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(-) Description

Title :  SOLUTION STRUCTURE OF RSGI RUH-053, AN APO-BIOTIN CARBOXY CARRIER PROTEIN FROM HUMAN TRANSCARBOXYLASE
 
Authors :  A. Z. M. Ruhul Momen, H. Hirota, F. Hayashi, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  25 Apr 06  (Deposition) - 25 Oct 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Biotin Required Enzyme, Transcarboxylase, Acetyl Coa Carboxylase, 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 :  A. Z. M. Ruhul Momen, H. Hirota, F. Hayashi, S. Yokoyama
Solution Structure Of Rsgi Ruh-053, An Apo-Biotin Carboxy Carrier Protein From Human Transcarboxylase
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ACETYL-COA CARBOXYLASE 2
    ChainsA
    EC Number6.4.1.2
    EngineeredYES
    Expression SystemCELL FREE SYNTHESIS
    Expression System PlasmidP050509-04
    Expression System Vector TypePLASMID
    FragmentBIOTINYL-BINDING DOMAIN, RESIDUES 8-94
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymBIOTIN CARBOXY CARRIER PROTEIN

 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 2DN8)

(-) Sites  (0, 0)

(no "Site" information available for 2DN8)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DN8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2DN8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DN8)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BIOTINYL_LIPOYLPS50968 Biotinyl/lipoyl domain profile.ACACB_HUMAN888-962  1A:11-85

