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(-) Description

Title :  SOLUTION STRUCTURE OF RNA BINDING DOMAIN IN HYPOTHETICAL PROTEIN LOC91801
 
Authors :  K. Tsuda, Y. Muto, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  19 May 05  (Deposition) - 19 Nov 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Rrm Domain, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Tsuda, Y. Muto, M. Inoue, T. Kigawa, T. Terada, M. Shirouzu, S. Yokoyama
Solution Structure Of Rna Binding Domain In Hypothetical Protein Loc91801
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN LOC91801
    ChainsA
    EngineeredYES
    Expression System PlasmidP041012-04
    Expression System Vector TypePLASMID
    FragmentRNA RECOGNITION MOTIF
    GeneLOC9180
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymHYPOTHETICAL PROTEIN BC015183

 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 2CQ2)

(-) Sites  (0, 0)

(no "Site" information available for 2CQ2)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2CQ2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2CQ2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2CQ2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2CQ2)

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2ENST000003895682ENSE00001724312chr11:107436244-10743617966ALKB8_HUMAN-00--
1.3ENST000003895683ENSE00001620533chr11:107435940-10743588853ALKB8_HUMAN-00--
1.4ENST000003895684ENSE00001769102chr11:107434462-107434273190ALKB8_HUMAN-00--
1.5ENST000003895685ENSE00001727109chr11:107433542-107433425118ALKB8_HUMAN-00--
1.6ENST000003895686ENSE00002152837chr11:107431625-107431491135ALKB8_HUMAN1-43431A:18-43 (gaps)42
1.7ENST000003895687ENSE00000990040chr11:107427729-107427492238ALKB8_HUMAN44-123801A:44-12380
1.8aENST000003895688aENSE00000930433chr11:107424704-107424573132ALKB8_HUMAN123-167451A:123-127 (gaps)14
1.9ENST000003895689ENSE00000930432chr11:107423929-10742383496ALKB8_HUMAN167-199331A:128-1314
1.10bENST0000038956810bENSE00000930431chr11:107422638-107422534105ALKB8_HUMAN199-234360--
1.11ENST0000038956811ENSE00001506233chr11:107420549-10742047971ALKB8_HUMAN234-257240--
1.12bENST0000038956812bENSE00001687648chr11:107403132-107403026107ALKB8_HUMAN258-293360--
1.13ENST0000038956813ENSE00001697189chr11:107396318-107396167152ALKB8_HUMAN293-344520--
1.14ENST0000038956814ENSE00001611673chr11:107393281-107393025257ALKB8_HUMAN344-429860--
1.15ENST0000038956815ENSE00001634419chr11:107381762-107381613150ALKB8_HUMAN430-479500--
1.16cENST0000038956816cENSE00001763825chr11:107375941-107375321621ALKB8_HUMAN480-6641850--

(-) 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:114
 aligned with ALKB8_HUMAN | Q96BT7 from UniProtKB/Swiss-Prot  Length:664

    Alignment length:197
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       
          ALKB8_HUMAN     2 DSNHQSNYKLSKTEKKFLRKQIKAKHTLLRHEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVEKVQWKELRPQALPPGLMVVEEIISSEEEKMLLESVDWTEDTDNQNSQKSLKHRRVKHFGYEFHYENNNVDKDKPLSG 198
               SCOP domains -----------------------d2cq2a1 A:25-125 Alkylation repair AlkB homolog 8, ALKBH8                                            ------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......----------------....hhhhhhh.........eeeee..hhhhh.hhhhhhhhhhhhh.eeeee.......eeeee.hhhhhhhhhhhh...eee.....eee.eeeee......---------.----------------------------------------------------------.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.6  PDB: A:18-43 (gaps) [INCOMPLETE]Exon 1.7  PDB: A:44-123 UniProt: 44-123                                         -------------------------------------------Exon 1.9  PDB: A:128-131         Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------------------------------Exon 1.8a  PDB: A:123-127 (gaps) [INCOMPLETE]------------------------------- Transcript 1 (2)
                 2cq2 A  18 GSSGSS----------------GAKHTLLRHEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVEKVQWS---------G----------------------------------------------------------PSSG 131
                                 |   -         -  |     31        41        51        61        71        81        91       101       111       121    |    -    |    -         -         -         -         -         -   |   
                                23               24                                                                                                   126       127                                                        128   

   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 2CQ2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2CQ2)

(-) Gene Ontology  (24, 24)

NMR Structure(hide GO term definitions)
Chain A   (ALKB8_HUMAN | Q96BT7)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    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:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016706    oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors    Catalysis of the reaction: A + 2-oxoglutarate + O2 = B + succinate + CO2. This is an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from 2-oxoglutarate and one other donor, and one atom of oxygen is incorporated into each donor.
    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).
    GO:0016300    tRNA (uracil) methyltransferase activity    Catalysis of the transfer of a methyl group from a donor to a uracil residue in a tRNA molecule.
    GO:0000049    tRNA binding    Interacting selectively and non-covalently with transfer RNA.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    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:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    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:0030488    tRNA methylation    The posttranscriptional addition of methyl groups to specific residues in a tRNA molecule.
    GO:0002098    tRNA wobble uridine modification    The process in which a uridine in position 34 of a tRNA is post-transcriptionally modified.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0015630    microtubule cytoskeleton    The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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)

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        ALKB8_HUMAN | Q96BT73thp 3tht

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