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(-) Description

Title :  BACTERIAL TRANSLATION INITIATION FACTOR IF2 (1-363), APO FORM
 
Authors :  A. Simonetti, A. Urzhumtsev, B. P. Klaholz
Date :  26 Jul 12  (Deposition) - 29 May 13  (Release) - 05 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
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: PET30B
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-363
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Other Details: DSM 579
    Strain: HB8
    Synonym: TRANSLATION INITIATION FACTOR IF2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:11 , GLU A:246 , PRO A:247 , TRP A:325 , HOH A:2156 , HOH A:2159 , HOH A:2169 , HOH A:2203BINDING SITE FOR RESIDUE GOL A1364
2AC2SOFTWARETHR A:135 , GLN A:160 , LYS A:174 , LEU A:233 , GLU A:237 , HOH A:2058 , HOH A:2089BINDING SITE FOR RESIDUE GOL A1365
3AC3SOFTWAREARG A:72 , VAL A:143 , ASP A:145 , LEU A:267 , GLN A:269 , HOH A:2050 , HOH A:2167 , HOH A:2204BINDING SITE FOR RESIDUE GOL A1366

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4B3X)

(-) Cis Peptide Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1Ala A:2 -Lys A:3
2Glu A:102 -Gly A:103
3Gly A:103 -Gly A:104
4Gly A:104 -Gly A:105
5Gly A:105 -Ile A:106
6Thr A:135 -Ile A:136
7Arg A:139 -Gly A:140
8Arg A:353 -Arg A:354
9Leu A:362 -Arg A:363

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4B3X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4B3X)

(-) Exons   (0, 0)

(no "Exon" information available for 4B3X)

(-) 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:363
 aligned with IF2_THET8 | P48515 from UniProtKB/Swiss-Prot  Length:571

    Alignment length:363
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360   
            IF2_THET8     1 MAKVRIYQLAKELGMETQELLELLDQMGVAYKSHASTLEEKDAEAVRELVKEQRGLQEKLAEEERRKSLPRRPPVVVIMGHVDHGKTTLLDYLRKSRIAEKEAGGITQHVGAFEVKTPQGTVVFIDTPGHEAFTTIRQRGAKVADIAVIVIAADDGIMPQTEEAIAHAKAAGAKLIFAINKIDLPQADPEKVKRQLMERGFVPEEYGGDAIVIPISAKTGQGVQDLLEMILLLAELEDYRADPNAEPRGVILESKLDKQAGIIANMLVQEGTFRVGDYVVAGEAYGRIRAMMDADGNQRKEAGPGSAVQVLGFQELPHAGDVVEWVPDLEAAKEIAEERKEERKAREEEEKARRPRTMAELLR 363
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eehhhhhhhhh.hhhhhhhhhhhhh........eehhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeee....hhhhhhhhhhhhhhh............eeeeee..eeeeee....................eeeeeee.....hhhhhhhhhhhhhh..eeeeeee.......hhhhhhhhhhhh....hhhh...eeee.......hhhhhhhhhhhhhhhhh.........eeeeeeeeee...eeeeeeeeee..ee...eeee..eeeeeeeee........ee....eeeeeee........eeeee.hhhhhhhhhhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b3x A   1 MAKVRIYQLAKELGMETQELLELLDQMGVAYKSHASTLEEKDAEAVRELVKEQRGLQEKLAEEERRKSLPRRPPVVVIMGHVDHGKTTLLDYLRKSRIAEKEGGGITQHVGAFEVKTPQGTVVFIDTPGHEAFTTIRQRGAKVADIAVIVIAADDGIMPQTEEAIAHAKAAGAKLIFAINKIDLPQADPEKVKRQLMERGFVPEEYGGDAIVIPISAKTGQGVQDLLEMILLLAELEDYRADPNAEPRGVILESKLDKQAGIIANMLVQEGTFRVGDYVVAGEAYGRIRAMMDADGNQRKEAGPGSAVQVLGFQELPHAGDVVEWVPDLEAAKEIAEERKEERKAREEEEKARRPRTMAELLR 363
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360
   Legend:   → Mismatch (orange background)
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  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 4B3X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4B3X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4B3X)

(-) 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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 Related Entries

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

UniProtKB/Swiss-Prot
        IF2_THET8 | P48515: 3j4j 4b43 4b44 4b47 4b48 4kjz 5lmv

(-) Related Entries Specified in the PDB File

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
4b47 BACTERIAL TRANSLATION INITIATION FACTOR IF2 (1-363), COMPLEX WITH GDP AT PH6.5
4b48 BACTERIAL TRANSLATION INITIATION FACTOR IF2 (1-363), COMPLEX WITH GTP