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003778481aENSE00002193931chr12:109577202-109577863662ACACB_HUMAN1-2182180--
1.2ENST000003778482ENSE00001592576chr12:109604666-109604798133ACACB_HUMAN218-262450--
1.3ENST000003778483ENSE00001645737chr12:109605701-109605839139ACACB_HUMAN263-309470--
1.4ENST000003778484ENSE00001696806chr12:109609610-109609719110ACACB_HUMAN309-345370--
1.5ENST000003778485ENSE00001659607chr12:109610080-10961016182ACACB_HUMAN346-373280--
1.6ENST000003778486ENSE00001752262chr12:109611937-10961203599ACACB_HUMAN373-406340--
1.7ENST000003778487ENSE00001658849chr12:109613736-109613845110ACACB_HUMAN406-442370--
1.8ENST000003778488ENSE00001745001chr12:109613958-109614068111ACACB_HUMAN443-479370--
1.9ENST000003778489ENSE00001659729chr12:109616893-109617102210ACACB_HUMAN480-549700--
1.10ENST0000037784810ENSE00001734325chr12:109617722-109617892171ACACB_HUMAN550-606570--
1.11ENST0000037784811ENSE00001678287chr12:109623384-109623545162ACACB_HUMAN607-660540--
1.12ENST0000037784812ENSE00001749990chr12:109625804-109625967164ACACB_HUMAN661-715550--
1.13ENST0000037784813ENSE00001780825chr12:109629418-109629568151ACACB_HUMAN715-765510--
1.14ENST0000037784814ENSE00001738467chr12:109629652-109629755104ACACB_HUMAN766-800350--
1.15ENST0000037784815ENSE00001614723chr12:109631453-10963153482ACACB_HUMAN800-827280--
1.16ENST0000037784816ENSE00001662933chr12:109634813-109634958146ACACB_HUMAN828-876491A:1-66
1.17ENST0000037784817ENSE00001682078chr12:109637207-109637357151ACACB_HUMAN876-926511A:7-49 (gaps)45
1.18ENST0000037784818ENSE00001599746chr12:109639372-109639506135ACACB_HUMAN927-971451A:50-9445
1.19ENST0000037784819ENSE00001711654chr12:109644515-109644661147ACACB_HUMAN972-1020491A:95-1006
1.20ENST0000037784820ENSE00001649091chr12:109646970-109647158189ACACB_HUMAN1021-1083630--
1.21ENST0000037784821ENSE00001641104chr12:109650641-109650741101ACACB_HUMAN1084-1117340--
1.22bENST0000037784822bENSE00001756818chr12:109654423-10965451189ACACB_HUMAN1117-1147310--
1.23bENST0000037784823bENSE00001595891chr12:109654601-109654725125ACACB_HUMAN1147-1188420--
1.25ENST0000037784825ENSE00001629446chr12:109660312-109660425114ACACB_HUMAN1189-1226380--
1.26ENST0000037784826ENSE00001802870chr12:109660604-109660717114ACACB_HUMAN1227-1264380--
1.27ENST0000037784827ENSE00001718675chr12:109661620-10966170990ACACB_HUMAN1265-1294300--
1.28ENST0000037784828ENSE00001732085chr12:109665176-109665294119ACACB_HUMAN1295-1334400--
1.29ENST0000037784829ENSE00001671433chr12:109670474-109670611138ACACB_HUMAN1334-1380470--
1.30ENST0000037784830ENSE00000754740chr12:109671553-109671652100ACACB_HUMAN1380-1413340--
1.31ENST0000037784831ENSE00000754741chr12:109671743-109671850108ACACB_HUMAN1414-1449360--
1.32ENST0000037784832ENSE00000754742chr12:109673118-10967317457ACACB_HUMAN1450-1468190--
1.33ENST0000037784833ENSE00000754743chr12:109673411-10967345242ACACB_HUMAN1469-1482140--
1.34ENST0000037784834ENSE00000410836chr12:109674970-109675185216ACACB_HUMAN1483-1554720--
1.35ENST0000037784835ENSE00001601824chr12:109677635-109677790156ACACB_HUMAN1555-1606520--
1.36ENST0000037784836ENSE00000754745chr12:109678883-109679086204ACACB_HUMAN1607-1674680--
1.37ENST0000037784837ENSE00001507550chr12:109680242-109680397156ACACB_HUMAN1675-1726520--
1.38ENST0000037784838ENSE00001197605chr12:109683431-109683553123ACACB_HUMAN1727-1767410--
1.39ENST0000037784839ENSE00000834687chr12:109683984-109684253270ACACB_HUMAN1768-1857900--
1.40ENST0000037784840ENSE00000834688chr12:109685411-10968550898ACACB_HUMAN1858-1890330--
1.41ENST0000037784841ENSE00000754750chr12:109687789-109687909121ACACB_HUMAN1890-1930410--
1.42ENST0000037784842ENSE00000754751chr12:109689851-109689961111ACACB_HUMAN1931-1967370--
1.43ENST0000037784843ENSE00000754752chr12:109690820-109690963144ACACB_HUMAN1968-2015480--
1.44ENST0000037784844ENSE00000754753chr12:109692019-109692139121ACACB_HUMAN2016-2056410--
1.45ENST0000037784845ENSE00000754755chr12:109693945-10969404197ACACB_HUMAN2056-2088330--
1.46ENST0000037784846ENSE00000754756chr12:109696073-10969616997ACACB_HUMAN2088-2120330--
1.47ENST0000037784847ENSE00000754757chr12:109696778-109696913136ACACB_HUMAN2121-2166460--
1.49ENST0000037784849ENSE00001654404chr12:109698285-109698462178ACACB_HUMAN2166-2225600--
1.50ENST0000037784850ENSE00000754759chr12:109700162-109700274113ACACB_HUMAN2225-2263390--
1.51ENST0000037784851ENSE00000754760chr12:109702037-109702191155ACACB_HUMAN2263-2314520--
1.52ENST0000037784852ENSE00000754761chr12:109702915-109703085171ACACB_HUMAN2315-2371570--
1.53ENST0000037784853ENSE00000754762chr12:109703194-109703330137ACACB_HUMAN2372-2417460--
1.54bENST0000037784854bENSE00001423352chr12:109704041-1097060281988ACACB_HUMAN2417-2458420--

(-) 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:100
 aligned with ACACB_HUMAN | O00763 from UniProtKB/Swiss-Prot  Length:2458

    Alignment length:115
                                   872       882       892       902       912       922       932       942       952       962       972     
          ACACB_HUMAN   863 GNSYTTYMKEEVDSYRITIGNKTCVFEKENDPTVLRSPSAGKLTQYTVEDGGHVEAGSSYAEMEVMKMIMTLNVQERGRVKYIKRPGAVLEAGCVVARLELDDPSKVHPAEPFTG 977
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......-------------.--...........eee....eeeeee.....eee....eeeeeee..eeeeee....eeeee......ee....eeeee................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------BIOTINYL_LIPOYL  PDB: A:11-85 UniProt: 888-962                             --------------- PROSITE
           Transcript 1 (1) Exon 1.16     --------------------------------------------------Exon 1.18  PDB: A:50-94 UniProt: 927-971     1.19   Transcript 1 (1)
           Transcript 1 (2) -------------Exon 1.17  PDB: A:7-49 (gaps) UniProt: 876-926     --------------------------------------------------- Transcript 1 (2)
                 2dn8 A   1 GSSGSS-------------G--TCVFEKENDPTVLRSPSAGKLTQYTVEDGGHVEAGSSYAEMEVMKMIMTLNVQERGRVKYIKRPGAVLEAGCVVARLELDDPSKVHPSGPSSG 100
                                 |   -         7  |     15        25        35        45        55        65        75        85        95     
                                 6             7  8                                                                                            

   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 2DN8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2DN8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DN8)

(-) Gene Ontology  (34, 34)

NMR Structure(hide GO term definitions)
Chain A   (ACACB_HUMAN | O00763)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003989    acetyl-CoA carboxylase activity    Catalysis of the reaction: ATP + acetyl-CoA + HCO3- = ADP + phosphate + malonyl-CoA.
    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: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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0006084    acetyl-CoA metabolic process    The chemical reactions and pathways involving acetyl-CoA, a derivative of coenzyme A in which the sulfhydryl group is acetylated; it is a metabolite derived from several pathways (e.g. glycolysis, fatty acid oxidation, amino-acid catabolism) and is further metabolized by the tricarboxylic acid cycle. It is a key intermediate in lipid and terpenoid biosynthesis.
    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:0006853    carnitine shuttle    The transfer of acyl groups to and from acyl-CoA molecules to form O-acylcarnitine, which can exchange across the mitochondrial inner membrane with unacylated carnitine.
    GO:0097009    energy homeostasis    Any process involved in the balance between food intake (energy input) and energy expenditure.
    GO:0006633    fatty acid biosynthetic process    The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.
    GO:0006631    fatty acid metabolic process    The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:2001295    malonyl-CoA biosynthetic process    The chemical reactions and pathways resulting in the formation of malonyl-CoA, the S-malonyl derivative of coenzyme A.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0043086    negative regulation of catalytic activity    Any process that stops or reduces the activity of an enzyme.
    GO:0031999    negative regulation of fatty acid beta-oxidation    Any process that stops, prevents, or reduces the frequency, rate or extent of fatty acid beta-oxidation.
    GO:0046322    negative regulation of fatty acid oxidation    Any process that stops, prevents, or reduces the frequency, rate or extent of fatty acid oxidation.
    GO:0010629    negative regulation of gene expression    Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0050995    negative regulation of lipid catabolic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of lipids.
    GO:0031325    positive regulation of cellular metabolic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.
    GO:0060421    positive regulation of heart growth    Any process that increases the rate or extent of heart growth. Heart growth is the increase in size or mass of the heart.
    GO:0010884    positive regulation of lipid storage    Any process that increases the rate, frequency or extent of lipid storage. Lipid storage is the accumulation and maintenance in cells or tissues of lipids, compounds soluble in organic solvents but insoluble or sparingly soluble in aqueous solvents. Lipid reserves can be accumulated during early developmental stages for mobilization and utilization at later stages of development.
    GO:0051289    protein homotetramerization    The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
    GO:0010906    regulation of glucose metabolic process    Any process that modulates the rate, frequency or extent of glucose metabolism. Glucose metabolic processes are the chemical reactions and pathways involving glucose, the aldohexose gluco-hexose.
    GO:0031667    response to nutrient levels    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus reflecting the presence, absence, or concentration of nutrients.
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:0012505    endomembrane system    A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005741    mitochondrial outer membrane    The outer, i.e. cytoplasm-facing, lipid bilayer of the mitochondrial envelope.
    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.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ACACB_HUMAN | O007632hjw 2kcc 3ff6 3gid 3glk 3jrw 3jrx 3tdc 4hq6 5kkn

(-) Related Entries Specified in the PDB File

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