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(-) Description

Title :  CRYSTAL STRUCTURE OF THE S. CEREVISIAE DEXH HELICASE SKI2 BOUND TO AMPPNP
 
Authors :  F. Halbach, M. Rode, E. Conti
Date :  20 Oct 11  (Deposition) - 21 Dec 11  (Release) - 28 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Atpase, Mrna 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
    EC Number: 3.6.4.13
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Cell Line: HIGH FIVE
    Expression System Common: CABBAGE LOOPER
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Fragment: RESIDUES 296-1287
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: SKI2, SUPERKILLER PROTEIN 2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1ANP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2EDO4Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:328 , GLU A:329 , ASP A:331 , GLN A:334 , HIS A:352 , THR A:353 , SER A:354 , ALA A:355 , GLY A:356 , LYS A:357 , THR A:358 , ARG A:763 , ARG A:767 , HOH A:2078 , HOH A:2080BINDING SITE FOR RESIDUE ANP A2288
2AC2SOFTWAREGLU A:640 , LYS A:683 , THR A:684 , VAL A:694 , HOH A:2133BINDING SITE FOR RESIDUE EDO A2289
3AC3SOFTWARELYS A:636 , GLY A:697 , THR A:722 , THR A:724 , HOH A:2067BINDING SITE FOR RESIDUE EDO A2290
4AC4SOFTWAREALA A:383 , LYS A:704 , GLU A:708BINDING SITE FOR RESIDUE EDO A2291
5AC5SOFTWARETYR A:1125 , LEU A:1127 , VAL A:1128 , GLU A:1200BINDING SITE FOR RESIDUE EDO A2292

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4A4Z)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:627 -Pro A:628

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4A4Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4A4Z)

(-) Exons   (0, 0)

(no "Exon" information available for 4A4Z)

(-) 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:874
 aligned with SKI2_YEAST | P35207 from UniProtKB/Swiss-Prot  Length:1287

