PDB entry 2vk8

View 2vk8 on RCSB PDB site
Description: Crystal structure of the Saccharomyces cerevisiae pyruvate decarboxylase variant E477Q in complex with its substrate
Class: lyase
Keywords: asymmetric active sites, phenylalanine catabolism, tryptophan catabolism, thiamine pyrophosphate, dimer of dimers, phosphorylation, allosteric enzyme, tdp, tpp, lyase, nucleus, pyruvate, branched-chain amino acid catabolism, substrate activation, thiamine diphosphate, magnesium, metal-binding, decarboxylase
Deposited on 2007-12-17, released 2009-01-27
The last revision prior to the SCOPe 2.07 freeze date was dated 2013-09-11, with a file datestamp of 2013-09-06.
Experiment type: XRAY
Resolution: 1.42 Å
R-factor: 0.181
AEROSPACI score: 0.67 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: pyruvate decarboxylase isozyme 1
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P06169 (Start-562)
      • engineered mutation (476)
      • conflict (205)
      • conflict (207)
      • conflict (537)
    Domains in SCOPe 2.07: d2vk8a1, d2vk8a2, d2vk8a3
  • Chain 'B':
    Compound: pyruvate decarboxylase isozyme 1
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P06169 (Start-562)
      • engineered mutation (476)
      • conflict (205)
      • conflict (207)
      • conflict (537)
    Domains in SCOPe 2.07: d2vk8b1, d2vk8b2, d2vk8b3
  • Chain 'C':
    Compound: pyruvate decarboxylase isozyme 1
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P06169 (Start-562)
      • engineered mutation (476)
      • conflict (205)
      • conflict (207)
      • conflict (537)
    Domains in SCOPe 2.07: d2vk8c1, d2vk8c2, d2vk8c3
  • Chain 'D':
    Compound: pyruvate decarboxylase isozyme 1
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P06169 (Start-562)
      • engineered mutation (476)
      • conflict (205)
      • conflict (207)
      • conflict (537)
    Domains in SCOPe 2.07: d2vk8d1, d2vk8d2, d2vk8d3
  • Heterogens: TPP, MG, 2OP, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >2vk8A (A:)
    mseitlgkylferlkqvnvntvfglpgdfnlslldkiyevegmrwagnanelnaayaadg
    yarikgmsciittfgvgelsalngiagsyaehvgvlhvvgvpsisaqakqlllhhtlgng
    dftvfhrmsanisettamitdiatapaeidrcirttyvtqrpvylglpanlvdlnvpakl
    lqtpidmslkpndaesekevidtilvldkdaknpviladaccsrhdvkaetkklidltqf
    pafvtpmgkgsideqhpryggvyvgtlskpevkeavesadlilsvgallsdfntgsfsys
    yktknivefhsdhmkirnatfpgvqmkfvlqkllttiadaakgykpvavpartpanaavp
    astplkqewmwnqlgnflqegdvviaetgtsafginqttfpnntygisqvlwgsigfttg
    atlgaafaaeeidpkkrvilfigdgslqltvqeistmirwglkpylfvlnndgytiqkli
    hgpkaqyneiqgwdhlsllptfgakdyethrvattgewdkltqdksfndnskirmievml
    pvfdapqnlveqakltaatnakq
    

    Sequence, based on observed residues (ATOM records): (download)
    >2vk8A (A:)
    seitlgkylferlkqvnvntvfglpgdfnlslldkiyevegmrwagnanelnaayaadgy
    arikgmsciittfgvgelsalngiagsyaehvgvlhvvgvpsisaqakqlllhhtlgngd
    ftvfhrmsanisettamitdiatapaeidrcirttyvtqrpvylglpanlvdlnvpakll
    qtpidmslkpndaesekevidtilvldkdaknpviladaccsrhdvkaetkklidltqfp
    afvtpmgkgsideqhpryggvyvgtlskpevkeavesadlilsvgallsdfntgsfsysy
    ktknivefhsdhmkirnatfpgvqmkfvlqkllttiadaakgykpvavpartpanaavpa
    stplkqewmwnqlgnflqegdvviaetgtsafginqttfpnntygisqvlwgsigfttga
    tlgaafaaeeidpkkrvilfigdgslqltvqeistmirwglkpylfvlnndgytiqklih
    gpkaqyneiqgwdhlsllptfgakdyethrvattgewdkltqdksfndnskirmievmlp
    vfdapqnlveqakltaatnakq
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >2vk8B (B:)
    mseitlgkylferlkqvnvntvfglpgdfnlslldkiyevegmrwagnanelnaayaadg
    yarikgmsciittfgvgelsalngiagsyaehvgvlhvvgvpsisaqakqlllhhtlgng
    dftvfhrmsanisettamitdiatapaeidrcirttyvtqrpvylglpanlvdlnvpakl
    lqtpidmslkpndaesekevidtilvldkdaknpviladaccsrhdvkaetkklidltqf
    pafvtpmgkgsideqhpryggvyvgtlskpevkeavesadlilsvgallsdfntgsfsys
    yktknivefhsdhmkirnatfpgvqmkfvlqkllttiadaakgykpvavpartpanaavp
    astplkqewmwnqlgnflqegdvviaetgtsafginqttfpnntygisqvlwgsigfttg
    atlgaafaaeeidpkkrvilfigdgslqltvqeistmirwglkpylfvlnndgytiqkli
    hgpkaqyneiqgwdhlsllptfgakdyethrvattgewdkltqdksfndnskirmievml
    pvfdapqnlveqakltaatnakq
    

