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(-) Description

Title :  DDX18 DEAD-DOMAIN
 
Authors :  P. Schutz, T. Karlberg, C. H. Arrowsmith, H. Berglund, C. Bountra, R. Co A. M. Edwards, S. Flodin, A. Flores, S. Graslund, M. Hammarstrom, A. Jo I. Johansson, A. Kallas, P. Kraulis, T. Kotenyova, A. Kotzsch, N. Mark M. Moche, T. K. Nielsen, P. Nordlund, T. Nyman, C. Persson, A. K. Roos, M. I. Siponen, L. Svensson, A. G. Thorsell, L. Tresaugues, S. Van Den E. Wahlberg, J. Weigelt, M. Welin, M. Wisniewska, H. M. Schuler, Struc Genomics Consortium (Sgc)
Date :  26 Feb 10  (Deposition) - 12 May 10  (Release) - 27 Oct 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Alpha-Beta, Structural Genomics, Structural Genomics Consortium, Sgc, Atp-Binding, Helicase, Hydrolase, Nucleotide-Binding, Rna-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Schutz, T. Karlberg, S. Van Den Berg, R. Collins, L. Lehtio, M. Hogbom, L. Holmberg-Schiavone, W. Tempel, H. W. Park, M. Hammarstrom, M. Moche, A. G. Thorsell, H. Schuler
Comparative Structural Analysis Of Human Dead-Box Rna Helicases.
Plos One V. 5 12791 2010
PubMed-ID: 20941364  |  Reference-DOI: 10.1371/JOURNAL.PONE.0012791

(-) Compounds

Molecule 1 - ATP-DEPENDENT RNA HELICASE DDX18
    Chains: A, B
    EC Number: 3.6.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC-BSA4
    Expression System Strain: BL21(DE3) GOLD PRARE2
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: DEAD-DOMAIN, RESIDUES 149-387
    Gene: DDX18
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DEAD BOX PROTEIN 18, MYC-REGULATED DEAD BOX PROTEIN, MRDB

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2PO41Ligand/IonPHOSPHATE ION
3SCN2Ligand/IonTHIOCYANATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2PO41Ligand/IonPHOSPHATE ION
3SCN1Ligand/IonTHIOCYANATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2PO4-1Ligand/IonPHOSPHATE ION
3SCN1Ligand/IonTHIOCYANATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:225 , GLY A:226 , SER A:227 , GLY A:228 , LYS A:229 , THR A:230BINDING SITE FOR RESIDUE PO4 A 1
2AC2SOFTWAREGLY A:342 , GLU A:346BINDING SITE FOR RESIDUE MG A 388
3AC3SOFTWAREALA A:223 , LYS A:229 , GLU A:334 , SER A:364 , ALA A:365BINDING SITE FOR RESIDUE MG A 389
4AC4SOFTWARETHR A:308 , GLY A:310 , ARG A:311BINDING SITE FOR RESIDUE SCN A 390
5AC5SOFTWARETHR B:308 , GLY B:310 , ARG B:311BINDING SITE FOR RESIDUE SCN B 2

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LY5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3LY5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LY5)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEAD_ATP_HELICASEPS00039 DEAD-box subfamily ATP-dependent helicases signature.DDX18_HUMAN331-339
 		  2A:331-339
B:331-339
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEAD_ATP_HELICASEPS00039 DEAD-box subfamily ATP-dependent helicases signature.DDX18_HUMAN331-339
 		  1A:331-339
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEAD_ATP_HELICASEPS00039 DEAD-box subfamily ATP-dependent helicases signature.DDX18_HUMAN331-339
 		  1-
B:331-339

(-) Exons   (0, 0)

(no "Exon" information available for 3LY5)

(-) 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:211
 aligned with DDX18_HUMAN | Q9NVP1 from UniProtKB/Swiss-Prot  Length:670

    Alignment length:216
                                   180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380      
          DDX18_HUMAN   171 TGAFEDTSFASLCNLVNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNGTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQKLGNGINIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILDVGFEEELKQIIKLLPTRRQTMLFSATQTRKVEDLARISLKKEPLYV 386
               SCOP domains d3ly5a_ A     : automated matches                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhh.-----..hhhhhhhhhhh.....hhhhhhhhhhhhhh...ee......hhhhhhhhhhhhhhhhh..hhhhh..eeee..hhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhh..eeeehhhhhhhhhhhh.........eeee.hhhhhhhh.hhhhhhhhhhhh....eeeee....hhhhhhhhhhhh....ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------DEAD_ATP_----------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ly5 A 171 TGAFEDTSF-----LVNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNGTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQKLGNGINIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILDVGFEEELKQIIKLLPTRRQTMLFSATQTRKVEDLARISLKKEPLYV 386
                                    |-    |  190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380      
                                  179   185                                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:213
 aligned with DDX18_HUMAN | Q9NVP1 from UniProtKB/Swiss-Prot  Length:670

    Alignment length:218
                                   178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378        
          DDX18_HUMAN   169 GLTGAFEDTSFASLCNLVNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNGTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQKLGNGINIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILDVGFEEELKQIIKLLPTRRQTMLFSATQTRKVEDLARISLKKEPLYV 386
               SCOP domains d3ly5b_ B:      automated matches                                                                                                                                                                                          SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------------DEAD-3ly5B01 B:203-374                                                                                                                                                      ------------ Pfam domains (1)
           Pfam domains (2) ----------------------------------DEAD-3ly5B02 B:203-374                                                                                                                                                      ------------ Pfam domains (2)
         Sec.struct. author .....hhhhh.-----..hhhhhhhhhh......hhhhhhhhhhhhhh...ee......hhhhhhhhhhhhhhhhh.........eeee..hhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhh...eeeehhhhhhhhhhhh.........eeee.hhhhhhhh.hhhhhhhhhhhh....eeeee....hhhhhhhhhhhh....ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------DEAD_ATP_----------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ly5 B 169 GLTGAFEDTSF-----LVNENTLKAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFMPRNGTGVLILSPTRELAMQTFGVLKELMTHHVHTYGLIMGGSNRSAEAQKLGNGINIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILDVGFEEELKQIIKLLPTRRQTMLFSATQTRKVEDLARISLKKEPLYV 386
                                   178|     |188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378        
                                    179   185
   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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LY5)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: P-loop_NTPase (1112)
(-)
Family: DEAD (41)
(-)
Homo sapiens (Human) (12)
1aDEAD-3ly5B01B:203-374
1bDEAD-3ly5B02B:203-374

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (DDX18_HUMAN | Q9NVP1)
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: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:0010501    RNA secondary structure unwinding    The process in which a secondary structure of RNA are broken or 'melted'.
cellular component
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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