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Protein

Glyceraldehyde-3-phosphate dehydrogenase

Gene

gap

Organism
Aquifex aeolicus (strain VF5)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the oxidative phosphorylation of glyceraldehyde 3-phosphate (G3P) to 1,3-bisphosphoglycerate (BPG) using the cofactor NAD. The first reaction step involves the formation of a hemiacetal intermediate between G3P and a cysteine residue, and this hemiacetal intermediate is then oxidized to a thioester, with concomitant reduction of NAD to NADH. The reduced NADH is then exchanged with the second NAD, and the thioester is attacked by a nucleophilic inorganic phosphate to produce BPG.By similarity

Catalytic activityi

D-glyceraldehyde 3-phosphate + phosphate + NAD+ = 3-phospho-D-glyceroyl phosphate + NADH.By similarity

Pathwayi: glycolysis

This protein is involved in step 1 of the subpathway that synthesizes pyruvate from D-glyceraldehyde 3-phosphate.Curated
Proteins known to be involved in the 5 steps of the subpathway in this organism are:
  1. Glyceraldehyde-3-phosphate dehydrogenase (gap)
  2. Phosphoglycerate kinase (pgk)
  3. Probable 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (apgM)
  4. Enolase (eno)
  5. no protein annotated in this organism
This subpathway is part of the pathway glycolysis, which is itself part of Carbohydrate degradation.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes pyruvate from D-glyceraldehyde 3-phosphate, the pathway glycolysis and in Carbohydrate degradation.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei34 – 341NAD1 Publication
Binding sitei78 – 781NAD; via carbonyl oxygen1 Publication
Binding sitei120 – 1201NAD1 Publication
Active sitei152 – 1521NucleophileBy similarity
Sitei179 – 1791Activates thiol group during catalysisBy similarity
Binding sitei182 – 1821Glyceraldehyde 3-phosphateBy similarity
Binding sitei183 – 1831NADBy similarity
Binding sitei197 – 1971Glyceraldehyde 3-phosphateBy similarity
Binding sitei233 – 2331Glyceraldehyde 3-phosphateBy similarity
Binding sitei322 – 3221NAD1 Publication

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi12 – 132NAD1 Publication

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Glycolysis

Keywords - Ligandi

NAD, Nucleotide-binding

Enzyme and pathway databases

BioCyciAAEO224324:GJBH-759-MONOMER.
UniPathwayiUPA00109; UER00184.

Names & Taxonomyi

Protein namesi
Recommended name:
Glyceraldehyde-3-phosphate dehydrogenaseBy similarity (EC:1.2.1.12By similarity)
Short name:
GAPDHBy similarity
Alternative name(s):
NAD-dependent glyceraldehyde-3-phosphate dehydrogenaseBy similarity
Gene namesi
Name:gap
Ordered Locus Names:aq_1065
OrganismiAquifex aeolicus (strain VF5)
Taxonomic identifieri224324 [NCBI]
Taxonomic lineageiBacteriaAquificaeAquificalesAquificaceaeAquifex
Proteomesi
  • UP000000798 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 342342Glyceraldehyde-3-phosphate dehydrogenasePRO_0000145629Add
BLAST

Proteomic databases

PRIDEiO67161.

Interactioni

Subunit structurei

Homotetramer.1 Publication

Protein-protein interaction databases

STRINGi224324.aq_1065.

Structurei

Secondary structure

1
342
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 85Combined sources
Helixi12 – 2110Combined sources
Beta strandi28 – 336Combined sources
Helixi38 – 469Combined sources
Turni49 – 513Combined sources
Beta strandi58 – 603Combined sources
Beta strandi62 – 676Combined sources
Beta strandi70 – 756Combined sources
Helixi80 – 823Combined sources
Helixi86 – 883Combined sources
Beta strandi91 – 955Combined sources
Beta strandi97 – 993Combined sources
Helixi103 – 1064Combined sources
Turni107 – 1093Combined sources
Helixi110 – 1123Combined sources
Beta strandi115 – 1217Combined sources
Beta strandi127 – 1293Combined sources
Turni132 – 1343Combined sources
Helixi136 – 1383Combined sources
Turni141 – 1433Combined sources
Beta strandi146 – 1483Combined sources
Helixi152 – 16817Combined sources
Beta strandi170 – 18011Combined sources
Beta strandi185 – 1895Combined sources
Turni195 – 1984Combined sources
Helixi201 – 2033Combined sources
Beta strandi206 – 2083Combined sources
Helixi214 – 2185Combined sources
Helixi221 – 2233Combined sources
Turni224 – 2263Combined sources
Beta strandi227 – 2359Combined sources
Beta strandi240 – 25011Combined sources
Helixi255 – 27016Combined sources
Helixi275 – 2773Combined sources
Beta strandi280 – 2845Combined sources
Helixi290 – 2934Combined sources
Beta strandi299 – 3035Combined sources
Helixi304 – 3063Combined sources
Beta strandi308 – 3103Combined sources
Beta strandi313 – 3208Combined sources
Helixi324 – 33916Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2EP7X-ray2.30A/B1-342[»]
ProteinModelPortaliO67161.
SMRiO67161. Positions 2-340.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO67161.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni151 – 1533Glyceraldehyde 3-phosphate bindingBy similarity
Regioni210 – 2112Glyceraldehyde 3-phosphate bindingBy similarity