    Sequence, based on observed residues (ATOM records): (download)
    >2vk8B (B:)
    seitlgkylferlkqvnvntvfglpgdfnlslldkiyevegmrwagnanelnaayaadgy
    arikgmsciittfgvgelsalngiagsyaehvgvlhvvgvpsisaqakqlllhhtlgngd
    ftvfhrmsanisettamitdiatapaeidrcirttyvtqrpvylglpanlvdlnvpakll
    qtpidmslkpndaesekevidtilvldkdaknpviladaccsrhdvkaetkklidltqfp
    afvtpmgkgsideqhpryggvyvgtlskpevkeavesadlilsvgallsdfntgsfsysy
    ktknivefhsdhmkirnatfpgvqmkfvlqkllttiadaakgykpvavpartpanaavpa
    stplkqewmwnqlgnflqegdvviaetgtsafginqttfpnntygisqvlwgsigfttga
    tlgaafaaeeidpkkrvilfigdgslqltvqeistmirwglkpylfvlnndgytiqklih
    gpkaqyneiqgwdhlsllptfgakdyethrvattgewdkltqdksfndnskirmievmlp
    vfdapqnlveqakltaatnakq
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >2vk8C (C:)
    mseitlgkylferlkqvnvntvfglpgdfnlslldkiyevegmrwagnanelnaayaadg
    yarikgmsciittfgvgelsalngiagsyaehvgvlhvvgvpsisaqakqlllhhtlgng
    dftvfhrmsanisettamitdiatapaeidrcirttyvtqrpvylglpanlvdlnvpakl
    lqtpidmslkpndaesekevidtilvldkdaknpviladaccsrhdvkaetkklidltqf
    pafvtpmgkgsideqhpryggvyvgtlskpevkeavesadlilsvgallsdfntgsfsys
    yktknivefhsdhmkirnatfpgvqmkfvlqkllttiadaakgykpvavpartpanaavp
    astplkqewmwnqlgnflqegdvviaetgtsafginqttfpnntygisqvlwgsigfttg
    atlgaafaaeeidpkkrvilfigdgslqltvqeistmirwglkpylfvlnndgytiqkli
    hgpkaqyneiqgwdhlsllptfgakdyethrvattgewdkltqdksfndnskirmievml
    pvfdapqnlveqakltaatnakq
    

    Sequence, based on observed residues (ATOM records): (download)
    >2vk8C (C:)
    seitlgkylferlkqvnvntvfglpgdfnlslldkiyevegmrwagnanelnaayaadgy
    arikgmsciittfgvgelsalngiagsyaehvgvlhvvgvpsisaqakqlllhhtlgngd
    ftvfhrmsanisettamitdiatapaeidrcirttyvtqrpvylglpanlvdlnvpakll
    qtpidmslkpndaesekevidtilvldkdaknpviladaccsrhdvkaetkklidltqfp
    afvtpmgkgsideqhpryggvyvgtlskpevkeavesadlilsvgallsdfntgsfsysy
    ktknivefhsdhmkirnatfpgvqmkfvlqkllttiadaakgykpvavpartpanaavpa
    stplkqewmwnqlgnflqegdvviaetgtsafginqttfpnntygisqvlwgsigfttga
    tlgaafaaeeidpkkrvilfigdgslqltvqeistmirwglkpylfvlnndgytiqklih
    gpkaqyneiqgwdhlsllptfgakdyethrvattgewdkltqdksfndnskirmievmlp
    vfdapqnlveqakltaatnakq
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >2vk8D (D:)
    mseitlgkylferlkqvnvntvfglpgdfnlslldkiyevegmrwagnanelnaayaadg
    yarikgmsciittfgvgelsalngiagsyaehvgvlhvvgvpsisaqakqlllhhtlgng
    dftvfhrmsanisettamitdiatapaeidrcirttyvtqrpvylglpanlvdlnvpakl
    lqtpidmslkpndaesekevidtilvldkdaknpviladaccsrhdvkaetkklidltqf
    pafvtpmgkgsideqhpryggvyvgtlskpevkeavesadlilsvgallsdfntgsfsys
    yktknivefhsdhmkirnatfpgvqmkfvlqkllttiadaakgykpvavpartpanaavp
    astplkqewmwnqlgnflqegdvviaetgtsafginqttfpnntygisqvlwgsigfttg
    atlgaafaaeeidpkkrvilfigdgslqltvqeistmirwglkpylfvlnndgytiqkli
    hgpkaqyneiqgwdhlsllptfgakdyethrvattgewdkltqdksfndnskirmievml
    pvfdapqnlveqakltaatnakq
    

    Sequence, based on observed residues (ATOM records): (download)
    >2vk8D (D:)
    seitlgkylferlkqvnvntvfglpgdfnlslldkiyevegmrwagnanelnaayaadgy
    arikgmsciittfgvgelsalngiagsyaehvgvlhvvgvpsisaqakqlllhhtlgngd
    ftvfhrmsanisettamitdiatapaeidrcirttyvtqrpvylglpanlvdlnvpakll
    qtpidmslkpndaesekevidtilvldkdaknpviladaccsrhdvkaetkklidltqfp
    afvtpmgkgsideqhpryggvyvgtlskpevkeavesadlilsvgallsdfntgsfsysy
    ktknivefhsdhmkirnatfpgvqmkfvlqkllttiadaakgykpvavpartpanaavpa
    stplkqewmwnqlgnflqegdvviaetgtsafginqttfpnntygisqvlwgsigfttga
    tlgaafaaeeidpkkrvilfigdgslqltvqeistmirwglkpylfvlnndgytiqklih
    gpkaqyneiqgwdhlsllptfgakdyethrvattgewdkltqdksfndnskirmievmlp
    vfdapqnlveqakltaatnakq