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P0A9T0

- SERA_ECOLI

UniProt

P0A9T0 - SERA_ECOLI

Protein

D-3-phosphoglycerate dehydrogenase

Gene

serA

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 91 (01 Oct 2014)
      Sequence version 2 (23 Jan 2007)
      Previous versions | rss
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    Functioni

    Catalytic activityi

    3-phospho-D-glycerate + NAD+ = 3-phosphonooxypyruvate + NADH.
    2-hydroxyglutarate + NAD+ = 2-oxoglutarate + NADH.

    Enzyme regulationi

    In bacteria displays feedback inhibition by L-serine.

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei181 – 1811NADBy similarity
    Active sitei240 – 2401
    Binding sitei264 – 2641NADBy similarity
    Active sitei269 – 2691
    Active sitei292 – 2921Proton donor

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi161 – 1622NADBy similarity
    Nucleotide bindingi238 – 2403NADBy similarity
    Nucleotide bindingi292 – 2954NADBy similarity

    GO - Molecular functioni

    1. 2-hydroxyglutarate dehydrogenase activity Source: EcoCyc
    2. identical protein binding Source: EcoCyc
    3. NAD binding Source: InterPro
    4. phosphoglycerate dehydrogenase activity Source: EcoCyc
    5. serine binding Source: EcoCyc

    GO - Biological processi

    1. L-serine biosynthetic process Source: EcoCyc

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Amino-acid biosynthesis, Serine biosynthesis

    Keywords - Ligandi

    NAD

    Enzyme and pathway databases

    BioCyciEcoCyc:PGLYCDEHYDROG-MONOMER.
    ECOL316407:JW2880-MONOMER.
    MetaCyc:PGLYCDEHYDROG-MONOMER.
    SABIO-RKP0A9T0.
    UniPathwayiUPA00135; UER00196.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    D-3-phosphoglycerate dehydrogenase (EC:1.1.1.95)
    Short name:
    PGDH
    Gene namesi
    Name:serA
    Ordered Locus Names:b2913, JW2880
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG10944. serA.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed1 Publication
    Chaini2 – 410409D-3-phosphoglycerate dehydrogenasePRO_0000075999Add
    BLAST

    Proteomic databases

    PaxDbiP0A9T0.
    PRIDEiP0A9T0.

    PTM databases

    PhosSiteiP0810437.

    Expressioni

    Gene expression databases

    GenevestigatoriP0A9T0.

    Interactioni

    Subunit structurei

    Homotetramer.

    Protein-protein interaction databases

    DIPiDIP-10851N.
    IntActiP0A9T0. 3 interactions.
    STRINGi511145.b2913.

    Structurei

    Secondary structure

    1
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Turni6 – 83
    Beta strandi9 – 113
    Beta strandi13 – 153
    Helixi21 – 299
    Beta strandi35 – 373
    Helixi44 – 507
    Beta strandi55 – 595
    Beta strandi61 – 633
    Helixi67 – 726
    Beta strandi78 – 814
    Helixi91 – 966
    Turni105 – 1084
    Helixi109 – 12517
    Helixi127 – 13610
    Helixi143 – 1453
    Beta strandi153 – 1575
    Helixi161 – 17212
    Beta strandi176 – 1805
    Helixi197 – 2037
    Beta strandi205 – 2095
    Turni215 – 2195
    Helixi223 – 2286
    Beta strandi233 – 2375
    Beta strandi241 – 2444
    Helixi246 – 2549
    Beta strandi257 – 2648
    Turni276 – 2783
    Helixi279 – 2813
    Beta strandi287 – 2904
    Helixi298 – 31821
    Beta strandi324 – 3274
    Beta strandi336 – 34611
    Helixi350 – 36011
    Beta strandi364 – 3729
    Beta strandi374 – 38411
    Helixi387 – 39812
    Beta strandi403 – 4108

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1PSDX-ray2.75A/B2-410[»]
    1SC6X-ray2.09A/B/C/D7-410[»]
    1YBAX-ray2.24A/B/C/D1-410[»]
    2P9CX-ray2.46A/B1-410[»]
    2P9EX-ray2.60A/B/C/D1-410[»]
    2P9GX-ray2.80A/B1-410[»]
    2PA3X-ray2.74A1-410[»]
    ProteinModelPortaliP0A9T0.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP0A9T0.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini339 – 41072ACTPROSITE-ProRule annotationAdd
    BLAST

    Sequence similaritiesi

    Contains 1 ACT domain.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiCOG0111.
    HOGENOMiHOG000136696.
    KOiK00058.
    OMAiKFVKYSD.
    OrthoDBiEOG6VXFC3.
    PhylomeDBiP0A9T0.

