phosphateADP3-Phospho-D-glyceroyl phosphateGlycerone phosphateEnediol form of glycerone phosphate
Typedivalent metal (Ca2+, Mg2+)amine group,nucleotidecarbohydrate,carboxyl group,phosphate group/phosphate ioncarbohydrate,phosphate group/phosphate ionamine group,nucleotidecarbohydrate,phosphate group/phosphate ioncarbohydrate,phosphate group/phosphate ion
ChEBI18420
15422
17794
29052
16761
16001
16108

PubChem888
5957
439183
439168
6022
439191
668

                
1vpeA01UnboundUnboundBound:3PGUnboundUnboundUnboundUnboundUnbound
1vpeA02Bound:_MGAnalogue:ANPUnboundUnboundUnboundUnboundUnboundUnbound
1b9bAUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound
1b9bBUnboundUnboundUnboundUnboundUnboundUnboundUnboundUnbound

Active-site residues
resource
Swiss-prot;P36204, literature [3], [4], [6], [7]
pdbCatalytic residuesCofactor-binding residuesMain-chain involved in catalysis
           
1vpeA01ARG  36                        
 
 
1vpeA02LYS 201;ASN 317                
ASP 355
GLY 354;GLY 377
1b9bAASN  10;LYS  12;HIS  96;GLU 168
 
 
1b9bBASN 510;LYS 512;HIS 596;GLU 668
 
 

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[4]p.4431-4435

references
[1]
PubMed ID9165089
JournalBiol Chem
Year1997
Volume378
Pages327-9
AuthorsAuerbach G, Jacob U, Grattinger M, Schurig H, Jaenicke R
TitleCrystallographic analysis of phosphoglycerate kinase from the hyperthermophilic bacterium Thermotoga maritima.
[2]
PubMed ID9278147
JournalBiol Chem
Year1997
Volume378
Pages679-85
AuthorsBeaucamp N, Schurig H, Jaenicke R
TitleThe PGK-TIM fusion protein from Thermotoga maritima and its constituent parts are intrinsically stable and fold independently.
[3]
CommentsX-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF PGK, AND REVISIONS.
Medline ID98046096
PubMed ID9384563
JournalStructure
Year1997
Volume5
Pages1475-83
AuthorsAuerbach G, Huber R, Grattinger M, Zaiss K, Schurig H, Jaenicke R, Jacob U
TitleClosed structure of phosphoglycerate kinase from Thermotoga maritima reveals the catalytic mechanism and determinants of thermal stability.
Related PDB1vpe
Related UniProtKBP36204
[4]
PubMed ID9521762
JournalBiochemistry
Year1998
Volume37
Pages4429-36
AuthorsBernstein BE, Hol WG
TitleCrystal structures of substrates and products bound to the phosphoglycerate kinase active site reveal the catalytic mechanism.
[5]
Medline ID99315861
PubMed ID10383424
JournalJ Biol Chem
Year1999
Volume274
Pages19181-7
AuthorsAlvarez M, Wouters J, Maes D, Mainfroid V, Rentier-Delrue F, Wyns L, Depiereux E, Martial JA
TitleLys13 plays a crucial role in the functional adaptation of the thermophilic triose-phosphate isomerase from Bacillus stearothermophilus to high temperatures.
[6]
CommentsX-RAY CRYSTALLOGRAPHY (2.85 ANGSTROMS) OF TIM.
Medline ID20058648
PubMed ID10591103
JournalProteins
Year1999
Volume37
Pages441-53
AuthorsMaes D, Zeelen JP, Thanki N, Beaucamp N, Alvarez M, Thi MH, Backmann J, Martial JA, Wyns L, Jaenicke R, Wierenga RK
TitleThe crystal structure of triosephosphate isomerase (TIM) from Thermotoga maritima: a comparative thermostability structural analysis of ten different TIM structures.
Related PDB1b9b
Related UniProtKBP36204
[7]
PubMed ID11243785
JournalJ Mol Biol
Year2001
Volume306
Pages745-57
AuthorsWalden H, Bell GS, Russell RJ, Siebers B, Hensel R, Taylor GL
TitleTiny TIM: a small, tetrameric, hyperthermostable triosephosphate isomerase.
[8]
PubMed ID11265486
JournalMethods Enzymol
Year2001
Volume331
Pages90-104
AuthorsCrowhurst G, McHarg J, Littlechild JA
TitlePhosphoglycerate kinases from bacteria and archaea.
[9]
PubMed ID12102622
JournalBiochemistry
Year2002
Volume41
Pages8796-806
AuthorsKovari Z, Flachner B, Naray-Szabo G, Vas M
TitleCrystallographic and thiol-reactivity studies on the complex of pig muscle phosphoglycerate kinase with ATP analogues: correlation between nucleotide binding mode and helix flexibility.
[10]
PubMed ID14997553
JournalProteins
Year2004
Volume55
Pages198-209
AuthorsKovari Z, Vas M
TitleProtein conformer selection by sequence-dependent packing contacts in crystals of 3-phosphoglycerate kinase.

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):

createdupdated
2006-01-242014-07-08


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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)
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