Reviewed, UniProtKB/Swiss-Prot P0A9B2 (G3P1_ECOLI)

Names and origin

Protein names

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

Gene names

Name:	gapA
Ordered Locus Names:	b1779, JW1768

Organism

Escherichia coli (strain K12) [Complete proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	331 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.14
Subcellular location	Cytoplasm.
Sequence similarities	Belongs to the glyceraldehyde-3-phosphate dehydrogenase family.

Ontologies

Keywords
Biological process	Glycolysis
Cellular component	Cytoplasm
Ligand	NAD
Molecular function	Oxidoreductase
PTM	Acetylation
Technical term	3D-structure Complete proteome 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	cytosol Inferred from direct assay. Source: UniProtKB membrane Inferred from direct assay. Source: UniProtKB
Molecular function	NAD or NADH binding Inferred from electronic annotation. Source: InterPro glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) activity Inferred from electronic annotation. Source: EC protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
cheZ	P0A9H9	1	EBI-368904,EBI-546726
yfjJ	P52125	1	EBI-368904,EBI-1123506

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.6 Ref.7

Chain

2 – 331

330

Glyceraldehyde-3-phosphate dehydrogenase A

PRO_0000145648

Regions

Nucleotide binding

12 – 13

2

NAD By similarity

Region

149 – 151

3

Glyceraldehyde 3-phosphate binding

Region

209 – 210

2

Glyceraldehyde 3-phosphate binding

Sites

Active site

150

1

Nucleophile

Binding site

34

1

NAD

Binding site

78

1

NAD; via carbonyl oxygen

Binding site

180

1

Glyceraldehyde 3-phosphate

Binding site

232

1

Glyceraldehyde 3-phosphate

Binding site

314

1

NAD

Site

177

1

Activates thiol group during catalysis

Amino acid modifications

Modified residue

132

1

N6-acetyllysine Ref.12

Modified residue

138

1

N6-acetyllysine Ref.12

Modified residue

192

1

N6-acetyllysine Ref.12

Modified residue

249

1

N6-acetyllysine Ref.12

Natural variations

Natural variant

43

1

Y → I in strain: ECOR 70.

Natural variant

266

1

G → D in strain: E830587.

Natural variant

267

1

E → A in strain: E2666-74.

Experimental info

Mutagenesis

177

1

H → N: Reduces activity about 50-fold. Ref.11

Secondary structure

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331

Helix Strand Turn

Details...

Beta strand

3 – 8

6

Helix

12 – 22

11

Beta strand

25 – 36

12

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 – 111

9

Beta strand

115 – 121

7

Beta strand

124 – 126

3

Turn

132 – 134

3

Beta strand

143 – 146

4

Helix

150 – 166

17

Beta strand

168 – 178

11

Beta strand

183 – 187

5

Helix

195 – 197

3

Turn

200 – 202

3

Beta strand

205 – 208

4

Helix

211 – 218

8

Helix

220 – 222

3

Turn

223 – 225

3

Beta strand

226 – 234

9

Beta strand

239 – 249

11

Helix

253 – 265

13

Turn

266 – 271

6

Beta strand

272 – 275

4

Helix

281 – 284

4

Beta strand

289 – 294

6

Turn

295 – 297

3

Beta strand

299 – 302

4

Beta strand

305 – 312

8

Helix

316 – 328

13

Sequences

	Sequence		Length	Mass (Da)
	P0A9B2-1 [UniParc]. Last modified January 23, 2007. Version 2. Checksum: B3A460AA6D59E46D	FASTA	331	35,532
	10 20 30 40 50 60 MTIKVGINGF GRIGRIVFRA AQKRSDIEIV AINDLLDADY MAYMLKYDST HGRFDGTVEV 70 80 90 100 110 120 KDGHLIVNGK KIRVTAERDP ANLKWDEVGV DVVAEATGLF LTDETARKHI TAGAKKVVMT 130 140 150 160 170 180 GPSKDNTPMF VKGANFDKYA GQDIVSNASC TTNCLAPLAK VINDNFGIIE GLMTTVHATT 190 200 210 220 230 240 ATQKTVDGPS HKDWRGGRGA SQNIIPSSTG AAKAVGKVLP ELNGKLTGMA FRVPTPNVSV 250 260 270 280 290 300 VDLTVRLEKA ATYEQIKAAV KAAAEGEMKG VLGYTEDDVV STDFNGEVCT SVFDAKAGIA 310 320 330 LNDNFVKLVS WYDNETGYSN KVLDLIAHIS K

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Nucleotide sequence of the Escherichia coli gap gene. Different evolutionary behavior of the NAD+-binding domain and of the catalytic domain of D-glyceraldehyde-3-phosphate dehydrogenase." Branlant G., Branlant C. Eur. J. Biochem. 150:61-66(1985) [PubMed: 2990926] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	Nelson K. Submitted (SEP-1990) to the EMBL/GenBank/DDBJ databases Cited for: SEQUENCE REVISION TO 295-300.
[3]	"A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 28.0-40.1 min region on the linkage map." Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Itoh T., Kasai H., Kashimoto K., Kimura S., Kitakawa M., Kitagawa M., Makino K., Miki T., Mizobuchi K., Mori H., Mori T., Motomura K. , Nakade S., Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G., Seki Y., Sivasundaram S., Tagami H., Takeda J., Takemoto K., Takeuchi Y., Wada C., Yamamoto Y., Horiuchi T. DNA Res. 3:363-377(1996) [PubMed: 9097039] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed: 9278503] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[5]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed: 16738553] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[6]	Pasquali C., Sanchez J.-C., Ravier F., Golaz O., Hughes G.J., Frutiger S., Paquet N., Wilkins M., Appel R.D., Bairoch A., Hochstrasser D.F. Submitted (SEP-1994) to UniProtKB Cited for: PROTEIN SEQUENCE OF 2-13. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[7]	"Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12." Link A.J., Robison K., Church G.M. Electrophoresis 18:1259-1313(1997) [PubMed: 9298646] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-13. Strain: K12 / EMG2.
[8]	"Nucleotide polymorphism and evolution in the glyceraldehyde-3-phosphate dehydrogenase gene (gapA) in natural populations of Salmonella and Escherichia coli." Nelson K., Whittam T.S., Selander R.K. Proc. Natl. Acad. Sci. U.S.A. 88:6667-6671(1991) [PubMed: 1862091] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 7-314. Strain: A8190, E2666-74, E3406, E830587, E851819, ECOR 14, ECOR 32, ECOR 40, ECOR 52, ECOR 58, ECOR 64 and ECOR 70.
[9]	"Detecting selective sweeps in naturally occurring Escherichia coli." Guttman D.S., Dykhuizen D.E. Genetics 138:993-1003(1994) [PubMed: 7896119] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 10-321. Strain: ECOR 10, ECOR 16, ECOR 38, ECOR 39, ECOR 4, ECOR 40, ECOR 49, ECOR 65, ECOR 68, ECOR 8 and O2:HN / ECOR 50 / P97 / UPEC.
[10]	"A naturally occurring horizontal gene transfer from a eukaryote to a prokaryote." Doolittle R.F., Feng D.F., Anderson K.L., Alberro M.R. J. Mol. Evol. 31:383-388(1990) [PubMed: 2124629] [Abstract] Cited for: GENE TRANSFER DISCUSSION.
[11]	"Role of the histidine 176 residue in glyceraldehyde-3-phosphate dehydrogenase as probed by site-directed mutagenesis." Soukri A., Mougin A., Corbier C., Wonacott A., Branlant C., Branlant G. Biochemistry 28:2586-2592(1989) [PubMed: 2659073] [Abstract] Cited for: MUTAGENESIS OF HIS-177.
[12]	"Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli." Zhang J., Sprung R., Pei J., Tan X., Kim S., Zhu H., Liu C.F., Grishin N.V., Zhao Y. Mol. Cell. Proteomics 8:215-225(2009) [PubMed: 18723842] [Abstract] Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-132; LYS-138; LYS-192 AND LYS-249, MASS SPECTROMETRY.
[13]	"Comparison of the structures of wild-type and a N313T mutant of Escherichia coli glyceraldehyde 3-phosphate dehydrogenases: implication for NAD binding and cooperativity." Duee E., Olivier-Deyris L., Fanchon E., Corbier C., Branlant G., Dideberg O. J. Mol. Biol. 257:814-838(1996) [PubMed: 8636984] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
[14]	"Structural analysis of glyceraldehyde 3-phosphate dehydrogenase from Escherichia coli: direct evidence of substrate binding and cofactor-induced conformational changes." Yun M., Park C.-G., Kim J.-Y., Park H.-W. Biochemistry 39:10702-10710(2000) [PubMed: 10978154] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEX WITH NAD AND GLYCERALDEHYDE 3-PHOSPHATE, SUBUNIT.

Cross-references

Sequence databases

EMBLGenBankDDBJ

X02662 Genomic DNA. Translation: CAA26498.1.
U00096 Genomic DNA. Translation: AAC74849.1.
AP009048 Genomic DNA. Translation: BAA15576.1.
M66870 Genomic DNA. Translation: AAA23838.1.
M66871 Genomic DNA. Translation: AAA23839.1.
M66872 Genomic DNA. Translation: AAA02930.1.
M66873 Genomic DNA. Translation: AAA23840.1.
M66874 Genomic DNA. Translation: AAA23841.1.
M66875 Genomic DNA. Translation: AAA23842.1.
M66876 Genomic DNA. Translation: AAA23843.1.
M66877 Genomic DNA. Translation: AAA23844.1.
M66878 Genomic DNA. Translation: AAA23845.1.
M66879 Genomic DNA. Translation: AAA23846.1.
M66880 Genomic DNA. Translation: AAA23847.1.
M66881 Genomic DNA. Translation: AAA23848.1.
M66882 Genomic DNA. Translation: AAA23849.1.
U07750 Genomic DNA. Translation: AAC43271.1.
U07751 Genomic DNA. Translation: AAC43272.1.
U07752 Genomic DNA. Translation: AAC43273.1.
U07754 Genomic DNA. Translation: AAC43274.1.
U07765 Genomic DNA. Translation: AAC43284.1.
U07768 Genomic DNA. Translation: AAC43285.1.
U07769 Genomic DNA. Translation: AAC43286.1.
U07770 Genomic DNA. Translation: AAC43287.1.
U07771 Genomic DNA. Translation: AAC43288.1.
U07772 Genomic DNA. Translation: AAC43289.1.
U07773 Genomic DNA. Translation: AAC43290.1.

PIR

DEECG3. A25209.

RefSeq

AP_002398.1.
NP_416293.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1DC3	X-ray	2.50	A/B	2-331	[»]
1DC4	X-ray	2.50	A/B	2-331	[»]
1DC5	X-ray	2.00	A/B	2-331	[»]
1DC6	X-ray	2.00	A/B	2-331	[»]
1GAD	X-ray	1.80	O/P	2-331	[»]
1GAE	X-ray	2.17	O/P	2-331	[»]
1S7C	X-ray	2.04	A	2-330	[»]
2VYN	X-ray	2.20	A/B/C	1-331	[»]
2VYV	X-ray	2.38	A/B/C	1-331	[»]

ModBase

Search...

Protein-protein interaction databases

IntAct

P0A9B2. 23 interactions.

2-D gel databases

SWISS-2DPAGE

P0A9B2.

2DBase-Ecoli

P0A9B2.

ECO2DBASE

H034.3. 6TH EDITION.
I033.5. 6TH EDITION.

Genome annotation databases

GeneID

947679.

GenomeReviews

Gene locus JW1768 in contig AP009048_GR.
Gene locus b1779 in contig U00096_GR.

KEGG

ecj:JW1768.
eco:b1779.

Organism-specific databases

EchoBASE

EB0362.

EcoGene

EG10367. gapA.

CMR

Search...

Phylogenomic databases

HOGENOM

P0A9B2.

OMA

P0A9B2. KEICTEV.

Enzyme and pathway databases

BioCyc

EcoCyc:GAPDH-A-MON.
MetaCyc:GAPDH-A-MON.

Family and domain databases

InterPro

IPR000173. GlycerAld_3-P_DH.
IPR006424. Glyceraldehyde-3-P_DH_1.
[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.

TIGRFAMs

TIGR01534. GAPDH-I. 1 hit.

PROSITE

PS00071. GAPDH. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

G3P1_ECOLI

Accession

Primary (citable) accession number: P0A9B2
Secondary accession number(s): P06977

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 1, 1988
Last sequence update:	January 23, 2007
Last modified:	June 16, 2009
This is version 50 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

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