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Protein

Glyceraldehyde-3-phosphate dehydrogenase

Gene

gap

Organism
Geobacillus stearothermophilus (Bacillus stearothermophilus)
Status
Reviewed-Annotation score: Annotation score: 5 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.2 Publications

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), Phosphoglycerate kinase (pgk), Phosphoglycerate kinase (pgk), Phosphoglycerate kinase (pgk)
  3. 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (gpmI), 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (gpmI), 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (gpmI_1), 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (gpmI)
  4. Enolase (eno), Enolase (eno), Enolase (eno)
  5. Pyruvate kinase (pyk), Pyruvate kinase (AA904_05055), Pyruvate kinase (pyk), Pyruvate kinase (GT94_09925), Pyruvate kinase (B4114_2369)
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 – 341NAD4 Publications
Binding sitei78 – 781NAD; via carbonyl oxygen4 Publications
Binding sitei120 – 1201NAD4 Publications
Active sitei152 – 1521Nucleophile1 Publication1 Publication
Sitei179 – 1791Activates thiol group during catalysisBy similarity
Binding sitei182 – 1821Glyceraldehyde 3-phosphate5 Publications
Binding sitei183 – 1831NAD4 Publications
Binding sitei197 – 1971Glyceraldehyde 3-phosphate3 Publications
Binding sitei233 – 2331Glyceraldehyde 3-phosphate5 Publications
Binding sitei315 – 3151NAD4 Publications

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi12 – 132NAD4 Publications

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

BRENDAi1.2.1.12. 623.
SABIO-RKP00362.
UniPathwayiUPA00109; UER00184.

Names & Taxonomyi

Protein namesi
Recommended name:
Glyceraldehyde-3-phosphate dehydrogenase1 Publication (EC:1.2.1.12By similarity)
Short name:
GAPDH1 Publication
Alternative name(s):
NAD-dependent glyceraldehyde-3-phosphate dehydrogenase1 Publication
Gene namesi
Name:gap
OrganismiGeobacillus stearothermophilus (Bacillus stearothermophilus)
Taxonomic identifieri1422 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeGeobacillus

Subcellular locationi

  • Cytoplasm 1 Publication

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi35 – 373LTD → TGG in mutant B-S, the recognition of NAD is slightly affected; when associated with A-190 and S-191. 1 Publication
Mutagenesisi152 – 1521C → A: Loss of dehydrogenase activity. 2 Publications
Mutagenesisi152 – 1521C → S: Possess a low residual dehydrogenase activity. 1 Publication
Mutagenesisi190 – 1901L → A in mutant D32G-S, a strong alteration of the affinity for NAD is observed; when associated with S-191. In mutant B-S, the recognition of NAD is slightly affected; when associated with 35-T--G-37 and S-191. 1 Publication
Mutagenesisi191 – 1911P → S in mutant D32G-S, a strong alteration of the affinity for NAD is observed; when associated with A-190. In mutant B-S, the recognition of NAD is slightly affected; when associated with 35-T--G-37 and A-190. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemoved1 Publication
Chaini2 – 335334Glyceraldehyde-3-phosphate dehydrogenasePRO_0000145633Add
BLAST

Proteomic databases

PRIDEiP00362.

