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(-) Description

Title :  CRYSTAL STRUCTURE OF THE N-TERMINAL REGION OF THE BIOTIN ACCEPTOR DOMAIN OF HUMAN PROPIONYL-COA CARBOXYLASE
 
Authors :  S. Healy, W. W. Yue, G. Kochan, E. S. Pilka, J. W. Murray, A. K. Roos, P. Filippakopoulos, F. Von Delft, C. Arrowsmith, M. Wikstrom, A. Edwards, C. Bountra, R. A. Gravel, U. Oppermann
Date :  30 Aug 08  (Deposition) - 09 Sep 08  (Release) - 04 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Ligase, Biotin, Atp-Binding, Disease Mutation, Nucleotide-Binding, Mitochondrion, Phosphoprotein, Transit Peptide (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Healy, M. K. Mcdonald, X. Wu, W. W. Yue, G. Kochan, U. Oppermann, R. A. Gravel
Structural Impact Of Human And Escherichia Coli Biotin Carboxyl Carrier Proteins On Biotin Attachment.
Biochemistry V. 49 4687 2010
PubMed-ID: 20443544  |  Reference-DOI: 10.1021/BI901612Y

(-) Compounds

Molecule 1 - PROPIONYL-COA CARBOXYLASE ALPHA CHAIN, MITOCHONDRIAL
    ChainsA
    EC Number6.4.1.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC28-BSA4
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantR3-PRARE2
    FragmentBIOTIN ACCEPTOR DOMAIN, RESIDUES 633-703
    OrganelleMITOCHONDRIA
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPROPANOYL-COA:CARBON DIOXIDE LIGASE SUBUNIT ALPHA

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1PG42Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:634 , VAL A:636 , ALA A:647 , GLU A:661 , VAL A:664BINDING SITE FOR RESIDUE PG4 A1668
2AC2SOFTWAREARG A:638 , GLU A:658 , GLY A:659 , HOH A:2058BINDING SITE FOR RESIDUE PG4 A1669

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2JKU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_009101G668RPCCA_HUMANDisease (PA-1)771438170AG643R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BIOTINPS00188 Biotin-requiring enzymes attachment site.PCCA_HUMAN684-701  1A:659-667

(-) Exons   (2, 2)

Asymmetric/Biological Unit (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003762851aENSE00001685308chr13:100741337-100741479143PCCA_HUMAN1-35350--
1.2ENST000003762852ENSE00001697964chr13:100755137-10075521478PCCA_HUMAN36-61260--
1.3ENST000003762853ENSE00001723053chr13:100764095-10076414248PCCA_HUMAN62-77160--
1.4ENST000003762854ENSE00001739393chr13:100764247-10076431569PCCA_HUMAN78-100230--
1.7ENST000003762857ENSE00001690014chr13:100807233-100807346114PCCA_HUMAN101-138380--
1.8ENST000003762858ENSE00001722625chr13:100809541-10080959454PCCA_HUMAN139-156180--
1.10ENST0000037628510ENSE00001805607chr13:100861586-100861717132PCCA_HUMAN157-200440--
1.11ENST0000037628511ENSE00001638065chr13:100888096-10088813237PCCA_HUMAN201-213130--
1.12ENST0000037628512ENSE00001673087chr13:100909849-10090992779PCCA_HUMAN213-239270--
1.13ENST0000037628513ENSE00001698412chr13:100914983-100915085103PCCA_HUMAN239-273350--
1.14ENST0000037628514ENSE00001713098chr13:100920943-10092103795PCCA_HUMAN274-305320--
1.15ENST0000037628515ENSE00001593748chr13:100925450-100925600151PCCA_HUMAN305-355510--
1.17ENST0000037628517ENSE00001652442chr13:100953714-100953857144PCCA_HUMAN356-403480--
1.18ENST0000037628518ENSE00001804646chr13:100955178-10095525275PCCA_HUMAN404-428250--
1.20ENST0000037628520ENSE00001629467chr13:100959446-10095951469PCCA_HUMAN429-451230--
1.21ENST0000037628521ENSE00001665361chr13:100962087-10096216276PCCA_HUMAN452-477260--
1.22ENST0000037628522ENSE00001696369chr13:100982815-100982925111PCCA_HUMAN477-514380--
1.23ENST0000037628523ENSE00002154556chr13:100992411-100992513103PCCA_HUMAN514-548350--
1.24aENST0000037628524aENSE00002179391chr13:101020726-101020828103PCCA_HUMAN548-582350--
1.25ENST0000037628525ENSE00002195459chr13:101077887-10107798599PCCA_HUMAN583-615330--
1.26ENST0000037628526ENSE00001758999chr13:101101506-10110155954PCCA_HUMAN616-633180--
1.28ENST0000037628528ENSE00001622034chr13:101167681-101167821141PCCA_HUMAN634-680471A:633-65523
1.30ENST0000037628530ENSE00001648714chr13:101179929-10118000678PCCA_HUMAN681-706261A:656-66712
1.31ENST0000037628531ENSE00001696675chr13:101182352-101182686335PCCA_HUMAN707-728220--

(-) 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
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Chain A from PDB  Type:PROTEIN  Length:35
 aligned with PCCA_HUMAN | P05165 from UniProtKB/Swiss-Prot  Length:728

    Alignment length:35
                                   667       677       687     
           PCCA_HUMAN   658 TSSVLRSPMPGVVVAVSVKPGDAVAEGQEICVIEA 692
               SCOP domains ----------------------------------- SCOP domains
               CATH domains ----------------------------------- CATH domains
               Pfam domains --Biotin_lipoyl-2jkuA01 A:635-667   Pfam domains
         Sec.struct. author ...........eeeee..............eeee. Sec.struct. author
                 SAPs(SNPs) ----------R------------------------ SAPs(SNPs)
                    PROSITE --------------------------BIOTIN    PROSITE
               Transcript 1 Exon 1.28 [INCOMPLETE] Exon 1.30    Transcript 1
                 2jku A 633 TSSVLRSPMPGVVVAVSVKPGDAVAEGQEICVIEA 667
                                   642       652       662     

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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2JKU)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2JKU)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Hybrid (58)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PCCA_HUMAN | P05165)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0009374    biotin binding    Interacting selectively and non-covalently with biotin (cis-tetrahydro-2-oxothieno(3,4-d)imidazoline-4-valeric acid), the (+) enantiomer of which is very widely distributed in cells and serves as a carrier in a number of enzymatic beta-carboxylation reactions.
    GO:0004075    biotin carboxylase activity    Catalysis of the reaction: ATP + biotin-carboxyl-carrier protein + CO2 = ADP + phosphate + carboxybiotin-carboxyl-carrier protein.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0004658    propionyl-CoA carboxylase activity    Catalysis of the reaction: ATP + propanoyl-CoA + HCO3- = ADP + phosphate + (S)-methylmalonyl-CoA.
biological process
    GO:0006768    biotin metabolic process    The chemical reactions and pathways involving biotin, cis-tetrahydro-2-oxothieno(3,4-d)imidazoline-4-valeric acid; the (+) enantiomer is very widely distributed in cells and serves as a carrier in a number of enzymatic beta-carboxylation reactions.
    GO:0019626    short-chain fatty acid catabolic process    The chemical reactions and pathways resulting in the breakdown of fatty acids with a chain length of less than C6.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005759    mitochondrial matrix    The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PCCA_HUMAN | P051652cqy

(-) Related Entries Specified in the PDB File

2cqy SOLUTION STRUCTURE OF B DOMAIN FROM HUMAN PROPIONYL-COACARBOXYLASE ALPHA SUBUNIT