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4105C17. Bacteria.
COG0057. LUCA.
HOGENOMiHOG000071679.
InParanoidiO67161.
KOiK00134.
OMAiFVRVLSW.
OrthoDBiEOG66TG3S.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
InterProiIPR020831. GlycerAld/Erythrose_P_DH.
IPR020830. GlycerAld_3-P_DH_AS.
IPR020829. GlycerAld_3-P_DH_cat.
IPR020828. GlycerAld_3-P_DH_NAD(P)-bd.
IPR006424. Glyceraldehyde-3-P_DH_1.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PANTHERiPTHR10836. PTHR10836. 1 hit.
PfamiPF02800. Gp_dh_C. 1 hit.
PF00044. Gp_dh_N. 1 hit.
[Graphical view]
PIRSFiPIRSF000149. GAP_DH. 1 hit.
PRINTSiPR00078. G3PDHDRGNASE.
SMARTiSM00846. Gp_dh_N. 1 hit.
[Graphical view]
SUPFAMiSSF51735. SSF51735. 1 hit.
TIGRFAMsiTIGR01534. GAPDH-I. 1 hit.
PROSITEiPS00071. GAPDH. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

O67161-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAIKVGINGF GRIGRSFFRA SWGREEIEIV AINDLTDAKH LAHLLKYDSV
60 70 80 90 100
HGIFKGSVEA KDDSIVVDGK EIKVFAQKDP SQIPWGDLGV DVVIEATGVF
110 120 130 140 150
RDRENASKHL QGGAKKVIIT APAKNPDITV VLGVNEEKYN PKEHNIISNA
160 170 180 190 200
SCTTNCLAPC VKVLNEAFGV EKGYMVTVHA YTNDQRLLDL PHKDFRRARA
210 220 230 240 250
AAINIVPTTT GAAKAIGEVI PELKGKLDGT ARRVPVPDGS LIDLTVVVNK
260 270 280 290 300
APSSVEEVNE KFREAAQKYR ESGKVYLKEI LQYCEDPIVS TDIVGNPHSA
310 320 330 340
IFDAPLTQVI DNLVHIAAWY DNEWGYSCRL RDLVIYLAER GL
Length:342
Mass (Da):37,613
Last modified:August 1, 1998 - v1
Checksum:i4A6E070088985DAA
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000657 Genomic DNA. Translation: AAC07122.1.
PIRiF70391.
RefSeqiNP_213724.1. NC_000918.1.
WP_010880662.1. NC_000918.1.

Genome annotation databases

EnsemblBacteriaiAAC07122; AAC07122; aq_1065.
GeneIDi1193795.
KEGGiaae:aq_1065.
PATRICi20959410. VBIAquAeo85532_0825.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000657 Genomic DNA. Translation: AAC07122.1.
PIRiF70391.
RefSeqiNP_213724.1. NC_000918.1.
WP_010880662.1. NC_000918.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2EP7X-ray2.30A/B1-342[»]
ProteinModelPortaliO67161.
SMRiO67161. Positions 2-340.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224324.aq_1065.

Proteomic databases

PRIDEiO67161.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC07122; AAC07122; aq_1065.
GeneIDi1193795.
KEGGiaae:aq_1065.
PATRICi20959410. VBIAquAeo85532_0825.

Phylogenomic databases

eggNOGiENOG4105C17. Bacteria.
COG0057. LUCA.
HOGENOMiHOG000071679.
InParanoidiO67161.
KOiK00134.
OMAiFVRVLSW.
OrthoDBiEOG66TG3S.

Enzyme and pathway databases

UniPathwayiUPA00109; UER00184.
BioCyciAAEO224324:GJBH-759-MONOMER.

Miscellaneous databases

EvolutionaryTraceiO67161.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
InterProiIPR020831. GlycerAld/Erythrose_P_DH.
IPR020830. GlycerAld_3-P_DH_AS.
IPR020829. GlycerAld_3-P_DH_cat.
IPR020828. GlycerAld_3-P_DH_NAD(P)-bd.
IPR006424. Glyceraldehyde-3-P_DH_1.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PANTHERiPTHR10836. PTHR10836. 1 hit.
PfamiPF02800. Gp_dh_C. 1 hit.
PF00044. Gp_dh_N. 1 hit.
[Graphical view]
PIRSFiPIRSF000149. GAP_DH. 1 hit.
PRINTSiPR00078. G3PDHDRGNASE.
SMARTiSM00846. Gp_dh_N. 1 hit.
[Graphical view]
SUPFAMiSSF51735. SSF51735. 1 hit.
TIGRFAMsiTIGR01534. GAPDH-I. 1 hit.
PROSITEiPS00071. GAPDH. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: VF5.
  2. "Structural study of Project ID aq_1065 from Aquifex aeolicus VF5."
    RIKEN structural genomics initiative (RSGI)
    Submitted (MAR-2007) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) IN COMPLEX WITH NAD, SUBUNIT.

Entry informationi

Entry nameiG3P_AQUAE
AccessioniPrimary (citable) accession number: O67161
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 15, 1998
Last sequence update: August 1, 1998
Last modified: December 9, 2015
This is version 106 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.