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(-) Description

Title :  BACTERIAL TRANSLATION INITIATION FACTOR IF2 (1-363), APO FORM, DOUBLE MUTANT K86L H130A
 
Authors :  A. Simonetti, A. Urzhumtsev, B. P. Klaholz
Date :  27 Jul 12  (Deposition) - 18 Sep 13  (Release) - 18 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.94
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Keywords :  Translation, Initiation, Gtp Hydrolysis Mechanism (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Simonetti, S. Marzi, A. Fabbretti, A. G. Myasnikov, I. Hazemann, L. Jenner, A. Urzhumtsev, C. O. Gualerzi, B. P. Klaholz
Molecular Basis Of Gtp Hydrolysis By Bacterial Translation Initiation Factor If2
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TRANSLATION INITIATION FACTOR IF-2
    Atcc: 27634
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-30B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-363
    Mutation: YES
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Other Details: DSM 579
    Strain: HB8
    Synonym: TRANSLATION INITIATION FACTOR IF2

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric Unit (3, 12)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2IOD7Ligand/IonIODIDE ION
3MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (2, 11)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2IOD7Ligand/IonIODIDE ION
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:282 , VAL A:322 , GLU A:324 , ARG A:339 , HOH A:2252BINDING SITE FOR RESIDUE MG A1361
02AC2SOFTWARELYS A:11 , GLU A:246 , PRO A:247 , TRP A:325 , HOH A:2188 , HOH A:2203 , HOH A:2253BINDING SITE FOR RESIDUE GOL A1362
03AC3SOFTWARETYR A:7 , HIS A:34 , TRP A:325 , PRO A:327 , HOH A:2009 , HOH A:2020 , HOH A:2022 , HOH A:2253 , HOH A:2254BINDING SITE FOR RESIDUE GOL A1363
04AC4SOFTWAREGLU A:39 , GLU A:114 , LYS A:116 , ASP A:293 , ASP A:295 , HOH A:2104 , HOH A:2113 , HOH A:2223BINDING SITE FOR RESIDUE GOL A1364
05AC5SOFTWAREARG A:72 , LYS A:142 , VAL A:143 , ASP A:145 , GLN A:269 , HOH A:2086 , HOH A:2127BINDING SITE FOR RESIDUE GOL A1365
06AC6SOFTWAREHOH A:2143BINDING SITE FOR RESIDUE IOD A1366
07AC7SOFTWAREASP A:183BINDING SITE FOR RESIDUE IOD A1367
08AC8SOFTWARELYS A:193 , HOH A:2162BINDING SITE FOR RESIDUE IOD A1368
09AC9SOFTWAREHOH A:2134 , HOH A:2136BINDING SITE FOR RESIDUE IOD A1369
10BC1SOFTWAREPRO A:73 , HOH A:2120BINDING SITE FOR RESIDUE IOD A1370
11BC2SOFTWARELYS A:255 , ASN A:265BINDING SITE FOR RESIDUE IOD A1371
12BC3SOFTWAREHOH A:2058 , HOH A:2142 , HOH A:2161BINDING SITE FOR RESIDUE IOD A1372

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4B43)

(-) Cis Peptide Bonds  (7, 7)

Asymmetric Unit
No.Residues
1Ala A:2 -Lys A:3
2Glu A:102 -Ala A:103
3Ala A:103 -Gly A:104
4Gly A:104 -Gly A:105
5Gly A:105 -Ile A:106
6Ala A:130 -Glu A:131
7Arg A:353 -Arg A:354

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4B43)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4B43)

(-) Exons   (0, 0)

(no "Exon" information available for 4B43)

(-) 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:346
 aligned with IF2_THET8 | P48515 from UniProtKB/Swiss-Prot  Length:571

    Alignment length:355
                                    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     
            IF2_THET8     1 MAKVRIYQLAKELGMETQELLELLDQMGVAYKSHASTLEEKDAEAVRELVKEQRGLQEKLAEEERRKSLPRRPPVVVIMGHVDHGKTTLLDYLRKSRIAEKEAGGITQHVGAFEVKTPQGTVVFIDTPGHEAFTTIRQRGAKVADIAVIVIAADDGIMPQTEEAIAHAKAAGAKLIFAINKIDLPQADPEKVKRQLMERGFVPEEYGGDAIVIPISAKTGQGVQDLLEMILLLAELEDYRADPNAEPRGVILESKLDKQAGIIANMLVQEGTFRVGDYVVAGEAYGRIRAMMDADGNQRKEAGPGSAVQVLGFQELPHAGDVVEWVPDLEAAKEIAEERKEERKAREEEEKARRP 355
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eehhhhhhhhh.hhhhhhhhhhhhh........eehhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeee.hhhhhhhhhhhhhhh...............eeeeee..eeeeee......---------.....eeeeeee.....hhhhhhhhhhhhhh..eeeeeee.......hhhhhhhhhhhh....hhhh....eee.......hhhhhhhhhhhhhhhhh.........eeeeeeeeee...eeeeeeeeee..ee...eeee..eeeeeeeee........ee....eeeeeee........eeeee.hhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b43 A   1 MAKVRIYQLAKELGMETQELLELLDQMGVAYKSHASTLEEKDAEAVRELVKEQRGLQEKLAEEERRKSLPRRPPVVVIMGHVDHGLTTLLDYLRKSRIAEKEAGGITQHVGAFEVKTPQGTVVFIDTPGAE---------AKVADIAVIVIAADDGIMPQTEEAIAHAKAAGAKLIFAINKIDLPQADPEKVKRQLMERGFVPEEYGGDAIVIPISAKTGQGVQDLLEMILLLAELEDYRADPNAEPRGVILESKLDKQAGIIANMLVQEGTFRVGDYVVAGEAYGRIRAMMDADGNQRKEAGPGSAVQVLGFQELPHAGDVVEWVPDLEAAKEIAEERKEERKAREEEEKARRP 355
                                    10        20        30        40        50        60        70        80        90       100       110       120       130|        -|      150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350     
                                                                                                                                                            131       141
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 4B43)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4B43)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4B43)

(-) Gene Ontology  (8, 8)

Asymmetric 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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  Cis Peptide Bonds
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    Arg A:353 - Arg A:354   [ RasMol ]  
    Glu A:102 - Ala A:103   [ RasMol ]  
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  4b43
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 Related Entries

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

UniProtKB/Swiss-Prot
        IF2_THET8 | P48515: 3j4j 4b3x 4b44 4b47 4b48 4kjz 5lmv

(-) Related Entries Specified in the PDB File

4b3x BACTERIAL TRANSLATION INITIATION FACTOR IF2 (1-363), APO FORM
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