Interactioni

Subunit structurei

Homotetramer.6 Publications

Structurei

Secondary structure

1
335
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 97Combined sources
Helixi12 – 2110Combined sources
Beta strandi27 – 337Combined sources
Helixi38 – 469Combined sources
Turni49 – 513Combined sources
Beta strandi58 – 614Combined sources
Beta strandi64 – 674Combined sources
Beta strandi70 – 756Combined sources
Helixi80 – 823Combined sources
Helixi86 – 883Combined sources
Beta strandi92 – 954Combined sources
Beta strandi97 – 993Combined sources
Helixi103 – 1064Combined sources
Helixi108 – 1114Combined 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
Turni201 – 2033Combined sources
Beta strandi206 – 2094Combined sources
Helixi212 – 2198Combined sources
Helixi221 – 2233Combined sources
Turni224 – 2263Combined sources
Beta strandi227 – 2359Combined sources
Beta strandi240 – 25011Combined sources
Helixi254 – 26613Combined sources
Turni267 – 2726Combined sources
Beta strandi273 – 2764Combined sources
Helixi282 – 2854Combined sources
Beta strandi290 – 2956Combined sources
Helixi296 – 2983Combined sources
Beta strandi300 – 3023Combined sources
Turni303 – 3053Combined sources
Beta strandi306 – 3138Combined sources
Helixi317 – 33216Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1DBVX-ray2.50O/P/Q/R2-335[»]
1GD1X-ray1.80O/P/Q/R2-335[»]
1NPTX-ray2.18O/P/Q/R2-335[»]
1NQ5X-ray2.11A/C/O/Q2-335[»]
1NQAX-ray2.20O/P/Q/R2-335[»]
1NQOX-ray2.01A/C/O/Q2-335[»]
2DBVX-ray2.20O/P/Q/R2-335[»]
2GD1X-ray2.50O/P/Q/R2-335[»]
3CMCX-ray1.77O/P/Q/R2-335[»]
3DBVX-ray2.45O/P/Q/R2-335[»]
4DBVX-ray2.50O/P/Q/R2-335[»]
ProteinModelPortaliP00362.
SMRiP00362. Positions 2-335.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP00362.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni151 – 1533Glyceraldehyde 3-phosphate binding5 Publications
Regioni210 – 2112Glyceraldehyde 3-phosphate binding4 Publications

Sequence similaritiesi

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.

Sequence processingi: The displayed sequence is further processed into a mature form.

P00362-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAVKVGINGF GRIGRNVFRA ALKNPDIEVV AVNDLTDANT LAHLLKYDSV
60 70 80 90 100
HGRLDAEVSV NGNNLVVNGK EIIVKAERDP ENLAWGEIGV DIVVESTGRF
110 120 130 140 150
TKREDAAKHL EAGAKKVIIS APAKNEDITI VMGVNQDKYD PKAHHVISNA
160 170 180 190 200
SCTTNCLAPF AKVLHEQFGI VRGMMTTVHS YTNDQRILDL PHKDLRRARA
210 220 230 240 250
AAESIIPTTT GAAKAVALVL PELKGKLNGM AMRVPTPNVS VVDLVAELEK
260 270 280 290 300
EVTVEEVNAA LKAAAEGELK GILAYSEEPL VSRDYNGSTV SSTIDALSTM
310 320 330
VIDGKMVKVV SWYDNETGYS HRVVDLAAYI ASKGL
Length:335
Mass (Da):36,075
Last modified:January 23, 2007 - v5
Checksum:iDBAAA2DD24497E18
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M24493 Genomic DNA. Translation: AAA22461.1.
PIRiJS0164. DEBSGF.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M24493 Genomic DNA. Translation: AAA22461.1.
PIRiJS0164. DEBSGF.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1DBVX-ray2.50O/P/Q/R2-335[»]
1GD1X-ray1.80O/P/Q/R2-335[»]
1NPTX-ray2.18O/P/Q/R2-335[»]
1NQ5X-ray2.11A/C/O/Q2-335[»]
1NQAX-ray2.20O/P/Q/R2-335[»]
1NQOX-ray2.01A/C/O/Q2-335[»]
2DBVX-ray2.20O/P/Q/R2-335[»]
2GD1X-ray2.50O/P/Q/R2-335[»]
3CMCX-ray1.77O/P/Q/R2-335[»]
3DBVX-ray2.45O/P/Q/R2-335[»]
4DBVX-ray2.50O/P/Q/R2-335[»]
ProteinModelPortaliP00362.
SMRiP00362. Positions 2-335.
ModBaseiSearch...
MobiDBiSearch...

Proteomic databases

PRIDEiP00362.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Enzyme and pathway databases

UniPathwayiUPA00109; UER00184.
BRENDAi1.2.1.12. 623.
SABIO-RKP00362.

Miscellaneous databases

EvolutionaryTraceiP00362.

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...

Entry informationi

Entry nameiG3P_GEOSE
AccessioniPrimary (citable) accession number: P00362
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: January 23, 2007
Last modified: December 9, 2015
This is version 131 of the entry and version 5 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Caution

PubMed:2684782 sequence was incorrect and retracted in PubMed:2227448.Curated

Keywords - Technical termi

3D-structure, Direct protein sequencing

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.