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(-) Description

Title :  CRYSTAL STRUCTURE OF TRANSLATION INITIATION FACTOR AIF2BETAGAMMA HETERODIMER
 
Authors :  M. Sokabe, M. Yao, N. Sakai, S. Toya, I. Tanaka
Date :  16 Nov 05  (Deposition) - 25 Jul 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein Complex, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Sokabe, M. Yao, N. Sakai, S. Toya, I. Tanaka
Structure Of Archaeal Translational Initiation Factor 2 Betagamma-Gdp Reveals Significant Conformational Change Of The Beta-Subunit And Switch 1 Region.
Proc. Natl. Acad. Sci. Usa V. 103 13016 2006
PubMed-ID: 16924118  |  Reference-DOI: 10.1073/PNAS.0604165103

(-) Compounds

Molecule 1 - TRANSLATION INITIATION FACTOR 2 GAMMA SUBUNIT
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET26B
    Expression System Strain: BL21(DE3)-CODONPLUS-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PF1717
    Mutation: YES
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 186497
    Strain: DSM 3638
    Synonym: EIF-2-GAMMA, AIF2-GAMMA
 
Molecule 2 - TRANSLATION INITIATION FACTOR 2 BETA SUBUNIT
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET26B
    Expression System Strain: BL21(DE3)-CODONPLUS-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PF0481
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 186497
    Strain: DSM 3638
    Synonym: EIF-2-BETA, AIF2-BETA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:61 , CYS A:64 , CYS A:73 , CYS A:76BINDING SITE FOR RESIDUE ZN A 1001
2AC2SOFTWARECYS B:107 , CYS B:110 , CYS B:128 , CYS B:131BINDING SITE FOR RESIDUE ZN B 1002

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1B:110 -B:131

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2D74)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2D74)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2D74)

(-) Exons   (0, 0)

(no "Exon" information available for 2D74)

(-) 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:403
 aligned with IF2G_PYRFU | Q8U082 from UniProtKB/Swiss-Prot  Length:411

    Alignment length:407
                                                                                                                                                                                                                                                                                                                                                                                                                                               411 
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405     | 
           IF2G_PYRFU     6 KTRQAEVNIGMVGHVDHGKTTLTKALTGVWTDTHSEELRRGITIKIGFADAEIRRCSNCGRYSTSPICPYCGHETEFIRRVSFIDSPGHEALMTTMLAGASLMDGAILVIAANEPCPRPQTREHLMALQIIGQKNIIIAQNKIELVDKEKALENYRQIKEFIKGTVAENAPIIPISALHGANIDVLVKAIEEFIPTPKRDSNKPPKMLVLRSFDVNKPGTPPEKLVGGVLGGSIVQGKLKVGDEIEIRPGVPYEEHGRIKYEPITTEIVSLQAGGQFVEEAYPGGLVGIGTKLDPYLTKGDLMAGNVVGKPGKLPPVWTDLRLEVHLLERVVGTEQELNVEPIKRKEVLLLNVGTARTMGLVTALGKDEIELKLQIPVCAEPGERVAISRQIGSRWRLIGYGIIKE-   -
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2d74A01 A:6-204 P-loop containing     nucleotide triphosphate hydrolases                                                                                                                               2d74A02 A:205-319 Translation factors                                                                              2d74A03 A:320-412 Translation factors                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee....hhhhhhhhhhhhhh..----.........eeeeeeeeee.....ee...........eeeeeeeeeee..hhhhhhhhhhhh.....eeeeeee......hhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhhhhhh........eeee......hhhhhhhhhhhh............eeeeeeee...............eeeeeeee..ee...eeee...ee........ee..eeeeeeeee..ee..ee.....eeeee..hhhhhhhhh....eee.......eeeeeee..ee......hhhhhh........eeeeee..eeeeeeeeee....eeeeeeeeee.....eeeeee......eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d74 A   6 KTRQAEVNIGMVGHVDHGKTTLTKALTGVWTDT----LRRGITIKIGFADAEIRRCSNCGRYSTSPICPYCGHETEFIRRVSFIDSPGHEALMTTMLAGASLMDGAILVIAANEPCPRPQTREHLMALQIIGQKNIIIAQNKIELVDKEKALENYRQIKEFIKGTVAENAPIIPISALHGANIDVLVKAIEEFIPTPKRDSNKPPKMLVLRSFDVNKPGTPPEKLVGGVLDGSIVQGKLKVGDEIEIRPGVPYEEHGRIKYEPITTEIVSLQAGGQFVEEAYPGGLVGIGTKLDPYLTKGDLMAGNVVGKPGKLPPVWTDLRLEVHLLERVVGTEQELNVEPIKRKEVLLLNVGTARTMGLVTALGKDEIELKLQIPVCAEPGERVAISRQIGSRWRLIGYGIIKEL 412
                                    15        25        35  |    |45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       
                                                           38   43                                                                                                                                                                                                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:137
 aligned with IF2B_PYRFU | Q8U3I5 from UniProtKB/Swiss-Prot  Length:140

    Alignment length:137
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       
           IF2B_PYRFU     3 IDYYDYEKLLEKAYQELPENVKHHKSRFEVPGALVTIEGNKTIIENFKDIADALNRDPQHLLKFLLREIATAGTLEGRRVVLQGRFTPYLIANKLKKYIKEYVICPVCGSPDTKIIKRDRFHFLKCEACGAETPIQH 139
               SCOP domains d2d74b1 B:3-103 automated matches                                                                    d2d74b2 B:104-139 automated matches  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhh.....hhhhhh...........eeee..eeee.hhhhhhhhhh..hhhhhhhhhhhh...eeee..eeee....hhhhhhhhhhhhhhhhh.................................. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d74 B   3 IDYYDYEKLLEKAYQELPENVKHHKSRFEVPGALVTIEGNKTIIENFKDIADALNRDPQHLLKFLLREIATAGTLEGRRVVLQGRFTPYLIANKLKKYIKEYVICPVCGSPDTKIIKRDRFHFLKCEACGAETPIQH 139
                                    12        22        32        42        52        62        72        82        92       102       112       122       132
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Small proteins (3458)

(-) CATH Domains  (2, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2D74)

(-) Gene Ontology  (8, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (IF2G_PYRFU | Q8U082)
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:0003746    translation elongation factor activity    Functions in chain elongation during polypeptide synthesis at the ribosome.
    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:0006414    translational elongation    The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis.
    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.

Chain B   (IF2B_PYRFU | Q8U3I5)
molecular function
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        IF2B_PYRFU | Q8U3I5: 2dcu
        IF2G_PYRFU | Q8U082: 2dcu

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