PDB entry 2w93

View 2w93 on RCSB PDB site
Description: Crystal structure of the Saccharomyces cerevisiae pyruvate decarboxylase variant E477Q in complex with the surrogate pyruvamide
Class: lyase
Keywords: substrate activation, substrate regulation, lyase, nucleus, magnesium, phosphoprotein, allosteric enzyme, thiamine pyrophosphate, phenylalanine catabolism, tryptophan catabolism, pyruvate decarboxylase, branched-chain amino acid catabolism, metal-binding, thiohemiketal, decarboxylase
Deposited on 2009-01-21, released 2009-02-03
The last revision prior to the SCOPe 2.06 freeze date was dated 2014-07-30, with a file datestamp of 2014-07-25.
Experiment type: XRAY
Resolution: 1.6 Å
R-factor: 0.181
AEROSPACI score: 0.51 (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
      • conflict (105)
      • conflict (335)
      • engineered mutation (476)
      • conflict (537)
    Domains in SCOPe 2.06: d2w93a1, d2w93a2, d2w93a3
  • Chain 'B':
    Compound: pyruvate decarboxylase isozyme 1
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P06169 (Start-562)
      • conflict (105)
      • conflict (335)
      • engineered mutation (476)
      • conflict (537)
    Domains in SCOPe 2.06: d2w93b1, d2w93b2, d2w93b3
  • Chain 'C':
    Compound: pyruvate decarboxylase isozyme 1
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P06169
      • conflict (105)
      • conflict (335)
      • engineered mutation (476)
      • conflict (537)
    Domains in SCOPe 2.06: d2w93c1, d2w93c2, d2w93c3
  • Chain 'D':
    Compound: pyruvate decarboxylase isozyme 1
    Species: Saccharomyces cerevisiae [TaxId:4932]
    Database cross-references and differences (RAF-indexed):
    • Uniprot P06169 (Start-562)
      • conflict (105)
      • conflict (335)
      • engineered mutation (476)
      • conflict (537)
    Domains in SCOPe 2.06: d2w93d1, d2w93d2, d2w93d3
  • Heterogens: TPP, MG, PY0, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download)
    >2w93A (A:)
    mseitlgkylferlkqvnvntvfglpgdfnlslldkiyevegmrwagnanelnaayaadg
    yarikgmsciittfgvgelsalngiagsyaehvgvlhvvgvpsissqakqlllhhtlgng
    dftvfhrmsanisettamitdiatapaeidrcirttyvtqrpvylglpanlvdlnvpakl
    lqtpidmslkpndaesekevidtilalvkdaknpviladaccsrhdvkaetkklidltqf
    pafvtpmgkgsideqhpryggvyvgtlskpevkeavesadlilsvgallsdfntgsfsys
    yktknivefhsdhmkirnatfpgvqmkfvlqklltniadaakgykpvavpartpanaavp
    astplkqewmwnqlgnflqegdvviaetgtsafginqttfpnntygisqvlwgsigfttg
    atlgaafaaeeidpkkrvilfigdgslqltvqeistmirwglkpylfvlnndgytiqkli
    hgpkaqyneiqgwdhlsllptfgakdyethrvattgewdkltqdksfndnskirmievml
    pvfdapqnlveqakltaatnakq
    

    Sequence, based on observed residues (ATOM records): (download)
    >2w93A (A:)
    seitlgkylferlkqvnvntvfglpgdfnlslldkiyevegmrwagnanelnaayaadgy
    arikgmsciittfgvgelsalngiagsyaehvgvlhvvgvpsissqakqlllhhtlgngd
    ftvfhrmsanisettamitdiatapaeidrcirttyvtqrpvylglpanlvdlnvpakll
    qtpidmslkpndaesekevidtilalvkdaknpviladaccsrhdvkaetkklidltqfp
    afvtpmgkgsideqhpryggvyvgtlskpevkeavesadlilsvgaltknivefhsdhmk
    irnatfpgvqmkfvlqklltniadaakgykpvavpartpanaavpastplkqewmwnqlg
    nflqegdvviaetgtsafginqttfpnntygisqvlwgsigfttgatlgaafaaeeidpk
    krvilfigdgslqltvqeistmirwglkpylfvlnndgytiqklihgpkaqyneiqgwdh
    lsllptfgakdyethrvattgewdkltqdksfndnskirmievmlpvfdapqnlveqakl
    taat
    

  • Chain 'B':
    Sequence, based on SEQRES records: (download)
    >2w93B (B:)
    mseitlgkylferlkqvnvntvfglpgdfnlslldkiyevegmrwagnanelnaayaadg
    yarikgmsciittfgvgelsalngiagsyaehvgvlhvvgvpsissqakqlllhhtlgng
    dftvfhrmsanisettamitdiatapaeidrcirttyvtqrpvylglpanlvdlnvpakl
    lqtpidmslkpndaesekevidtilalvkdaknpviladaccsrhdvkaetkklidltqf
    pafvtpmgkgsideqhpryggvyvgtlskpevkeavesadlilsvgallsdfntgsfsys
    yktknivefhsdhmkirnatfpgvqmkfvlqklltniadaakgykpvavpartpanaavp
    astplkqewmwnqlgnflqegdvviaetgtsafginqttfpnntygisqvlwgsigfttg
    atlgaafaaeeidpkkrvilfigdgslqltvqeistmirwglkpylfvlnndgytiqkli
    hgpkaqyneiqgwdhlsllptfgakdyethrvattgewdkltqdksfndnskirmievml
    pvfdapqnlveqakltaatnakq
    

