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(-) Description

Title :  CRYSTAL STRUCTURE OF INTACT ALPHA SUBUNIT OF AIF2 FROM PYROCOCCUS ABYSSI
 
Authors :  L. Yatime, E. Schmitt, S. Blanquet, Y. Mechulam
Date :  28 Feb 05  (Deposition) - 28 Jun 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.37
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta Barrel, Helical Domain And Alpha Beta Domain, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Yatime, E. Schmitt, S. Blanquet, Y. Mechulam
Structure-Function Relationships Of The Intact Aif2Alpha Subunit From The Archaeon Pyrococcus Abyssi
Biochemistry V. 44 8749 2005
PubMed-ID: 15952781  |  Reference-DOI: 10.1021/BI050373I
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROBABLE TRANSLATION INITIATION FACTOR 2 ALPHA SUBUNIT
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET3A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Organism Scientific: PYROCOCCUS ABYSSI
    Organism Taxid: 29292
    Synonym: EIF-2-ALPHA, AIF2

 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 1YZ6)

(-) Sites  (0, 0)

(no "Site" information available for 1YZ6)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YZ6)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala A:221 -Pro A:222

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1YZ6)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1S1PS50126 S1 domain profile.IF2A_PYRAB12-83  1A:12-83

(-) Exons   (0, 0)

(no "Exon" information available for 1YZ6)

(-) 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:261
 aligned with IF2A_PYRAB | Q9V0E4 from UniProtKB/Swiss-Prot  Length:275

    Alignment length:261
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264 
           IF2A_PYRAB     5 AREYPEEGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEGQKVVAKVIRVDPRKGHIDLSLRRVTQQQRKAKLQEFKRAQKAENLLKLAAEKLGKDFETAWREVWVPLEEEWGEVYAAFEDAAKDGIDVLKGHVPDEWLPVLKEIIDNYVEVPTVTIDAEFEITVPKPNGVEIIKEALIRARDRANKEKDVEVKFTYLGAPRYRIDITAPDYYKAEEVLESIAEEILRVIKEAGGEATLLRKEK 265
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------1yz6A01 A:13-85 Nucleic acid-binding proteins                            ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ---S1-1yz6A01 A:8-83                                                           ------------------------------------EIF_2_alpha-1yz6A02 A:120-233                                                                                     -------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeeeee..eeeeee......eeeee.hhh......hhhhh.....eeeeeeeeee....eeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh......eeeeeeee....hhhhhhhhhhhhhhhhhh........eeeee..eeeeee...hhhhhhhhhhhhhhhhhhhhhhh..eee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------S1  PDB: A:12-83 UniProt: 12-83                                         -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yz6 A   5 AREYPEEGEFVVATVKRIHNYGAFLELDEYPGKEAFMHISEVASTWVRNIRDYLKEGQKVVAKVIRVDPRKGHIDLSLRRVTQQQRKAKLQEFKRAQKAENLLKLAAEKLGKDFETAWREVWVPLEEEWGEVYAAFEDAAKDGIDVLKGHVPDEWLPVLKEIIDNYVEVPTVTIDAEFEITVPKPNGVEIIKEALIRARDRANKEKDVEVKFTYLGAPRYRIDITAPDYYKAEEVLESIAEEILRVIKEAGGEATLLRKEK 265
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264
   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 1YZ6)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: OB (224)
(-)
Clan: no clan defined [family: EIF_2_alpha] (5)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (IF2A_PYRAB | Q9V0E4)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0003743    translation initiation factor activity    Functions in the initiation of ribosome-mediated translation of mRNA into a polypeptide.
biological process
    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.

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  Cis Peptide Bonds
    Ala A:221 - Pro A:222   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        IF2A_PYRAB | Q9V0E4: 1yz7

(-) Related Entries Specified in the PDB File

1yz7 THE C-TERMINAL SEGMENT OF THE SAME PROTEIN