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(-) Description

Title :  CRYSTAL STRUCTURE OF BIOTIN CARBOXYLASE FROM S. AUREUS COMPLEXED WITH AMPPNP
 
Authors :  I. Mochalkin
Date :  03 Mar 08  (Deposition) - 09 Sep 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Bacteria, Atp-Grasp Domain, Biotin Carboxylase, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Mochalkin, J. R. Miller, A. Evdokimov, S. Lightle, C. Yan, C. K. Stover, G. L. Waldrop
Structural Evidence For Substrate-Induced Synergism And Half-Sites Reactivity In Biotin Carboxylase.
Protein Sci. V. 17 1706 2008
PubMed-ID: 18725455  |  Reference-DOI: 10.1110/PS.035584.108

(-) Compounds

Molecule 1 - ACETYL-COA CARBOXYLASE
    Chains: A, B
    EC Number: 6.3.4.14
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Synonym: BIOTIN CARBOXYLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1ANP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2CL2Ligand/IonCHLORIDE ION
3MG4Ligand/IonMAGNESIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS B:115 , ILE B:155 , LYS B:157 , GLY B:161 , GLY B:162 , GLY B:163 , GLY B:164 , ILE B:167 , GLU B:199 , LYS B:200 , PHE B:201 , ILE B:202 , HIS B:207 , GLN B:231 , MET B:234 , GLU B:274 , ILE B:276 , MET B:287 , GLU B:288 , ASN B:290 , MG B:1451 , MG B:1452 , HOH B:2155 , HOH B:2243 , HOH B:2393 , HOH B:2394 , HOH B:2397 , HOH B:2398BINDING SITE FOR RESIDUE ANP B1450
2AC2SOFTWARELYS A:115 , ILE A:155 , LYS A:157 , GLY A:161 , GLY A:162 , GLY A:163 , GLY A:164 , ILE A:167 , GLU A:199 , LYS A:200 , PHE A:201 , ILE A:202 , HIS A:207 , GLN A:231 , GLU A:274 , ILE A:276 , MET A:287 , GLU A:288 , ASN A:290 , MG A:1450 , MG A:1451 , HOH A:2172 , HOH A:2180 , HOH A:2266 , HOH A:2416 , HOH A:2417BINDING SITE FOR RESIDUE ANP A1449
3AC3SOFTWAREGLU B:274 , GLU B:288 , ANP B:1450 , HOH B:2398BINDING SITE FOR RESIDUE MG B1451
4AC4SOFTWAREGLU A:274 , GLU A:288 , ANP A:1449 , HOH A:2417BINDING SITE FOR RESIDUE MG A1450
5AC5SOFTWAREGLU B:288 , ASN B:290 , ANP B:1450 , HOH B:2155 , HOH B:2243BINDING SITE FOR RESIDUE MG B1452
6AC6SOFTWAREGLU A:288 , ASN A:290 , ANP A:1449 , HOH A:2172 , HOH A:2266BINDING SITE FOR RESIDUE MG A1451
7AC7SOFTWAREARG A:292 , GLN A:294 , VAL A:295 , HOH A:2270BINDING SITE FOR RESIDUE CL A1452
8AC8SOFTWAREARG B:292 , GLN B:294 , VAL B:295 , HOH B:2247BINDING SITE FOR RESIDUE CL B1453

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VPQ)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Tyr A:152 -Pro A:153
2Ala A:241 -Pro A:242
3Tyr B:152 -Pro B:153
4Ala B:241 -Pro B:242

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VPQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VPQ)

(-) Exons   (0, 0)

(no "Exon" information available for 2VPQ)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:447
 aligned with A0A0H3JRR2_S | A0A0H3JRR2 from UniProtKB/TrEMBL  Length:451

    Alignment length:447
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       
         A0A0H3JRR2_S     2 KKVLIANRGEIAVRIIRACRDLGIQTVAIYSEGDKDALHTQIADEAYCVGPTLSKDSYLNIPNILSIATSTGCDGVHPGYGFLAENADFAELCEACQLKFIGPSYQSIQKMGIKDVAKAEMIKANVPVVPGSDGLMKDVSEAKKIAKKIGYPVIIKATAGGGGKGIRVARDEKELETGFRMTEQEAQTAFGNGGLYMEKFIENFRHIEIQIVGDSYGNVIHLGERDCTIQRRMQKLVEEAPSPILDDETRREMGNAAVRAAKAVNYENAGTIEFIYDLNDNKFYFMEMNTRIQVEHPVTEMVTGIDLVKLQLQVAMGDVLPYKQEDIKLTGHAIEFRINAENPYKNFMPSPGKIEQYLAPGGYGVRIESACYTNYTIPPYYDSMVAKLIIHEPTRDEAIMAGIRALSEFVVLGIDTTIPFHIKLLNNDIFRSGKFNTNFLEQNSIMN 448
               SCOP domains d2vpqa1 A:2-114 automated matches                                                                                d2vpqa2 A:115-329 automated matches                                                                                                                                                                                    d2vpqa3 A:330-448 automated matches                                                                                     SCOP domains
               CATH domains 2vpqA01 A:2-84  [code=3.40.50.20, no name defined]                                 ---------------------------------------------2vpqA03 A:130-201 ATP-grasp fold, A domain                              ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..hhhhhhhhhhhhhhh..eeeeeee.hhh.hhhhhhh.eeeeee..hhhhh..hhhhhhhhhhhh...eee........hhhhhhhhhh...ee...hhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhh..eeeee........eeee.hhhhhhhhhhhhhhhhhhhhh...eeeee....eeeeeeeeee.....eeeeeeeeeeeee..eeeeeee.....hhhhhhhhhhhhhhhhhhh...eeeeeeeeee.....eeeeeee.....hhhhhhhhhh.hhhhhhhhhhh......hhhhh....eeeeeeee..hhhhh.........eee......eeee...............eeeeeeeee.hhhhhhhhhhhhhhh.eee....hhhhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vpq A   2 KKVLIANRGEIAVRIIRACRDLGIQTVAIYSEGDKDALHTQIADEAYCVGPTLSKDSYLNIPNILSIATSTGCDGVHPGYGFLAENADFAELCEACQLKFIGPSYQSIQKMGIKDVAKAEMIKANVPVVPGSDGLMKDVSEAKKIAKKIGYPVIIKATAGGGGKGIRVARDEKELETGFRMTEQEAQTAFGNGGLYMEKFIENFRHIEIQIVGDSYGNVIHLGERDCTIQRRMQKLVEEAPSPILDDETRREMGNAAVRAAKAVNYENAGTIEFIYDLNDNKFYFMEMNTRIQVEHPVTEMVTGIDLVKLQLQVAMGDVLPYKQEDIKLTGHAIEFRINAENPYKNFMPSPGKIEQYLAPGGYGVRIESACYTNYTIPPYYDSMVAKLIIHEPTRDEAIMAGIRALSEFVVLGIDTTIPFHIKLLNNDIFRSGKFNTNFLEQNSIMN 448
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       


