D-3-phosphoglycerate dehydrogenase - Escherichia coli (strain K12)

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P0A9T0 (SERA_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 80. History...

Clusters with 100%, 90%, 50% identity |

Documents (4) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
D-3-phosphoglycerate dehydrogenase
Short name=PGDH
EC=1.1.1.95

Gene names

Name:	serA
Ordered Locus Names:	b2913, JW2880

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia ›

Protein attributes

Sequence length	410 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	3-phospho-D-glycerate + NAD⁺ = 3-phosphonooxypyruvate + NADH. 2-hydroxyglutarate + NAD⁺ = 2-oxoglutarate + NADH.
Enzyme regulation	In bacteria displays feedback inhibition by L-serine.
Pathway	Amino-acid biosynthesis; L-serine biosynthesis; L-serine from 3-phospho-D-glycerate: step 1/3.
Subunit structure	Homotetramer.
Sequence similarities	Belongs to the D-isomer specific 2-hydroxyacid dehydrogenase family. Contains 1 ACT domain.

Ontologies

Keywords
Biological process	Amino-acid biosynthesis Serine biosynthesis
Ligand	NAD
Molecular function	Oxidoreductase
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	L-serine biosynthetic process Inferred from mutant phenotype PubMed 17012394. Source: EcoCyc
Molecular_function	2-hydroxyglutarate dehydrogenase activity Inferred from direct assay PubMed 8550422. Source: EcoCyc NAD binding Inferred from electronic annotation. Source: InterPro amino acid binding Inferred from electronic annotation. Source: InterPro phosphoglycerate dehydrogenase activity Inferred from direct assay PubMed 8550422. Source: EcoCyc
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

Removed Ref.6

Chain

2 – 410

409

D-3-phosphoglycerate dehydrogenase

PRO_0000075999

Regions

Domain

338 – 409

ACT

Nucleotide binding

161 – 162

NAD By similarity

Nucleotide binding

238 – 240

NAD By similarity

Nucleotide binding

292 – 295

NAD By similarity

Sites

Active site

240

Active site

269

Active site

292

Proton donor

Binding site

181

NAD By similarity

Binding site

264

NAD By similarity

Secondary structure

410

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P0A9T0 [UniParc].

Last modified January 23, 2007. Version 2.
Checksum: 61EF5EFC304DF6F0
Show »

FASTA

410

44,176

        10         20         30         40         50         60 
MAKVSLEKDK IKFLLVEGVH QKALESLRAA GYTNIEFHKG ALDDEQLKES IRDAHFIGLR 

        70         80         90        100        110        120 
SRTHLTEDVI NAAEKLVAIG CFCIGTNQVD LDAAAKRGIP VFNAPFSNTR SVAELVIGEL 

       130        140        150        160        170        180 
LLLLRGVPEA NAKAHRGVWN KLAAGSFEAR GKKLGIIGYG HIGTQLGILA ESLGMYVYFY 

       190        200        210        220        230        240 
DIENKLPLGN ATQVQHLSDL LNMSDVVSLH VPENPSTKNM MGAKEISLMK PGSLLINASR 

       250        260        270        280        290        300 
GTVVDIPALC DALASKHLAG AAIDVFPTEP ATNSDPFTSP LCEFDNVLLT PHIGGSTQEA 

       310        320        330        340        350        360 
QENIGLEVAG KLIKYSDNGS TLSAVNFPEV SLPLHGGRRL MHIHENRPGV LTALNKIFAE 