    Family and domain databases

    Gene3Di3.40.50.720. 2 hits.
    InterProiIPR002912. ACT_dom.
    IPR006139. D-isomer_2_OHA_DH_cat_dom.
    IPR006140. D-isomer_DH_NAD-bd.
    IPR016040. NAD(P)-bd_dom.
    IPR029015. PGDH_2.
    [Graphical view]
    PANTHERiPTHR10996:SF18. PTHR10996:SF18. 1 hit.
    PfamiPF00389. 2-Hacid_dh. 1 hit.
    PF02826. 2-Hacid_dh_C. 1 hit.
    PF01842. ACT. 1 hit.
    [Graphical view]
    PROSITEiPS51671. ACT. 1 hit.
    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]

    Sequencei

    Sequence statusi: Complete.

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

    P0A9T0-1 [UniParc]FASTAAdd to Basket

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    MAKVSLEKDK IKFLLVEGVH QKALESLRAA GYTNIEFHKG ALDDEQLKES    50
    IRDAHFIGLR SRTHLTEDVI NAAEKLVAIG CFCIGTNQVD LDAAAKRGIP 100
    VFNAPFSNTR SVAELVIGEL LLLLRGVPEA NAKAHRGVWN KLAAGSFEAR 150
    GKKLGIIGYG HIGTQLGILA ESLGMYVYFY DIENKLPLGN ATQVQHLSDL 200
    LNMSDVVSLH VPENPSTKNM MGAKEISLMK PGSLLINASR GTVVDIPALC 250
    DALASKHLAG AAIDVFPTEP ATNSDPFTSP LCEFDNVLLT PHIGGSTQEA 300
    QENIGLEVAG KLIKYSDNGS TLSAVNFPEV SLPLHGGRRL MHIHENRPGV 350
    LTALNKIFAE QGVNIAAQYL QTSAQMGYVV IDIEADEDVA EKALQAMKAI 400
    PGTIRARLLY 410
    Length:410
    Mass (Da):44,176
    Last modified:January 23, 2007 - v2
    Checksum:i61EF5EFC304DF6F0
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    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.
    PIRiA25200. DEECPG.
    RefSeqiNP_417388.1. NC_000913.3.
    YP_491113.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC75950; AAC75950; b2913.
    BAE76977; BAE76977; BAE76977.
    GeneIDi12932179.
    945258.
    KEGGiecj:Y75_p2844.
    eco:b2913.
    PATRICi32121238. VBIEscCol129921_3007.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    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 .
    PIRi A25200. DEECPG.
    RefSeqi NP_417388.1. NC_000913.3.
    YP_491113.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    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 7-410 [» ]
    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 [» ]
    ProteinModelPortali P0A9T0.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-10851N.
    IntActi P0A9T0. 3 interactions.
    STRINGi 511145.b2913.

    PTM databases

    PhosSitei P0810437.

    Proteomic databases

    PaxDbi P0A9T0.
    PRIDEi P0A9T0.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC75950 ; AAC75950 ; b2913 .
    BAE76977 ; BAE76977 ; BAE76977 .
    GeneIDi 12932179.
    945258.
    KEGGi ecj:Y75_p2844.
    eco:b2913.
    PATRICi 32121238. VBIEscCol129921_3007.

    Organism-specific databases

    EchoBASEi EB0937.
    EcoGenei EG10944. serA.

    Phylogenomic databases

    eggNOGi COG0111.
    HOGENOMi HOG000136696.
    KOi K00058.
    OMAi KFVKYSD.
    OrthoDBi EOG6VXFC3.
    PhylomeDBi P0A9T0.

    Enzyme and pathway databases

    UniPathwayi UPA00135 ; UER00196 .
    BioCyci EcoCyc:PGLYCDEHYDROG-MONOMER.
    ECOL316407:JW2880-MONOMER.
    MetaCyc:PGLYCDEHYDROG-MONOMER.
    SABIO-RK P0A9T0.

    Miscellaneous databases

    EvolutionaryTracei P0A9T0.
    PROi P0A9T0.

    Gene expression databases

    Genevestigatori P0A9T0.

    Family and domain databases

    Gene3Di 3.40.50.720. 2 hits.
    InterProi IPR002912. ACT_dom.
    IPR006139. D-isomer_2_OHA_DH_cat_dom.
    IPR006140. D-isomer_DH_NAD-bd.
    IPR016040. NAD(P)-bd_dom.
    IPR029015. PGDH_2.
    [Graphical view ]
    PANTHERi PTHR10996:SF18. PTHR10996:SF18. 1 hit.
    Pfami PF00389. 2-Hacid_dh. 1 hit.
    PF02826. 2-Hacid_dh_C. 1 hit.
    PF01842. ACT. 1 hit.
    [Graphical view ]
    PROSITEi PS51671. ACT. 1 hit.
    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 ]
    ProtoNeti Search...

    Publicationsi

    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. 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).

    Entry informationi

    Entry nameiSERA_ECOLI
    AccessioniPrimary (citable) accession number: P0A9T0
    Secondary accession number(s): P08328, Q2M9S9, Q47633
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 1, 1988
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 91 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3