Reviewed, UniProtKB/Swiss-Prot P00362 (G3P_BACST)

Names and origin

Protein names

Recommended name:
    Glyceraldehyde-3-phosphate dehydrogenase
      Short name=GAPDH
    EC=1.2.1.12

Gene names

Name:

gap

Organism

Bacillus stearothermophilus (Geobacillus stearothermophilus)

Taxonomic identifier

1422 [NCBI]

Taxonomic lineage

Bacteria › Firmicutes › Bacillales › Bacillaceae › Geobacillus

Protein attributes

Sequence length	335 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

General annotation (Comments)

Catalytic activity	D-glyceraldehyde 3-phosphate + phosphate + NAD+ = 3-phospho-D-glyceroyl phosphate + NADH.
Pathway	Carbohydrate degradation; glycolysis; pyruvate from D-glyceraldehyde 3-phosphate: step 1/5.
Subunit structure	Homotetramer. Ref.6 Ref.7
Subcellular location	Cytoplasm.
Sequence similarities	Belongs to the glyceraldehyde-3-phosphate dehydrogenase family.
Caution	Ref.1 sequence was incorrect and retracted in Ref.2.

Ontologies

Keywords
Biological process	Glycolysis
Cellular component	Cytoplasm
Ligand	NAD
Molecular function	Oxidoreductase
Technical term	3D-structure Direct protein sequencing
Gene Ontology (GO)
Biological process	glycolysis Inferred from electronic annotation. Source: UniProtKB-KW oxidation reduction Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	NAD or NADH binding Inferred from electronic annotation. Source: InterPro glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.4

Chain

2 – 335

334

Glyceraldehyde-3-phosphate dehydrogenase

PRO_0000145633

Regions

Nucleotide binding

12 – 13

2

NAD

Region

151 – 153

3

Glyceraldehyde 3-phosphate binding

Sites

Active site

152

1

Nucleophile

Binding site

34

1

NAD

Binding site

78

1

NAD; via carbonyl oxygen

Binding site

120

1

NAD

Binding site

182

1

Glyceraldehyde 3-phosphate

Binding site

197

1

Glyceraldehyde 3-phosphate

Binding site

233

1

Glyceraldehyde 3-phosphate

Binding site

315

1

NAD

Site

179

1

Activates thiol group during catalysis

Experimental info

Mutagenesis

152

1

C → A: Loss of activity. Ref.7

Secondary structure

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335

Helix Strand Turn

Details...

Beta strand

3 – 8

6

Helix

12 – 21

10

Beta strand

25 – 33

9

Helix

38 – 46

9

Turn

49 – 51

3

Beta strand

58 – 61

4

Beta strand

64 – 67

4

Beta strand

70 – 75

6

Helix

80 – 82

3

Helix

85 – 88

4

Beta strand

92 – 95

4

Beta strand

97 – 99

3

Helix

103 – 106

4

Helix

108 – 111

4

Beta strand

115 – 121

7

Beta strand

127 – 129

3

Turn

132 – 134

3

Helix

136 – 138

3

Turn

141 – 143

3

Beta strand

146 – 148

3

Helix

152 – 168

17

Beta strand

170 – 180

11

Beta strand

185 – 189

5

Turn

195 – 198

4

Turn

201 – 203

3

Beta strand

206 – 209

4

Helix

214 – 218

5

Helix

221 – 223

3

Turn

224 – 226

3

Beta strand

227 – 235

9

Beta strand

240 – 250

11

Helix

254 – 266

13

Turn

267 – 269

3

Beta strand

273 – 276

4

Helix

282 – 285

4

Beta strand

290 – 295

6

Helix

296 – 298

3

Beta strand

300 – 302

3

Turn

303 – 305

3

Beta strand

306 – 313

8

Helix

317 – 332

16

Sequences

	Sequence		Length	Mass (Da)
	P00362-1 [UniParc]. Last modified January 23, 2007. Version 5. Checksum: DBAAA2DD24497E18	FASTA	335	36,075
	10 20 30 40 50 60 MAVKVGINGF GRIGRNVFRA ALKNPDIEVV AVNDLTDANT LAHLLKYDSV HGRLDAEVSV 70 80 90 100 110 120 NGNNLVVNGK EIIVKAERDP ENLAWGEIGV DIVVESTGRF TKREDAAKHL EAGAKKVIIS 130 140 150 160 170 180 APAKNEDITI VMGVNQDKYD PKAHHVISNA SCTTNCLAPF AKVLHEQFGI VRGMMTTVHS 190 200 210 220 230 240 YTNDQRILDL PHKDLRRARA AAESIIPTTT GAAKAVALVL PELKGKLNGM AMRVPTPNVS 250 260 270 280 290 300 VVDLVAELEK EVTVEEVNAA LKAAAEGELK GILAYSEEPL VSRDYNGSTV SSTIDALSTM 310 320 330 VIDGKMVKVV SWYDNETGYS HRVVDLAAYI ASKGL

