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(-) Description

Title :  CRYSTAL STRUCTURE OF THE S. CEREVISIAE SKI2 INSERTION DOMAIN
 
Authors :  F. Halbach, M. Rode, E. Conti
Date :  17 Oct 11  (Deposition) - 21 Dec 11  (Release) - 28 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.25
Chains :  Asym. Unit :  A,C,E,G,I
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  C  (1x)
Biol. Unit 3:  E  (1x)
Biol. Unit 4:  G  (1x)
Biol. Unit 5:  I  (1x)
Keywords :  Dexh Helicase, Hydrolase, Rna Degradation, Exosome (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Halbach, M. Rode, E. Conti
The Crystal Structure Of S. Cerevisiae Ski2, A Dexh Helicase Associated With The Cytoplasmic Functions Of The Exosome.
Rna V. 18 124 2012
PubMed-ID: 22114319  |  Reference-DOI: 10.1261/RNA.029553.111

(-) Compounds

Molecule 1 - ANTIVIRAL HELICASE SKI2
    Chains: A, C, E, G, I
    EC Number: 3.6.4.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: GOLD PLYSS
    Fragment: RESIDUES 835-1085
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: SKI2, SUPERKILLER PROTEIN 2

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ACEGI
Biological Unit 1 (1x): A    
Biological Unit 2 (1x):  C   
Biological Unit 3 (1x):   E  
Biological Unit 4 (1x):    G 
Biological Unit 5 (1x):     I

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric Unit (1, 5)
No.NameCountTypeFull Name
1ZN5Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 5 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:861 , CYS A:864 , CYS A:1054 , HIS A:1060BINDING SITE FOR RESIDUE ZN A2083
2AC2SOFTWARECYS C:861 , CYS C:864 , CYS C:1054 , HIS C:1060BINDING SITE FOR RESIDUE ZN C2083
3AC3SOFTWARECYS E:861 , CYS E:864 , CYS E:1054 , HIS E:1060BINDING SITE FOR RESIDUE ZN E2083
4AC4SOFTWARECYS G:861 , CYS G:864 , CYS G:1054 , HIS G:1060BINDING SITE FOR RESIDUE ZN G2083
5AC5SOFTWARECYS I:861 , CYS I:864 , CYS I:1054 , HIS I:1060BINDING SITE FOR RESIDUE ZN I2083

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4A4K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4A4K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4A4K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4A4K)

(-) Exons   (0, 0)

(no "Exon" information available for 4A4K)

(-) 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:246
 aligned with SKI2_YEAST | P35207 from UniProtKB/Swiss-Prot  Length:1287

    Alignment length:246
                                   846       856       866       876       886       896       906       916       926       936       946       956       966       976       986       996      1006      1016      1026      1036      1046      1056      1066      1076      
          SKI2_YEAST    837 TLQPEHEKQIKVLQEELQTIEYKSCEICDNDIEKFLELMLAYKEATVNLMQEMVKSPSILHILKEGRLVAFRDPNDCLKLGFVFKVSLKDAVCVIMTFTKPYKLPNGEPNHLIYFPKADGYRRRNFPKFQKTDFYMEEVPVTAIEVITKRKFAAPLGKVIKKDVAALNEFNAETNNILDGKTLKEAINIEKQGLKIHQILLDRTNIRDEIFKLKSIKCPNLSQHIVPKFKAHVIKKKIEELYHLMS 1082
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhh...hhhhhh...eeeeee.....eeeeeeeeee....eeeeeeee..................hhhhhhhhh....eeeeeeeeee.hhh.eeeeee...hhhhhhh.hhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4a4k A  837 TLQPEHEKQIKVLQEELQTIEYKSCEICDNDIEKFLELMLAYKEATVNLMQEMVKSPSILHILKEGRLVAFRDPNDCLKLGFVFKVSLKDAVCVIMTFTKPYKLPNGEPNHLIYFPKADGYRRRNFPKFQKTDFYMEEVPVTAIEVITKRKFAAPLGKVIKKDVAALNEFNAETNNILDGKTLKEAINIEKQGLKIHQILLDRTNIRDEIFKLKSIKCPNLSQHIVPKFKAHVIKKKIEELYHLMS 1082
                                   846       856       866       876       886       896       906       916       926       936       946       956       966       976       986       996      1006      1016      1026      1036      1046      1056      1066      1076      


Chain C from PDB  Type:PROTEIN  Length:245
 aligned with SKI2_YEAST | P35207 from UniProtKB/Swiss-Prot  Length:1287

