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(-) Description

Title :  DEAD-BOX HELICASE MSS116 BOUND TO SSRNA AND GDP-BEF
 
Authors :  A. L. Mallam, D. J. Sidote, A. M. Lambowitz
Date :  09 Jul 14  (Deposition) - 31 Dec 14  (Release) - 04 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dead-Box, Rna Helicase, Hydrolase, Rna Binding Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. L. Mallam, D. J. Sidote, A. M. Lambowitz
Molecular Insights Into Rna And Dna Helicase Evolution From The Determinants Of Specificity For A Dead-Box Rna Helicase
Elife V. 3 04630 2014
PubMed-ID: 25497230  |  Reference-DOI: 10.7554/ELIFE.04630

(-) Compounds

Molecule 1 - ATP-DEPENDENT RNA HELICASE MSS116, MITOCHONDRIAL
    Chains: A
    EC Number: 3.6.4.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMAL-CT2
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 88-596
    Gene: MSS116, YDR194C, YD9346.05C
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
 
Molecule 2 - RNA (5'-R(*AP*AP*AP*AP*AP*AP*A)-3')
    Chains: B
    Engineered: YES
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1BEF1Ligand/IonBERYLLIUM TRIFLUORIDE ION
2GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
3MG1Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:126 , GLY A:128 , THR A:130 , GLN A:133 , GLY A:155 , THR A:156 , GLY A:157 , LYS A:158 , THR A:159 , PHE A:160 , ASP A:441 , ARG A:469 , SER A:470 , BEF A:602 , MG A:603 , HOH A:709binding site for residue GDP A 601
2AC2SOFTWARETHR A:154 , LYS A:158 , GLU A:268 , GLY A:439 , ARG A:466 , ARG A:469 , GDP A:601 , MG A:603 , HOH A:709 , HOH A:715 , HOH A:719 , HOH A:732 , HOH A:733binding site for residue BEF A 602
3AC3SOFTWAREGDP A:601 , BEF A:602 , HOH A:709 , HOH A:715 , HOH A:716 , HOH A:733binding site for residue MG A 603

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4TZ0)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys A:138 -Pro A:139
2Glu A:144 -Asp A:145

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4TZ0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4TZ0)

(-) Exons   (0, 0)

(no "Exon" information available for 4TZ0)

(-) Sequences/Alignments

Asymmetric/Biological 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    
   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:508
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.........hhhhhhh....hhhhhhhhhh......hhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhhhhh.........eeee..hhhhhhhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhh....eeeeehhhhhh...hhhhhhhhhhhhhhhh.......eeeeee....hhhhhhh.......eeeee.............eeeeeeee...hhhhhhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh..eeeee.hhhh.........eeeee......hhhhhhhh........eeeeeeee..hhhhhhhhhhh......eeeee..hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh......eeehhhhhhhhhhhhhhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tz0 A  88 SKLIHVPKEDNSKEVTLDSLLEEGVLDKEIHKAITRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFDSQYMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHERIDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELEDAKNIVIAKQEKYEPSEEIKSEVLEAVTEEPEDISDIVISLISSYRSCIKEYRFSERRILPEIASTYGVLLNDPQLKIPVSRRFLDKLGLSRSPIGKAMFEIR 595
                                    97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587        


Chain B from PDB  Type:RNA  Length:7
                                       
                 4tz0 B   1 AAAAAAA   7
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 4TZ0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4TZ0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4TZ0)

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)

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    Glu A:144 - Asp A:145   [ RasMol ]  
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  4tz0
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  MS116_YEAST | P15424
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  3.6.4.13
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 Related Entries

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

UniProtKB/Swiss-Prot
        MS116_YEAST | P15424: 3i5x 3i5y 3i61 3i62 3sqw 3sqx 4db2 4db4 4tyn 4tyw 4tyy 4tz6

(-) Related Entries Specified in the PDB File

4tyn 4tyw 4tyy 4tz6