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(-) Description

Title :  STRUCTURE OF THE RNA BINDING DOMAIN (RESIDUES 404-479) OF THE BACILLUS SUBTILIS YXIN PROTEIN
 
Authors :  D. B. Mckay
Date :  11 Feb 06  (Deposition) - 18 Apr 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Rna Recognition Motif, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Wang, Y. Hu, M. T. Overgaard, F. V. Karginov, O. C. Uhlenbeck, D. B. Mckay
The Domain Of The Bacillus Subtilis Dead-Box Helicase Yxin That Is Responsible For Specific Binding Of 23S Rrna Has An Rna Recognition Motif Fold.
Rna V. 12 959 2006
PubMed-ID: 16611943  |  Reference-DOI: 10.1261/RNA.5906

(-) Compounds

Molecule 1 - ATP-DEPENDENT RNA HELICASE DBPA
    Chains: A
    EC Number: 3.6.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RNA BINDING DOMAIN
    Gene: DBPA, DEAD
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:424 , LYS A:427 , VAL A:467 , HOH A:1022 , HOH A:1035BINDING SITE FOR RESIDUE SO4 A 2001
2AC2SOFTWARELYS A:427 , LYS A:454 , ASN A:478 , HOH A:1017 , HOH A:1020BINDING SITE FOR RESIDUE SO4 A 2003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2G0C)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2G0C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2G0C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2G0C)

(-) Exons   (0, 0)

(no "Exon" information available for 2G0C)

(-) Sequences/Alignments

Asymmetric 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    
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:68
 aligned with DBPA_BACSU | P42305 from UniProtKB/Swiss-Prot  Length:479

    Alignment length:75
                                   413       423       433       443       453       463       473     
           DBPA_BACSU   404 MKLYFNGGKKKKIRAVDFVGTIAKIDGVSADDIGIITIMDNASYVEILNGKGPHVLKVMKNTTVKGKQLKVNKAN 478
               SCOP domains --------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....----hhhhhhhhhh....hhh.eeeeee....eeeee...hhhhhhhhhh....---...eee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                 2g0c A 404 MKLYFNGGKK----AVDFVGTIAKIDGVSADDIGIITIMDNASYVEILNGKGPHVLKVMKNTTV---QLKVNKAN 478
                                   413    |  423       433       443       453       463   |   473     
                                   413  418                                              467 471
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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 2G0C)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2G0C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2G0C)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A   (DBPA_BACSU | P42305)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0034459    ATP-dependent 3'-5' RNA helicase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction drives the unwinding of an RNA helix in the direction 3' to 5'.
    GO:0004004    ATP-dependent RNA helicase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction drives the unwinding of an RNA helix.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003724    RNA helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a RNA helix.
    GO:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    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.
biological process
    GO:0010501    RNA secondary structure unwinding    The process in which a secondary structure of RNA are broken or 'melted'.
    GO:0000027    ribosomal large subunit assembly    The aggregation, arrangement and bonding together of constituent RNAs and proteins to form the large ribosomal subunit.
    GO:0042254    ribosome biogenesis    A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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        DBPA_BACSU | P42305: 2hjv 3moj

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