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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DEADC DOMAIN OF HUMAN TRANSLATION INITIATION FACTOR 4A-2
 
Authors :  S. Dimov, B. Hong, W. Tempel, F. Mackenzie, T. Karlberg, C. H. Arrowsmit A. M. Edwards, J. Weigelt, A. Bochkarev, H. Park, Structural Genomic Consortium (Sgc)
Date :  17 Dec 07  (Deposition) - 01 Jan 08  (Release) - 27 Oct 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A
Keywords :  Translation Initiation, Dead Box, Structural Genomics, Helicase, Atp- Binding, Host-Virus Interaction, Hydrolase, Initiation Factor, Nucleotide-Binding, Protein Biosynthesis, Rna-Binding, Structural Genomics Consortium, Sgc (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 - HUMAN INITIATION FACTOR 4A-II
    Chains: A
    EC Number: 3.6.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28-MHL
    Expression System Strain: BL21-CODONPLUS(DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: EIF4A2, DDX2B, EIF4F
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ATP-DEPENDENT RNA HELICASE EIF4A-2, EIF4A-II, EIF-4A-II

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3BOR)

(-) Sites  (0, 0)

(no "Site" information available for 3BOR)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

Asymmetric/Biological Unit (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_052158Q93HIF4A2_HUMANPolymorphism11538616AQ93H
2UniProtVAR_035838V181LIF4A2_HUMANUnclassified  ---AV181L
3CancerSNPVAR_IF4A2_HUMAN_CCDS3282_1_01 *V181LIF4A2_HUMANDisease (Breast cancer)  ---AV181L
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1Q_MOTIFPS51195 DEAD-box RNA helicase Q motif profile.IF4A2_HUMAN33-61  1A:33-61
2DEAD_ATP_HELICASEPS00039 DEAD-box subfamily ATP-dependent helicases signature.IF4A2_HUMAN181-189  1A:181-189

(-) Exons   (5, 5)

Asymmetric/Biological Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1dENST000003239631dENSE00001842826chr3:186501336-18650142893IF4A2_HUMAN1-10100--
1.2dENST000003239632dENSE00001681065chr3:186502221-18650226646IF4A2_HUMAN10-25160--
1.2gENST000003239632gENSE00001694426chr3:186502353-186502485133IF4A2_HUMAN26-70451A:30-7041
1.2kENST000003239632kENSE00001695930chr3:186502751-186502890140IF4A2_HUMAN70-116471A:70-11647
1.2qENST000003239632qENSE00001609130chr3:186503672-186503840169IF4A2_HUMAN117-173571A:117-173 (gaps)57
1.2vENST000003239632vENSE00001790780chr3:186503953-186504062110IF4A2_HUMAN173-209371A:173-20937
1.2zENST000003239632zENSE00001697839chr3:186504291-186504434144IF4A2_HUMAN210-257481A:210-23627
1.2abENST000003239632abENSE00001633517chr3:186504916-186505053138IF4A2_HUMAN258-303460--
1.2aiENST000003239632aiENSE00001735148chr3:186505284-18650537390IF4A2_HUMAN304-333300--
1.2amENST000003239632amENSE00001617255chr3:186505592-18650567180IF4A2_HUMAN334-360270--
1.2ayENST000003239632ayENSE00001874691chr3:186506914-186507689776IF4A2_HUMAN360-407480--

(-) 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:194
 aligned with IF4A2_HUMAN | Q14240 from UniProtKB/Swiss-Prot  Length:407

    Alignment length:207
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       
          IF4A2_HUMAN    30 EIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQLEIEFKETQALVLAPTRELAQQIQKVILALGDYMGATCHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSRGFKDQIYEIFQKLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRIL 236
               SCOP domains d3bora_ A: automated matches                                                                                                                                                                                    SCOP domains
               CATH domains 3borA00 A:30-236 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh..hhhhhhhhhhhh....hhhhhhhhhhhhh...eee....hhhhhhhhhhhhhhhh........eeee..hhhhhhhhhhhhhhhh......eeee..-------------....eeeehhhhhhhhhhh.........eeeeehhhhhhhh.hhhhhhhhhhhh....eeeee....hhhhhhhhhhhh...eee. Sec.struct. author
             SAPs(SNPs) (1) ---------------------------------------------------------------H---------------------------------------------------------------------------------------L------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------------------------------------------------------------------------------------------------------------------------------------L------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE ---Q_MOTIF  PDB: A:33-61        -----------------------------------------------------------------------------------------------------------------------DEAD_ATP_----------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2g  PDB: A:30-70 UniProt: 26-70   ----------------------------------------------Exon 1.2q  PDB: A:117-173 (gaps) UniProt: 117-173        ------------------------------------Exon 1.2z  PDB: A:210-236   Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------Exon 1.2k  PDB: A:70-116 UniProt: 70-116       --------------------------------------------------------Exon 1.2v  PDB: A:173-209            --------------------------- Transcript 1 (2)
                 3bor A  30 EIVDNFDDMNLKESLLRGIYAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQLEIEFKETQALVLAPTRELAQQIQKVILALGDYMGATCHACIG-------------EAPHIVVGTPGRVFDMLNRRYLSPKWIKMFVLDEADEMLSRGFKDQIYEIFQKLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRIL 236
                                    39        49        59        69        79        89        99       109       119       129       | -         - |     159       169       179       189       199       209       219       229       
                                                                                                                                     137           151
   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, 1)

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

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3BOR)

(-) Gene Ontology  (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (IF4A2_HUMAN | Q14240)
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:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    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).
    GO:0003743    translation initiation factor activity    Functions in the initiation of ribosome-mediated translation of mRNA into a polypeptide.
biological process
    GO:0010501    RNA secondary structure unwinding    The process in which a secondary structure of RNA are broken or 'melted'.
    GO:1900260    negative regulation of RNA-directed 5'-3' RNA polymerase activity    Any process that stops, prevents or reduces the frequency, rate or extent of RNA-directed 5'-3' RNA polymerase activity.
    GO:0000289    nuclear-transcribed mRNA poly(A) tail shortening    Shortening of the poly(A) tail of a nuclear-transcribed mRNA from full length to an oligo(A) length.
    GO:0006446    regulation of translational initiation    Any process that modulates the frequency, rate or extent of translational initiation.
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
    GO:0006413    translational initiation    The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0016281    eukaryotic translation initiation factor 4F complex    The eukaryotic translation initiation factor 4F complex is composed of eIF4E, eIF4A and eIF4G; it is involved in the recognition of the mRNA cap, ATP-dependent unwinding of the 5'-terminal secondary structure and recruitment of the mRNA to the ribosome.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.

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