    Alignment length:245
                                   846       856       866       876       886       896       906       916       926       936       946       956       966       976       986       996      1006      1016      1026      1036      1046      1056      1066      1076     
          SKI2_YEAST    837 TLQPEHEKQIKVLQEELQTIEYKSCEICDNDIEKFLELMLAYKEATVNLMQEMVKSPSILHILKEGRLVAFRDPNDCLKLGFVFKVSLKDAVCVIMTFTKPYKLPNGEPNHLIYFPKADGYRRRNFPKFQKTDFYMEEVPVTAIEVITKRKFAAPLGKVIKKDVAALNEFNAETNNILDGKTLKEAINIEKQGLKIHQILLDRTNIRDEIFKLKSIKCPNLSQHIVPKFKAHVIKKKIEELYHLM 1081
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhh...hhhhhh...eeeeee.....eeeeeeeeee....eeeeeeee..................hhhhhhhhh....eeeeeeeeee.hhh.eeeeee...hhhhhhh.hhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4a4k C  837 TLQPEHEKQIKVLQEELQTIEYKSCEICDNDIEKFLELMLAYKEATVNLMQEMVKSPSILHILKEGRLVAFRDPNDCLKLGFVFKVSLKDAVCVIMTFTKPYKLPNGEPNHLIYFPKADGYRRRNFPKFQKTDFYMEEVPVTAIEVITKRKFAAPLGKVIKKDVAALNEFNAETNNILDGKTLKEAINIEKQGLKIHQILLDRTNIRDEIFKLKSIKCPNLSQHIVPKFKAHVIKKKIEELYHLM 1081
                                   846       856       866       876       886       896       906       916       926       936       946       956       966       976       986       996      1006      1016      1026      1036      1046      1056      1066      1076     


Chain E from PDB  Type:PROTEIN  Length:244
 aligned with SKI2_YEAST | P35207 from UniProtKB/Swiss-Prot  Length:1287

    Alignment length:244
                                   847       857       867       877       887       897       907       917       927       937       947       957       967       977       987       997      1007      1017      1027      1037      1047      1057      1067      1077    
          SKI2_YEAST    838 LQPEHEKQIKVLQEELQTIEYKSCEICDNDIEKFLELMLAYKEATVNLMQEMVKSPSILHILKEGRLVAFRDPNDCLKLGFVFKVSLKDAVCVIMTFTKPYKLPNGEPNHLIYFPKADGYRRRNFPKFQKTDFYMEEVPVTAIEVITKRKFAAPLGKVIKKDVAALNEFNAETNNILDGKTLKEAINIEKQGLKIHQILLDRTNIRDEIFKLKSIKCPNLSQHIVPKFKAHVIKKKIEELYHLM 1081
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhh...hhhhhh...eeeeeee...eeeeeeeeeee....eeeeeeee..................hhhhhhhhh....eeeeeeeeee.hhh.eeeeee...hhhhhhh.hhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4a4k E  838 LQPEHEKQIKVLQEELQTIEYKSCEICDNDIEKFLELMLAYKEATVNLMQEMVKSPSILHILKEGRLVAFRDPNDCLKLGFVFKVSLKDAVCVIMTFTKPYKLPNGEPNHLIYFPKADGYRRRNFPKFQKTDFYMEEVPVTAIEVITKRKFAAPLGKVIKKDVAALNEFNAETNNILDGKTLKEAINIEKQGLKIHQILLDRTNIRDEIFKLKSIKCPNLSQHIVPKFKAHVIKKKIEELYHLM 1081
                                   847       857       867       877       887       897       907       917       927       937       947       957       967       977       987       997      1007      1017      1027      1037      1047      1057      1067      1077    


Chain G from PDB  Type:PROTEIN  Length:246
 aligned with SKI2_YEAST | P35207 from UniProtKB/Swiss-Prot  Length:1287