    Sequence, based on observed residues (ATOM records): (download)
    >2w93B (B:)
    seitlgkylferlkqvnvntvfglpgdfnlslldkiyevegmrwagnanelnaayaadgy
    arikgmsciittfgvgelsalngiagsyaehvgvlhvvgvpsissqakqlllhhtlgngd
    ftvfhrmsanisettamitdiatapaeidrcirttyvtqrpvylglpanlvdlnvpakll
    qtpidmslkpndaesekevidtilalvkdaknpviladaccsrhdvkaetkklidltqfp
    afvtpmgkgsideqhpryggvyvgtlskpevkeavesadlilsvgallsdfntgsfsysy
    ktknivefhsdhmkirnatfpgvqmkfvlqklltniadaakgykpvavpartpanaavpa
    stplkqewmwnqlgnflqegdvviaetgtsafginqttfpnntygisqvlwgsigfttga
    tlgaafaaeeidpkkrvilfigdgslqltvqeistmirwglkpylfvlnndgytiqklih
    gpkaqyneiqgwdhlsllptfgakdyethrvattgewdkltqdksfndnskirmievmlp
    vfdapqnlveqakltaatnakq
    

  • Chain 'C':
    Sequence, based on SEQRES records: (download)
    >2w93C (C:)
    mseitlgkylferlkqvnvntvfglpgdfnlslldkiyevegmrwagnanelnaayaadg
    yarikgmsciittfgvgelsalngiagsyaehvgvlhvvgvpsissqakqlllhhtlgng
    dftvfhrmsanisettamitdiatapaeidrcirttyvtqrpvylglpanlvdlnvpakl
    lqtpidmslkpndaesekevidtilalvkdaknpviladaccsrhdvkaetkklidltqf
    pafvtpmgkgsideqhpryggvyvgtlskpevkeavesadlilsvgallsdfntgsfsys
    yktknivefhsdhmkirnatfpgvqmkfvlqklltniadaakgykpvavpartpanaavp
    astplkqewmwnqlgnflqegdvviaetgtsafginqttfpnntygisqvlwgsigfttg
    atlgaafaaeeidpkkrvilfigdgslqltvqeistmirwglkpylfvlnndgytiqkli
    hgpkaqyneiqgwdhlsllptfgakdyethrvattgewdkltqdksfndnskirmievml
    pvfdapqnlveqakltaatnakq
    

    Sequence, based on observed residues (ATOM records): (download)
    >2w93C (C:)
    seitlgkylferlkqvnvntvfglpgdfnlslldkiyevegmrwagnanelnaayaadgy
    arikgmsciittfgvgelsalngiagsyaehvgvlhvvgvpsissqakqlllhhtlgngd
    ftvfhrmsanisettamitdiatapaeidrcirttyvtqrpvylglpanlvdlnvpakll
    qtpidmslkpndaesekevidtilalvkdaknpviladaccsrhdvkaetkklidltqfp
    afvtpmgkgsideqhpryggvyvgtlskpevkeavesadlilsvgallsdfntgsfsysy
    ktknivefhsdhmkirnatfpgvqmkfvlqklltniadaakgykpvavpartpanaavpa
    stplkqewmwnqlgnflqegdvviaetgtsafginqttfpnntygisqvlwgsigfttga
    tlgaafaaeeidpkkrvilfigdgslqltvqeistmirwglkpylfvlnndgytiqklih
    gpkaqyneiqgwdhlsllptfgakdyethrvattgewdkltqdksfndnskirmievmlp
    vfdapqnlveqakltaa
    

  • Chain 'D':
    Sequence, based on SEQRES records: (download)
    >2w93D (D:)
    mseitlgkylferlkqvnvntvfglpgdfnlslldkiyevegmrwagnanelnaayaadg
    yarikgmsciittfgvgelsalngiagsyaehvgvlhvvgvpsissqakqlllhhtlgng
    dftvfhrmsanisettamitdiatapaeidrcirttyvtqrpvylglpanlvdlnvpakl
    lqtpidmslkpndaesekevidtilalvkdaknpviladaccsrhdvkaetkklidltqf
    pafvtpmgkgsideqhpryggvyvgtlskpevkeavesadlilsvgallsdfntgsfsys
    yktknivefhsdhmkirnatfpgvqmkfvlqklltniadaakgykpvavpartpanaavp
    astplkqewmwnqlgnflqegdvviaetgtsafginqttfpnntygisqvlwgsigfttg
    atlgaafaaeeidpkkrvilfigdgslqltvqeistmirwglkpylfvlnndgytiqkli
    hgpkaqyneiqgwdhlsllptfgakdyethrvattgewdkltqdksfndnskirmievml
    pvfdapqnlveqakltaatnakq
    

    Sequence, based on observed residues (ATOM records): (download)
    >2w93D (D:)
    seitlgkylferlkqvnvntvfglpgdfnlslldkiyevegmrwagnanelnaayaadgy
    arikgmsciittfgvgelsalngiagsyaehvgvlhvvgvpsissqakqlllhhtlgngd
    ftvfhrmsanisettamitdiatapaeidrcirttyvtqrpvylglpanlvdlnvpakll
    qtpidmslkpndaesekevidtilalvkdaknpviladaccsrhdvkaetkklidltqfp
    afvtpmgkgsideqhpryggvyvgtlskpevkeavesadlilsvgallsdfntgsfsysy
    ktknivefhsdhmkirnatfpgvqmkfvlqklltniadaakgykpvavpartpanaavpa
    stplkqewmwnqlgnflqegdvviaetgtsafginqttfpnntygisqvlwgsigfttga
    tlgaafaaeeidpkkrvilfigdgslqltvqeistmirwglkpylfvlnndgytiqklih
    gpkaqyneiqgwdhlsllptfgakdyethrvattgewdkltqdksfndnskirmievmlp
    vfdapqnlveqakltaatnakq