    Alignment length:989
                                   308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768       778       788       798       808       818       828       838       848       858       868       878       888       898       908       918       928       938       948       958       968       978       988       998      1008      1018      1028      1038      1048      1058      1068      1078      1088      1098      1108      1118      1128      1138      1148      1158      1168      1178      1188      1198      1208      1218      1228      1238      1248      1258      1268      1278         
          SKI2_YEAST    299 KKEWAHVVDLNHKIENFDELIPNPARSWPFELDTFQKEAVYHLEQGDSVFVAAHTSAGKTVVAEYAIAMAHRNMTKTIYTSPIKALSNQKFRDFKETFDDVNIGLITGDVQINPDANCLIMTTEILRSMLYRGADLIRDVEFVIFDEVHYVNDQDRGVVWEEVIIMLPQHVKFILLSATVPNTYEFANWIGRTKQKNIYVISTPKRPVPLEINIWAKKELIPVINQNSEFLEANFRKHKEILNGESAKGAPSKTDNGRGGSTARGGRGGSNTRDGRGGRGNSTRGGANRGGSRGAGAIGSNKRKFFTQDGPSKKTWPEIVNYLRKRELLPMVVFVFSKKRCEEYADWLEGINFCNNKEKSQIHMFIEKSITRLKKEDRDLPQILKTRSLLERGIAVHHGGLLPIVKELIEILFSKGFIKVLFATETFAMGLNLPTRTVIFSSIRKHDGNGLRELTPGEFTQMAGRAGRRGLDSTGTVIVMAYNSPLSIATFKEVTMGVPTRLQSQFRLTYNMILNLLRIEALRVEEMIKYSFSENAKETLQPEHEKQIKVLQEELQTIEYKSCEICDNDIEKFLELMLAYKEATVNLMQEMVKSPSILHILKEGRLVAFRDPNDCLKLGFVFKVSLKDAVCVIMTFTKPYKLPNGEPNHLIYFPKADGYRRRNFPKFQKTDFYMEEVPVTAIEVITKRKFAAPLGKVIKKDVAALNEFNAETNNILDGKTLKEAINIEKQGLKIHQILLDRTNIRDEIFKLKSIKCPNLSQHIVPKFKAHVIKKKIEELYHLMSDQNLSLLPDYEKRLAVLKDTEFIDQNHNVLLKGRVACEINSGYELVLTELILDNFLGSFEPEEIVALLSVFVYEGKTREEEPPIVTPRLAKGKQRIEEIYKKMLCVFNTHQIPLTQDEAEFLDRKRFAMMNVVYEWARGLSFKEIMEMSPEAEGTVVRVITWLDEICREVKTASIIIGNSTLHMKMSRAQELIKRDIVFAASLYL 1287
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee........hhhhhh...........hhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhh..--..eeee....ee.....eeeeehhhhhhhhhhh.hhhh.eeeeee..............hhhhhhhh....eeeeee....hhhhhhhhhhhhhh..eeeee.......eeeeeee..eeeeee......hhhhhhhhhhhhh-----------------------------------------------------------------.....hhhhhhhhhhhhh....eeee..hhhhhhhhhhh.......hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhh....eeee.hhhhhh......eeee...eeee..eeee..hhhhhhhhhhh........eeeeee......hhhhhhhhhhh...........hhhhhhhhhhhh.hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh--------------hhhhhhhhhhhhhhhhhhhhh...hhhhhh...eeeeee.....eeeeeeeeee....eeeeee-.....----------....hhhhhhhhh........eeeeee..-..eeeeee..-hhhhhhh....hhhhhhhhhhhhhhh......------.hhhhhhhhhhhhhhhh------------..hhhhhhhhhhhhhhhhhhhhhhh.---hhhhhhhhhhhhhhhh.........hhhhhhhh.....hhhhhhhhhh.hhhh...hhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh.hhhh....hhhhhhhhhh..hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4a4z A  299 KKEWAHVVDLNHKIENFDELIPNPARSWPFELDTFQKEAVYHLEQGDSVFVAAHTSAGKTVVAEYAIAMAHRNMTKTIYTSPIKALSNQKFRDFKETF--VNIGLITGDVQINPDANCLIMTTEILRSMLYRGADLIRDVEFVIFDEVHYVNDQDRGVVWEEVIIMLPQHVKFILLSATVPNTYEFANWIGRTKQKNIYVISTPKRPVPLEINIWAKKELIPVINQNSEFLEANFRKHKEILN-----------------------------------------------------------------DGPSKKTWPEIVNYLRKRELLPMVVFVFSKKRCEEYADWLEGINFCNNKEKSQIHMFIEKSITRLKKEDRDLPQILKTRSLLERGIAVHHGGLLPIVKELIEILFSKGFIKVLFATETFAMGLNLPTRTVIFSSIRKHDGNGLRELTPGEFTQMAGRAGRRGLDSTGTVIVMAYNSPLSIATFKEVTMGVPTRLQSQFRLTYNMILNLLRIEALRVEEMIKYSFSENAKETLQPEHEKQIKVLQEELQT--------------KFLELMLAYKEATVNLMQEMVKSPSILHILKEGRLVAFRDPNDCLKLGFVFKVSLKDAVCVIMT-TKPYK----------YFPKADGYRRRNFPKFQKTDFYMEEVPVT-IEVITKRKFA-PLGKVIKKDVAALNEFNAETNNILDGKTLKEA------GLKIHQILLDRTNIRDE------------SQHIVPKFKAHVIKKKIEELYHLMSD---SLLPDYEKRLAVLKDTEFIDQNHNVLLKGRVACEINSGYELVLTELILDNFLGSFEPEEIVALLSVFVYEGKTREEEPPIVTPRLAKGKQRIEEIYKKMLCVFNTHQIPLTQDEAEFLDRKRFAMMNVVYEWARGLSFKEIMEMSPEAEGTVVRVITWLDEICREVKTASIIIGNSTLHMKMSRAQELIKRDIVFAASLYL 1287
                                   308       318       328       338       348       358       368       378       388       | -|      408       418       428       438       448       458       468       478       488       498       508       518       528       538  |      -         -         -         -         -         -       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768       778       788       798       808       818       828       838       848      |  -         - |     878       888       898       908       918       928    | |938|        - |     958       968       978 |     988| |    998      1008      1018   |     -|     1038      |  -      1058      1068      1078    | 1088      1098      1108      1118      1128      1138      1148      1158      1168      1178      1188      1198      1208      1218      1228      1238      1248      1258      1268      1278         
                                                                                                                           396  |                                                                                                                                           541                                                               607                                                                                                                                                                                                                                                     855            870                                                            933 | 939        950                         978 |      989 |                           1022   1029            1045         1058                     1083   |                                                                                                                                                                                                        
                                                                                                                              399                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     935                                          980        991                                                                                            1087
   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 4A4Z)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4A4Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4A4Z)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (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: 4a4k 4buj 5mc6

(-) Related Entries Specified in the PDB File

4a4k CRYSTAL STRUCTURE OF THE S. CEREVISIAE SKI2 INSERTION DOMAIN