References

[1]	"Nucleotide sequences of genes encoding heat-stable and heat-labile glyceraldehyde-3-phosphate dehydrogenases; amino acid sequence and protein thermostability." Tesfay H.S., Amelunxen R.E., Goldberg I.D. Gene 82:237-248(1989) [PubMed: 2684782] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	Erratum Tesfay H.S., Amelunxen R.E., Goldberg I.D. Gene 94:144-144(1990) [PubMed: 2227448] [Abstract] Cited for: RETRACTION.
[3]	"Nucleotide sequence determination of the DNA region coding for Bacillus stearothermophilus glyceraldehyde-3-phosphate dehydrogenase and of the flanking DNA regions required for its expression in Escherichia coli." Branlant C., Oster T., Branlant G. Gene 75:145-155(1989) [PubMed: 2656407] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[4]	"D-glyceraldehyde-3-phosphate dehydrogenase. Complete amino-acid sequence of the enzyme from Bacillus stearothermophilus." Walker J.E., Carne A.F., Runswick M.J., Bridgen J., Harris J.I. Eur. J. Biochem. 108:549-565(1980) [PubMed: 7408868] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-335.
[5]	"Sequence and structure of D-glyceraldehyde 3-phosphate dehydrogenase from Bacillus stearothermophilus." Biesecker G., Harris J.I., Thierry J.-C., Walker J.E., Wonacott A.J. Nature 266:328-333(1977) [PubMed: 193030] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS).
[6]	"Structure of holo-glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus at 1.8-A resolution." Skarzynski T., Moody P.C.E., Wonacott A.J. J. Mol. Biol. 193:171-187(1987) [PubMed: 3586018] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) IN COMPLEX WITH NAD, SUBUNIT.
[7]	"A crystallographic comparison between mutated glyceraldehyde-3-phosphate dehydrogenases from Bacillus stearothermophilus complexed with either NAD+ or NADP+." Didierjean C., Rahuel-Clermont S., Vitoux B., Dideberg O., Branlant G., Aubry A. J. Mol. Biol. 268:739-759(1997) [PubMed: 9175858] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.45 ANGSTROMS) IN COMPLEX WITH NAD, MUTAGENESIS OF CYS-152, SUBUNIT.
[8]	"Crystal structure of two ternary complexes of phosphorylating glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus with NAD and D-glyceraldehyde 3-phosphate." Didierjean C., Corbier C., Fatih M., Favier F., Boschi-Muller S., Branlant G., Aubry A. J. Biol. Chem. 278:12968-12976(2003) [PubMed: 12569100] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.11 ANGSTROMS) IN COMPLEX WITH NAD AND GLYCERALDEHYDE 3-PHOSPHATE.

Cross-references

Sequence databases

EMBLGenBankDDBJ

M24493 Genomic DNA. Translation: AAA22461.1.

PIR

DEBSGF. JS0164.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1DBV	X-ray	2.50	O/P/Q/R	2-335	[»]
1GD1	X-ray	1.80	O/P/Q/R	2-335	[»]
1NPT	X-ray	2.18	O/P/Q/R	2-335	[»]
1NQ5	X-ray	2.11	A/C/O/Q	2-335	[»]
1NQA	X-ray	2.20	O/P/Q/R	2-335	[»]
1NQO	X-ray	2.01	A/C/O/Q	2-335	[»]
2DBV	X-ray	2.20	O/P/Q/R	2-335	[»]
2GD1	X-ray	2.50	O/P/Q/R	2-334	[»]
3CMC	X-ray	1.77	O/P/Q/R	2-335	[»]
3DBV	X-ray	2.45	O/P/Q/R	2-335	[»]
4DBV	X-ray	2.50	O/P/Q/R	2-335	[»]

ModBase

Search...

Enzyme and pathway databases

BRENDA

1.2.1.12. 266715.

Family and domain databases

InterPro

IPR020830. GlycerAld_3-P_DH_AS.
IPR020829. GlycerAld_3-P_DH_cat.
IPR020832. GlycerAld_3-P_DH_cat_sub.
IPR020831. GlycerAld_3-P_DH_family.
IPR020828. GlycerAld_3-P_DH_NAD(P)_bd.
IPR000173. GlycerAld_3-P_DH_subfam.
IPR006424. Glyceraldehyde-3-P_DH_1.
IPR016040. NAD(P)-bd_dom.
[Graphical view]

PANTHER

PTHR10836. GAP_DH. 1 hit.

Pfam

PF02800. Gp_dh_C. 1 hit.
PF00044. Gp_dh_N. 1 hit.
[Graphical view]

PIRSF

PIRSF000149. GAP_DH. 1 hit.

PRINTS

PR00078. G3PDHDRGNASE.

SMART

SM00846. Gp_dh_N. 1 hit.
[Graphical view]

TIGRFAMs

TIGR01534. GAPDH-I. 1 hit.

PROSITE

PS00071. GAPDH. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

G3P_BACST

Accession

Primary (citable) accession number: P00362

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	January 23, 2007
Last modified:	November 24, 2009
This is version 95 of the entry and version 5 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)