    Alignment length:246
                                   846       856       866       876       886       896       906       916       926       936       946       956       966       976       986       996      1006      1016      1026      1036      1046      1056      1066      1076      
          SKI2_YEAST    837 TLQPEHEKQIKVLQEELQTIEYKSCEICDNDIEKFLELMLAYKEATVNLMQEMVKSPSILHILKEGRLVAFRDPNDCLKLGFVFKVSLKDAVCVIMTFTKPYKLPNGEPNHLIYFPKADGYRRRNFPKFQKTDFYMEEVPVTAIEVITKRKFAAPLGKVIKKDVAALNEFNAETNNILDGKTLKEAINIEKQGLKIHQILLDRTNIRDEIFKLKSIKCPNLSQHIVPKFKAHVIKKKIEELYHLMS 1082
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhh...hhhhhh...eeeeeee...eeeeeeeeeee....eeeeeeee..................hhhhhhhhh....eeeeeeeeee.hhh.eeeeee...hhhhhhh.hhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4a4k G  837 TLQPEHEKQIKVLQEELQTIEYKSCEICDNDIEKFLELMLAYKEATVNLMQEMVKSPSILHILKEGRLVAFRDPNDCLKLGFVFKVSLKDAVCVIMTFTKPYKLPNGEPNHLIYFPKADGYRRRNFPKFQKTDFYMEEVPVTAIEVITKRKFAAPLGKVIKKDVAALNEFNAETNNILDGKTLKEAINIEKQGLKIHQILLDRTNIRDEIFKLKSIKCPNLSQHIVPKFKAHVIKKKIEELYHLMS 1082
                                   846       856       866       876       886       896       906       916       926       936       946       956       966       976       986       996      1006      1016      1026      1036      1046      1056      1066      1076      


Chain I from PDB  Type:PROTEIN  Length:245
 aligned with SKI2_YEAST | P35207 from UniProtKB/Swiss-Prot  Length:1287

    Alignment length:245
                                   847       857       867       877       887       897       907       917       927       937       947       957       967       977       987       997      1007      1017      1027      1037      1047      1057      1067      1077     
          SKI2_YEAST    838 LQPEHEKQIKVLQEELQTIEYKSCEICDNDIEKFLELMLAYKEATVNLMQEMVKSPSILHILKEGRLVAFRDPNDCLKLGFVFKVSLKDAVCVIMTFTKPYKLPNGEPNHLIYFPKADGYRRRNFPKFQKTDFYMEEVPVTAIEVITKRKFAAPLGKVIKKDVAALNEFNAETNNILDGKTLKEAINIEKQGLKIHQILLDRTNIRDEIFKLKSIKCPNLSQHIVPKFKAHVIKKKIEELYHLMS 1082
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhh...hhhhhh...eeeeee.....eeeeeeeeee....eeeeeeee..................hhhhhhhhh....eeeeeeeeee.hhh.eeeeee...hhhhhhh.hhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4a4k I  838 LQPEHEKQIKVLQEELQTIEYKSCEICDNDIEKFLELMLAYKEATVNLMQEMVKSPSILHILKEGRLVAFRDPNDCLKLGFVFKVSLKDAVCVIMTFTKPYKLPNGEPNHLIYFPKADGYRRRNFPKFQKTDFYMEEVPVTAIEVITKRKFAAPLGKVIKKDVAALNEFNAETNNILDGKTLKEAINIEKQGLKIHQILLDRTNIRDEIFKLKSIKCPNLSQHIVPKFKAHVIKKKIEELYHLMS 1082
                                   847       857       867       877       887       897       907       917       927       937       947       957       967       977       987       997      1007      1017      1027      1037      1047      1057      1067      1077
   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 4A4K)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4A4K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4A4K)

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)
Chain A,C,E,G,I   (SKI2_YEAST | P35207)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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.
    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).
biological process
    GO:0006401    RNA catabolic process    The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
    GO:0051607    defense response to virus    Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
    GO:0070478    nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay    The chemical reactions and pathways resulting in the breakdown of the nuclear-transcribed mRNA transcript body of an mRNA in which an amino-acid codon has changed to a nonsense codon; occurs when the 3' end is not protected by a 3'-poly(A) tail; degradation proceeds in the 3' to 5' direction.
    GO:0034427    nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5'    The chemical reactions and pathways resulting in the breakdown of the mRNA transcript body that occurs when the 3' end is not protected by a 3'-poly(A) tail; degradation proceeds in the 3' to 5' direction.
    GO:0070481    nuclear-transcribed mRNA catabolic process, non-stop decay    The chemical reactions and pathways resulting in the breakdown of the transcript body of a nuclear-transcribed mRNA that is lacking a stop codon.
    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.
cellular component
    GO:0055087    Ski complex    A protein complex that regulates RNA degradation by the exosome complex. In Saccharomyces the complex has a heterotetrameric stoichiometry consisting of one copy each of Ski2p and Ski3 and two copies of Ski8p.
    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

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

UniProtKB/Swiss-Prot
        SKI2_YEAST | P35207: 4a4z 4buj 5mc6

(-) Related Entries Specified in the PDB File

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