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

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Reviewed, UniProtKB/Swiss-Prot P0A9T0 (SERA_ECOLI)

Last modified June 16, 2009. Version 45. History...

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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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) [Complete proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

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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.

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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-glyceric acid: step 1/3.
Subunit structure	Homotetramer.
Sequence similarities	Belongs to the D-isomer specific 2-hydroxyacid dehydrogenase family. Contains 1 ACT domain.

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Ontologies

Keywords
Biological process	Amino-acid biosynthesis Serine biosynthesis
Ligand	NAD
Molecular function	Oxidoreductase
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	L-serine biosynthetic process Inferred from electronic annotation. Source: UniProtKB-KW oxidation reduction Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	NAD or NADH binding Inferred from electronic annotation. Source: InterPro amino acid binding Inferred from electronic annotation. Source: InterPro phosphoglycerate dehydrogenase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

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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

Sites

Active site

240

Active site

269

Active site

292

Proton donor

Secondary structure

410

Helix Strand Turn

Details...

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Sequences

Sequence

Length

Mass (Da)

Tools

P0A9T0-1 [UniParc].

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

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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: 3017965] [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: 9278503] [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: 16738553] [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: 1917830] [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: 9298646] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-13. Strain: K12 / EMG2.
[7]	"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: 7719856] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.75 ANGSTROMS).
+	Additional computationally mapped references.

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Cross-references

Sequence databases

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

AP_003471.1.
NP_417388.1.

3D structure databases

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	[»]

ModBase

Search...

PTM databases

PhosSite

P0A9T0.

2-D gel databases

ECO2DBASE

G044.1. 6TH EDITION.

Genome annotation databases

GeneID

945258.

GenomeReviews

Gene locus JW2880 in contig AP009048_GR.
Gene locus b2913 in contig U00096_GR.

KEGG

ecj:JW2880.
eco:b2913.

Organism-specific databases

EchoBASE

EB0937.

EcoGene

EG10944. serA.

CMR

Search...

Phylogenomic databases

HOGENOM

P0A9T0.

OMA

P0A9T0. GIRSKTK.

Enzyme and pathway databases

BioCyc

EcoCyc:PGLYCDEHYDROG-MON.
MetaCyc:PGLYCDEHYDROG-MON.

Family and domain databases

InterPro

IPR002912. ACT_bd.
IPR006139. D-isomer_2_OHA_DH.
IPR006140. D-isomer_2_OHA_DH_NAD-bd.
IPR016040. NAD(P)-bd_dom.
[Graphical view]

Gene3D

G3DSA:3.40.50.720. NAD(P)-bd. 1 hit.

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...

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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:	June 16, 2009
This is version 45 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)

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