       370        380        390        400        410 
QGVNIAAQYL QTSAQMGYVV IDIEADEDVA EKALQAMKAI PGTIRARLLY

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The nucleotide sequence of the serA gene of Escherichia coli and the amino acid sequence of the encoded protein, D-3-phosphoglycerate dehydrogenase." Tobey K.L., Grant G.A. J. Biol. Chem. 261:12179-12183(1986) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[2]	"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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[3]	"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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]	Roy I., Leadlay P.F. Submitted (JUN-1992) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-99. Strain: K12.
[5]	"The tdh and serA operons of Escherichia coli: mutational analysis of the regulatory elements of leucine-responsive genes." Rex J.H., Aronson B.D., Somerville R.L. J. Bacteriol. 173:5944-5953(1991) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-29. Strain: K12.
[6]	"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] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-13. Strain: K12 / EMG2.
[7]	"Escherichia coli proteome analysis using the gene-protein database." VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C. Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY 2D-GEL.
[8]	"The allosteric ligand site in the Vmax-type cooperative enzyme phosphoglycerate dehydrogenase." Schuller D.J., Grant G.A., Banaszak L.J. Nat. Struct. Biol. 2:69-76(1995) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.75 ANGSTROMS).
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

L29397 Genomic DNA. Translation: AAA24625.1.
U28377 Genomic DNA. Translation: AAA69080.1.
U00096 Genomic DNA. Translation: AAC75950.1.
AP009048 Genomic DNA. Translation: BAE76977.1.
X66836 Genomic DNA. Translation: CAA47308.1.
M64630 Genomic DNA. Translation: AAA73016.1.

PIR

DEECPG. A25200.

RefSeq

NP_417388.1. NC_000913.2.
YP_491113.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1PSD	X-ray	2.75	A/B	2-410	[»]
1SC6	X-ray	2.09	A/B/C/D	7-409	[»]
1YBA	X-ray	2.24	A/B/C/D	1-410	[»]
2P9C	X-ray	2.46	A/B	1-410	[»]
2P9E	X-ray	2.60	A/B/C/D	1-410	[»]
2P9G	X-ray	2.80	A/B	1-410	[»]
2PA3	X-ray	2.74	A	1-410	[»]

ProteinModelPortal

P0A9T0.

SMR

P0A9T0. Positions 5-410.

ModBase

Search...

Protein-protein interaction databases

IntAct

P0A9T0. 3 interactions.

STRING

511145.b2913.

PTM databases

PhosSite

P0810437.

Proteomic databases

PaxDb

P0A9T0.

PRIDE

P0A9T0.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC75950; AAC75950; b2913.
BAE76977; BAE76977; BAE76977.

GeneID

12932179.
945258.

KEGG

ecj:Y75_p2844.
eco:b2913.

PATRIC

32121238. VBIEscCol129921_3007.

Organism-specific databases

EchoBASE

EB0937.

EcoGene

EG10944. serA.

Phylogenomic databases

eggNOG

COG0111.

HOGENOM

HOG000136696.

K00058.

OMA

RGGWLKS.

ProtClustDB

PRK11790.

Enzyme and pathway databases

BioCyc

EcoCyc:PGLYCDEHYDROG-MONOMER.
ECOL316407:JW2880-MONOMER.
MetaCyc:PGLYCDEHYDROG-MONOMER.

SABIO-RK

P0A9T0.

UniPathway

UPA00135; UER00196.

Gene expression databases

Genevestigator

P0A9T0.

Family and domain databases

Gene3D

3.40.50.720. 2 hits.

InterPro

IPR002912. ACT_dom.
IPR006139. D-isomer_2_OHA_DH_cat_dom.
IPR006140. D-isomer_2_OHA_DH_NAD-bd.
IPR016040. NAD(P)-bd_dom.
[Graphical view]

Pfam

PF00389. 2-Hacid_dh. 1 hit.
PF02826. 2-Hacid_dh_C. 1 hit.
PF01842. ACT. 1 hit.
[Graphical view]

PROSITE

PS00065. D_2_HYDROXYACID_DH_1. 1 hit.
PS00670. D_2_HYDROXYACID_DH_2. 1 hit.
PS00671. D_2_HYDROXYACID_DH_3. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P0A9T0.

Entry information

Entry name

SERA_ECOLI

Accession

Primary (citable) accession number: P0A9T0
Secondary accession number(s): P08328, Q2M9S9, Q47633

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 1, 1988
Last sequence update:	January 23, 2007
Last modified:	May 1, 2013
This is version 80 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

PATHWAY comments

Index of metabolic and biosynthesis pathways

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

PTM databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents