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(-) Description

Title :  SOLUTION STRUCTURE OF RSGI RUH-059, AN ACP DOMAIN OF ACYL CARRIER PROTEIN, MITOCHONDRIAL [PRECURSOR] FROM HUMAN CDNA
 
Authors :  T. Abe, H. Hirota, C. Kurosaki, M. Yoshida, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  26 Apr 06  (Deposition) - 26 Oct 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Acyl Carrier Protein, Acp, Fatty Acid Biosynthesis, Mitochondria, Nadh:Ubiquinone Oxidereductase, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Abe, H. Hirota, C. Kurosaki, M. Yoshida, S. Yokoyama
Solution Structure Of Rsgi Ruh-059, An Acp Domain Of Acyl Carrier Protein, Mitochondrial [Precursor] From Human Cdna
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ACYL CARRIER PROTEIN
    ChainsA
    EngineeredYES
    Expression SystemCELL FREE SYNTHESIS
    Expression System PlasmidP050704-29
    Expression System Vector TypePLASMID
    FragmentACYL CARRIER PROTEIN
    GeneNDUFAB1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymACP, NADH-UBIQUINONE OXIDOREDUCTASE 9.6 KDA SUBUNIT, CI-SDAP

 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 2DNW)

(-) Sites  (0, 0)

(no "Site" information available for 2DNW)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CARRIERPS50075 Carrier protein (CP) domain profile.ACPM_HUMAN77-152  1A:14-89
2PHOSPHOPANTETHEINEPS00012 Phosphopantetheine attachment site.ACPM_HUMAN107-122  1A:44-59

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000000075161aENSE00001921040chr16:23607677-23607444234ACPM_HUMAN1-56561A:1-55
1.3ENST000000075163ENSE00000428414chr16:23598640-23598518123ACPM_HUMAN57-97411A:6-3429
1.4ENST000000075164ENSE00000677025chr16:23596744-2359665788ACPM_HUMAN98-127301A:35-6430
1.5ENST000000075165ENSE00000829593chr16:23593696-23593597100ACPM_HUMAN127-156301A:64-9330
1.6bENST000000075166bENSE00000829594chr16:23592494-23592323172ACPM_HUMAN-00--

(-) 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
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Chain A from PDB  Type:PROTEIN  Length:99
 aligned with ACPM_HUMAN | O14561 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:126
                                                                                                                                                 156      
                                    46        56        66        76        86        96       106       116       126       136       146       156      
           ACPM_HUMAN    37 CSAGTQTRLGTLQPALVLAQVPGRVTQLCRQYSDMPPLTLEGIQDRVLYVLKLYDKIDPEKLSVNSHFMKDLGLDSLDQVEIIMAMEDEFGFEIPDIDAEKLMCPQEIVDYIADKKDVYE------   -
               SCOP domains d2dnw                           a_ A: automated matches                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....---------------------------......hhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhh....hhhhhh...hhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ----------------------------------------CARRIER  PDB: A:14-89 UniProt: 77-152                                       ---------- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------PHOSPHOPANTETHEI---------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1a  PDB: A:1-Exon 1.3  PDB: A:6-34 UniProt: 57-97     Exon 1.4  PDB: A:35-64        ----------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------Exon 1.5  PDB: A:64-93        ------ Transcript 1 (2)
                 2dnw A   1 GSSGS---------------------------SGMPPLTLEGIQDRVLYVLKLYDKIDPEKLSVNSHFMKDLGLDSLDQVEIIMAMEDEFGFEIPDIDAEKLMCPQEIVDYIADKKDVYESGPSSG  99
                                |    -         -         -  |     13        23        33        43        53        63        73        83        93      
                                5                           6                                                                                             

   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  (1, 1)

NMR Structure

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (18, 18)

NMR Structure(hide GO term definitions)
Chain A   (ACPM_HUMAN | O14561)
molecular function
    GO:0000036    ACP phosphopantetheine attachment site binding involved in fatty acid biosynthetic process    Interacting selectively and non-covalently with the attachment site of the phosphopantetheine prosthetic group of an acyl carrier protein (ACP) as part of the process of fatty acid biosynthesis.
    GO:0008137    NADH dehydrogenase (ubiquinone) activity    Catalysis of the reaction: NADH + H+ + ubiquinone = NAD+ + ubiquinol.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0005504    fatty acid binding    Interacting selectively and non-covalently with fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
biological process
    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:0046487    glyoxylate metabolic process    The chemical reactions and pathways involving glyoxylate, the anion of glyoxylic acid, HOC-COOH.
    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:0006120    mitochondrial electron transport, NADH to ubiquinone    The transfer of electrons from NADH to ubiquinone that occurs during oxidative phosphorylation, mediated by the multisubunit enzyme known as complex I.
    GO:0032981    mitochondrial respiratory chain complex I assembly    The aggregation, arrangement and bonding together of a set of components to form mitochondrial respiratory chain complex I.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0009249    protein lipoylation    The addition of a lipoyl group to an amino acid residue in a protein.
cellular component
    GO:0005743    mitochondrial inner membrane    The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
    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:0031966    mitochondrial membrane    Either of the lipid bilayers that surround the mitochondrion and form the mitochondrial envelope.
    GO:0005747    mitochondrial respiratory chain complex I    A protein complex located in the mitochondrial inner membrane that forms part of the mitochondrial respiratory chain. It contains about 25 different polypeptide subunits, including NADH dehydrogenase (ubiquinone), flavin mononucleotide and several different iron-sulfur clusters containing non-heme iron. The iron undergoes oxidation-reduction between Fe(II) and Fe(III), and catalyzes proton translocation linked to the oxidation of NADH by ubiquinone.
    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:0070469    respiratory chain    The protein complexes that form the electron transport system (the respiratory chain), associated with a cell membrane, usually the plasma membrane (in prokaryotes) or the inner mitochondrial membrane (on eukaryotes). The respiratory chain complexes transfer electrons from an electron donor to an electron acceptor and are associated with a proton pump to create a transmembrane electrochemical gradient.

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