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(-) Description

Title :  BACTERIAL TRANSLATION INITIATION FACTOR IF2 (1-363), COMPLEX WITH GDP AT PH6.5
 
Authors :  A. Simonetti, A. Urzhumtsev, B. P. Klaholz
Date :  27 Jul 12  (Deposition) - 29 May 13  (Release) - 11 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Translation, Initiation, Gtp Hydrolysis Mechanism (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Simonetti, S. Marzi, A. Fabbretti, I. Hazemann, L. Jenner, A. Urzhumtsev, C. O. Gualerzi, B. P. Klaholz
Structure Of The Protein Core Of Translation Initiation Factor 2 In Apo, Gtp-Bound And Gdp-Bound Forms
Acta Crystallogr. , Sect. D V. 69 925 2013
PubMed-ID: 23695237  |  Reference-DOI: 10.1107/S0907444913006422

(-) Compounds

Molecule 1 - TRANSLATION INITIATION FACTOR IF-2
    Atcc: 27634
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET-30B
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-363
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Other Details: DSM 579
    Strain: HB8

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:82 , ASP A:83 , HIS A:84 , GLY A:85 , LYS A:86 , THR A:87 , THR A:88 , ASN A:180 , LYS A:181 , ASP A:183 , LEU A:184 , SER A:216 , ALA A:217 , LYS A:218 , ARG A:354 , MG A:1357 , HOH A:2018 , HOH A:2046BINDING SITE FOR RESIDUE GDP A1356
2AC2SOFTWARETHR A:87 , ARG A:354 , GDP A:1356 , HOH A:2018BINDING SITE FOR RESIDUE MG A1357

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4B47)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ala A:103 -Gly A:104
2Gly A:104 -Gly A:105
3Gly A:105 -Ile A:106
4Gln A:138 -Arg A:139

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4B47)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4B47)

(-) Exons   (0, 0)

(no "Exon" information available for 4B47)

(-) 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:348
 aligned with IF2_THET8 | P48515 from UniProtKB/Swiss-Prot  Length:571

    Alignment length:354
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351    
            IF2_THET8     2 AKVRIYQLAKELGMETQELLELLDQMGVAYKSHASTLEEKDAEAVRELVKEQRGLQEKLAEEERRKSLPRRPPVVVIMGHVDHGKTTLLDYLRKSRIAEKEAGGITQHVGAFEVKTPQGTVVFIDTPGHEAFTTIRQRGAKVADIAVIVIAADDGIMPQTEEAIAHAKAAGAKLIFAINKIDLPQADPEKVKRQLMERGFVPEEYGGDAIVIPISAKTGQGVQDLLEMILLLAELEDYRADPNAEPRGVILESKLDKQAGIIANMLVQEGTFRVGDYVVAGEAYGRIRAMMDADGNQRKEAGPGSAVQVLGFQELPHAGDVVEWVPDLEAAKEIAEERKEERKAREEEEKARRP 355
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eehhhhhhhh..hhhhhhhhhhhhh........eehhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeee.....hhhhhhhhhhh................eeeeee..eeeeee......------........eeeeeee.....hhhhhhhhhhhhhh..eeeeeee.......hhhhhhhhhhhh....hhhh...eeee.......hhhhhhhhhhhhhhhhh.........eeeeeeeeee...eeeeeeeeee..ee...eeee..eeeeeeeee........ee....eeeeeee........eeeee.hhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4b47 A   2 AKVRIYQLAKELGMETQELLELLDQMGVAYKSHASTLEEKDAEAVRELVKEQRGLQEKLAEEERRKSLPRRPPVVVIMGHVDHGKTTLLDYLRKSRIAEKEAGGITQHVGAFEVKTPQGTVVFIDTPGHE------QRGAKVADIAVIVIAADDGIMPQTEEAIAHAKAAGAKLIFAINKIDLPQADPEKVKRQLMERGFVPEEYGGDAIVIPISAKTGQGVQDLLEMILLLAELEDYRADPNAEPRGVILESKLDKQAGIIANMLVQEGTFRVGDYVVAGEAYGRIRAMMDADGNQRKEAGPGSAVQVLGFQELPHAGDVVEWVPDLEAAKEIAEERKEERKAREEEEKARRP 355
                                    11        21        31        41        51        61        71        81        91       101       111       121       131      |141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351    
                                                                                                                                                           131    138
   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 4B47)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4B47)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4B47)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (IF2_THET8 | P48515)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003924    GTPase activity    Catalysis of the reaction: GTP + H2O = GDP + phosphate.
    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: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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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  4b47
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  IF2_THET8 | P48515
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 Related Entries

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

UniProtKB/Swiss-Prot
        IF2_THET8 | P48515: 3j4j 4b3x 4b43 4b44 4b48 4kjz 5lmv

(-) Related Entries Specified in the PDB File

4b3x BACTERIAL TRANSLATION INITIATION FACTOR IF2 (1-363), APO FORM
4b43 BACTERIAL TRANSLATION INITIATION FACTOR IF2 (1-363), APO FORM, DOUBLE MUTANT K86L H130A
4b44 BACTERIAL TRANSLATION INITIATION FACTOR IF2 (1-363), COMPLEX WITH GDP AT PH8.0
4b48 BACTERIAL TRANSLATION INITIATION FACTOR IF2 (1-363), COMPLEX WITH GTP