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(-) Description

Title :  MSS116P DEAD-BOX HELICASE DOMAIN 2 BOUND TO AN RNA DUPLEX
 
Authors :  A. L. Mallam, M. Del Campo, B. D. Gilman, D. J. Sidote, A. Lambowitz
Date :  13 Jan 12  (Deposition) - 29 Aug 12  (Release) - 10 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.16
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J
Biol. Unit 1:  A,C,E,F  (1x)
Biol. Unit 2:  B,D,I,J  (1x)
Biol. Unit 3:  G,H  (1x)
Keywords :  Dead-Box, Rna Helicase, Hydrolase, Rna Binding Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. L. Mallam, M. Del Campo, B. Gilman, D. J. Sidote, A. M. Lambowitz
Structural Basis For Rna-Duplex Recognition And Unwinding B The Dead-Box Helicase Mss116P.
Nature V. 490 121 2012
PubMed-ID: 22940866  |  Reference-DOI: 10.1038/NATURE11402

(-) Compounds

Molecule 1 - ATP-DEPENDENT RNA HELICASE MSS116, MITOCHONDRIAL
    Chains: A, B, C, D
    EC Number: 3.6.4.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMAL-C2T
    Expression System Strain: BL21 ROSETTA 2
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: DOMAIN 2 (UNP RESIDUES 342-596)
    Gene: MSS116, YDR194C, YD9346.05C
    Organelle: MITOCHONDRION
    Organism Common: YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: MSS116P
 
Molecule 2 - 5'-R(*GP*GP*GP*CP*GP*GP*GP*CP*CP*CP*GP*CP*CP*C)-3'
    Chains: E, F, G, H, I, J
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678910
Asymmetric Unit : ABCDEFGHIJ
Biological Unit 1 (1x): A C EF    
Biological Unit 2 (1x):  B D    IJ
Biological Unit 3 (1x):       GH  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4DB2)

(-) Sites  (0, 0)

(no "Site" information available for 4DB2)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4DB2)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly A:436 -Ala A:437

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4DB2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4DB2)

(-) Exons   (0, 0)

(no "Exon" information available for 4DB2)

(-) 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    
   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:256
 aligned with MS116_YEAST | P15424 from UniProtKB/Swiss-Prot  Length:664

    Alignment length:256
                                   350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590      
          MS116_YEAST   341 RIDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELEDAKNIVIAKQEKYEPSEEIKSEVLEAVTEEPEDISDIVISLISSYRSCIKEYRFSERRILPEIASTYGVLLNDPQLKIPVSRRFLDKLGLSRSPIGKAMFEIRD 596
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee...hhhhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh..eeeee..............eeeee......hhhhhhhh........eeeeeeee...hhhhhhhhhh......eeeee..hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh......eeehhhhhhhhh...hhhhhhheee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4db2 A 341 SIDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELEDAKNIVIAKQEKYEPSEEIKSEVLEAVTEEPEDISDIVISLISSYRSCIKEYRFSERRILPEIASTYGVLLNDPQLKIPVSRRFLDKLGLSRSPIGKAMFEIRD 596
                                   350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590      


Chain B from PDB  Type:PROTEIN  Length:256
 aligned with MS116_YEAST | P15424 from UniProtKB/Swiss-Prot  Length:664

    Alignment length:256
                                   350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590      
          MS116_YEAST   341 RIDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELEDAKNIVIAKQEKYEPSEEIKSEVLEAVTEEPEDISDIVISLISSYRSCIKEYRFSERRILPEIASTYGVLLNDPQLKIPVSRRFLDKLGLSRSPIGKAMFEIRD 596
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee...hhhhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh..eeeee..............eeeee......hhhhhhhh........eeeeeeee...hhhhhhhhhh......eeeee..hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.....eeehhhhhhhhh...hhhhhhheee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4db2 B 341 SIDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELEDAKNIVIAKQEKYEPSEEIKSEVLEAVTEEPEDISDIVISLISSYRSCIKEYRFSERRILPEIASTYGVLLNDPQLKIPVSRRFLDKLGLSRSPIGKAMFEIRD 596
                                   350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590      


Chain C from PDB  Type:PROTEIN  Length:256
 aligned with MS116_YEAST | P15424 from UniProtKB/Swiss-Prot  Length:664

    Alignment length:256
                                   351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591      
          MS116_YEAST   342 IDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELEDAKNIVIAKQEKYEPSEEIKSEVLEAVTEEPEDISDIVISLISSYRSCIKEYRFSERRILPEIASTYGVLLNDPQLKIPVSRRFLDKLGLSRSPIGKAMFEIRDY 597
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh..eeeee..............eeeee......hhhhhhhh.........eeeeeee...hhhhhhhhhh......eeeee..hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh......eeehhhhhhhhh...hhhhhhheee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4db2 C 342 IDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELEDAKNIVIAKQEKYEPSEEIKSEVLEAVTEEPEDISDIVISLISSYRSCIKEYRFSERRILPEIASTYGVLLNDPQLKIPVSRRFLDKLGLSRSPIGKAMFEIRDY 597
                                   351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591      