Chain B from PDB  Type:PROTEIN  Length:448
 aligned with A0A0H3JRR2_S | A0A0H3JRR2 from UniProtKB/TrEMBL  Length:451

    Alignment length:448
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441        
         A0A0H3JRR2_S     2 KKVLIANRGEIAVRIIRACRDLGIQTVAIYSEGDKDALHTQIADEAYCVGPTLSKDSYLNIPNILSIATSTGCDGVHPGYGFLAENADFAELCEACQLKFIGPSYQSIQKMGIKDVAKAEMIKANVPVVPGSDGLMKDVSEAKKIAKKIGYPVIIKATAGGGGKGIRVARDEKELETGFRMTEQEAQTAFGNGGLYMEKFIENFRHIEIQIVGDSYGNVIHLGERDCTIQRRMQKLVEEAPSPILDDETRREMGNAAVRAAKAVNYENAGTIEFIYDLNDNKFYFMEMNTRIQVEHPVTEMVTGIDLVKLQLQVAMGDVLPYKQEDIKLTGHAIEFRINAENPYKNFMPSPGKIEQYLAPGGYGVRIESACYTNYTIPPYYDSMVAKLIIHEPTRDEAIMAGIRALSEFVVLGIDTTIPFHIKLLNNDIFRSGKFNTNFLEQNSIMND 449
               SCOP domains d2vpqb1 B:2-114 automated matches                                                                                d2vpqb2 B:115-329 automated matches                                                                                                                                                                                    d2vpqb3 B:330-449 automated matches                                                                                      SCOP domains
               CATH domains 2vpqB01 B:2-84  [code=3.40.50.20, no name defined]                                 ---------------------------------------------2vpqB03 B:130-201 ATP-grasp fold, A domain                              -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..hhhhhhhhhhhhhhh..eeeeeee.hhh.hhhhhhh.eeeeee..hhhhh..hhhhhhhhhhhh...eee........hhhhhhhhhhh..ee...hhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhh..eeeee........eeee.hhhhhhhhhhhhhhhhhhhhh...eeeee....eeeeeeeeee.....eeeeeeeeeeeee..eeeeeee.....hhhhhhhhhhhhhhhhhhh...eeeeeeeeee....eeeeeeee.....hhhhhhhhhh.hhhhhhhhhhh......hhhhh....eeeeeeee..hhhhh.........eee......eeeee..............eeeeeeeee.hhhhhhhhhhhhhhhheee....hhhhhhhhhhhhhhhhh....hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vpq B   2 KKVLIANRGEIAVRIIRACRDLGIQTVAIYSEGDKDALHTQIADEAYCVGPTLSKDSYLNIPNILSIATSTGCDGVHPGYGFLAENADFAELCEACQLKFIGPSYQSIQKMGIKDVAKAEMIKANVPVVPGSDGLMKDVSEAKKIAKKIGYPVIIKATAGGGGKGIRVARDEKELETGFRMTEQEAQTAFGNGGLYMEKFIENFRHIEIQIVGDSYGNVIHLGERDCTIQRRMQKLVEEAPSPILDDETRREMGNAAVRAAKAVNYENAGTIEFIYDLNDNKFYFMEMNTRIQVEHPVTEMVTGIDLVKLQLQVAMGDVLPYKQEDIKLTGHAIEFRINAENPYKNFMPSPGKIEQYLAPGGYGVRIESACYTNYTIPPYYDSMVAKLIIHEPTRDEAIMAGIRALSEFVVLGIDTTIPFHIKLLNNDIFRSGKFNTNFLEQNSIMND 449
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (3, 6)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2VPQ)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2VPQ)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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(-) Related Entries Specified in the PDB File

2c00 CRYSTAL STRUCTURE OF BIOTIN CARBOXYLASE FROM PSEUDOMONAS AERUGINOSA IN APO FORM
2j9g CRYSTAL STRUCTURE OF BIOTIN CARBOXYLASE FROM E. COLI IN COMPLEX WITH AMPPNP AND ADP
2vqd CRYSTAL STRUCTURE OF BIOTIN CARBOXYLASE FROM PSEUDOMONAS AERUGINOSA COMPLEXED WITH AMPCP
2vr1 CRYSTAL STRUCTURE OF BIOTIN CARBOXYLASE FROM E. COLI IN COMPLEX WITH ATP ANALOG, ADPCF2P.