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(-) Description

Title :  SOLUTION STRUCTURE OF B DOMAIN FROM HUMAN PROPIONYL-COA CARBOXYLASE ALPHA SUBUNIT
 
Authors :  T. Suetake, F. Hayashi, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  20 May 05  (Deposition) - 20 Nov 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Pcca, B Domain, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Suetake, F. Hayashi, S. Yokoyama
Solution Structure Of B Domain From Human Propionyl-Coa Carboxylase Alpha Subunit
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROPIONYL-COA CARBOXYLASE ALPHA CHAIN, MITOCHONDRIAL
    ChainsA
    EC Number6.4.1.3
    EngineeredYES
    Expression System PlasmidP040712-08
    Expression System Vector TypePLASMID
    FragmentB DOMAIN
    GenePCCA
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL FREE PROTEIN SYNTHESIS

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2CQY)

(-) Sites  (0, 0)

(no "Site" information available for 2CQY)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 20)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Tyr A:46 -Pro A:47

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

NMR Structure (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_023843G197EPCCA_HUMANDisease (PA-1)  ---AG29E
2UniProtVAR_009091M229KPCCA_HUMANDisease (PA-1)  ---AM61K

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CPSASE_1PS00866 Carbamoyl-phosphate synthase subdomain signature 1.PCCA_HUMAN214-228  1A:46-60

(-) Exons   (6, 6)

NMR Structure (6, 6)
 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_HUMAN101-138381A:1-66
1.8ENST000003762858ENSE00001722625chr13:100809541-10080959454PCCA_HUMAN139-156180--
1.10ENST0000037628510ENSE00001805607chr13:100861586-100861717132PCCA_HUMAN157-200441A:7-3226
1.11ENST0000037628511ENSE00001638065chr13:100888096-10088813237PCCA_HUMAN201-213131A:33-4513
1.12ENST0000037628512ENSE00001673087chr13:100909849-10090992779PCCA_HUMAN213-239271A:45-7127
1.13ENST0000037628513ENSE00001698412chr13:100914983-100915085103PCCA_HUMAN239-273351A:71-10333
1.14ENST0000037628514ENSE00001713098chr13:100920943-10092103795PCCA_HUMAN274-305321A:104-1085
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_HUMAN634-680470--
1.30ENST0000037628530ENSE00001648714chr13:101179929-10118000678PCCA_HUMAN681-706260--
1.31ENST0000037628531ENSE00001696675chr13:101182352-101182686335PCCA_HUMAN707-728220--

(-) Sequences/Alignments

NMR Structure
   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:108
 aligned with PCCA_HUMAN | P05165 from UniProtKB/Swiss-Prot  Length:728

    Alignment length:168
                                   122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272        
           PCCA_HUMAN   113 GPAPTSKSYLNMDAIMEAIKKTRAQAVHPGYGFLSENKEFARCLAAEDVVFIGPDTHAIQAMGDKIESKLLAKKAEVNTIPGFDGVVKDAEEAVRIAREIGYPVMIKASAGGGGKGMRIAWDDEETRDGFRLSSQEAASSFGDDRLLIEKFIDNPRHIEIQVLGDKHG 280
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains -------------------------------------------------------------------------------2cqyA01 A:24-95 ATP-grasp fold, A domain                                ----------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......--------------------------------------------------------..........................hhhhhhhhhhhhh..eeeee.........eee.hhhhhhhhhhhhhhhhhhhh....eeeee.........----..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------E-------------------------------K--------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------CPSASE_1       ---------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.7  PDB: A:1-6      Exon 1.8  PDB: -  Exon 1.10  PDB: A:7-32 UniProt: 157-200     Exon 1.11    -------------------------Exon 1.13  PDB: A:71-103           1.14    Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------Exon 1.12  PDB: A:45-71    ----------------------------------------- Transcript 1 (2)
                 2cqy A   1 GSSGSS--------------------------------------------------------GDKIESKLLAKKAEVNTIPGFDGVVKDAEEAVRIAREIGYPVMIKASAGGGGKGMRIAWDDEETRDGFRLSSQEAASSFGDDRLLIEKFIDNPRHIS----GPSSG 108
                                 |   -         -         -         -         -         -  |     14        24        34        44        54        64        74        84        94        |-   |    
                                 6                                                        7                                                                                             103  104    

   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  (0, 0)

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

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

NMR Structure(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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    Tyr A:46 - Pro A:47   [ RasMol ]  
 

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        PCCA_HUMAN | P051652jku

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