Chain D from PDB  Type:PROTEIN  Length:237
 aligned with MS116_YEAST | P15424 from UniProtKB/Swiss-Prot  Length:664

    Alignment length:256
                                   351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591      
          MS116_YEAST   342 IDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDVGARGMDFPNVHEVLQIGVPSELANYIHRIGRTARSGKEGSSVLFICKDELPFVRELEDAKNIVIAKQEKYEPSEEIKSEVLEAVTEEPEDISDIVISLISSYRSCIKEYRFSERRILPEIASTYGVLLNDPQLKIPVSRRFLDKLGLSRSPIGKAMFEIRDY 597
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...hhhhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh..eeeee...---------..eeeee....hhhhhhhhhh----------.eeeee...hhhhhhhhhh......eeeee..hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh......eeehhhhhhhhh...hhhhhhheee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4db2 D 342 IDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTSFLCSILKNEFKKDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDV---------VHEVLQIGVPSELANYIHRIG----------SVLFICKDELPFVRELEDAKNIVIAKQEKYEPSEEIKSEVLEAVTEEPEDISDIVISLISSYRSCIKEYRFSERRILPEIASTYGVLLNDPQLKIPVSRRFLDKLGLSRSPIGKAMFEIRDY 597
                                   351       361       371       381       391       401       411       421       431   |     -   |   451       461   |     -    |  481       491       501       511       521       531       541       551       561       571       581       591      
                                                                                                                       435       445                 465        476                                                                                                                         


Chain E from PDB  Type:RNA  Length:14
                                              
                 4db2 E  -3 GGGCGGGCCCGCCC  10
                                     6    


Chain F from PDB  Type:RNA  Length:14
                                              
                 4db2 F   0 GGGCGGGCCCGCCC  13
                                     9    


Chain G from PDB  Type:RNA  Length:13
                                             
                 4db2 G   1 GGGCGGGCCCGCC  13
                                    10   


Chain H from PDB  Type:RNA  Length:14
                                              
                 4db2 H   1 GGGCGGGCCCGCCC  14
                                    10    


Chain I from PDB  Type:RNA  Length:14
                                              
                 4db2 I  -2 GGGCGGGCCCGCCC  11
                                     7    


Chain J from PDB  Type:RNA  Length:14
                                              
                 4db2 J  -1 GGGCGGGCCCGCCC  12
                                     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 4DB2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4DB2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4DB2)

(-) Gene Ontology  (18, 18)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (MS116_YEAST | P15424)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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:0033592    RNA strand annealing activity    Facilitates the base-pairing of complementary single-stranded RNA.
    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:0000372    Group I intron splicing    The splicing of Group I introns. This occurs by a ribozymic mechanism where the intron sequence forms a distinct 3D structure, characteristic of Group I introns and involved in determining the locations of the splice sites (there do not appear to be consensus splice site sequences) as well as having a role in catalyzing the splicing reactions, though protein factors are also required in vivo. Splicing occurs by a series of two transesterification reactions, generally with exogenous guanosine as the initiating nucleophile. The intron is excised as a linear piece (though it may subsequently circularize).
    GO:0000373    Group II intron splicing    The splicing of Group II introns. This occurs by a ribozymic mechanism where the intron sequence forms a distinct 3D structure, characteristic of Group II introns and containing splice site consensus sequences, that is involved in catalyzing the splicing reactions, though protein factors are also required in vivo. Splicing occurs by a series of two transesterification reactions (mechanistically similar to those for splicing of nuclear mRNAs) initiated by a bulged adenosine residue within the intron sequence as the initiating nucleophile. The intron is excised as a lariat.
    GO:0034337    RNA folding    The process of assisting in the covalent and noncovalent assembly of single or multimeric RNAs into the correct tertiary structure.
    GO:0010501    RNA secondary structure unwinding    The process in which a secondary structure of RNA are broken or 'melted'.
    GO:0008380    RNA splicing    The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
    GO:0006397    mRNA processing    Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
    GO:0006417    regulation of translation    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:0006392    transcription elongation from mitochondrial promoter    The extension of an RNA molecule after transcription initiation and promoter clearance at mitochondrial promoter by the addition of ribonucleotides catalyzed by a mitchondrial RNA polymerase.
cellular component
    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: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.

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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 4db4 4tyn 4tyw 4tyy 4tz0 4tz6

(-) Related Entries Specified in the PDB File

4dax 4daz 4db4