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(-) Description

Title :  X-RAY STRUCTURE OF TRANSLATION INITIATION FACTOR IF2/EIF5B
 
Authors :  A. Roll-Mecak, C. Cao, T. E. Dever, S. K. Burley
Date :  14 Nov 00  (Deposition) - 06 Dec 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Translational Gtpase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Roll-Mecak, C. Cao, T. E. Dever, S. K. Burley
X-Ray Structures Of The Universal Translation Initiation Factor If2/Eif5B: Conformational Changes On Gdp And Gtp Binding.
Cell(Cambridge, Mass. ) V. 103 781 2000
PubMed-ID: 11114334  |  Reference-DOI: 10.1016/S0092-8674(00)00181-1
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRANSLATION INITIATION FACTOR IF2/EIF5B
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: FULL LENGTH
    Organism Scientific: METHANOTHERMOBACTER THERMAUTOTROPHICUS
    Organism Taxid: 145262

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 17)

Asymmetric/Biological Unit (1, 17)
No.NameCountTypeFull Name
1MSE17Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1G7R)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1G7R)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1G7R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1G7R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1G7R)

(-) Exons   (0, 0)

(no "Exon" information available for 1G7R)

(-) 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:559
 aligned with IF2P_METTH | O26359 from UniProtKB/Swiss-Prot  Length:594

    Alignment length:585
                                    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       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580     
           IF2P_METTH     1 MKIRSPIVSVLGHVDHGKTTLLDHIRGSAVASREAGGITQHIGATEIPMDVIEGICGDFLKKFSIRETLPGLFFIDTPGHEAFTTLRKRGGALADLAILIVDINEGFKPQTQEALNILRMYRTPFVVAANKIDRIHGWRVHEGRPFMETFSKQDIQVQQKLDTKVYELVGKLHEEGFESERFDRVTDFASQVSIIPISAITGEGIPELLTMLMGLAQQYLREQLKIEEDSPARGTILEVKEETGLGMTIDAVIYDGILRKDDTIAMMTSKDVISTRIRSLLKPRPLEEMRESRKKFQKVDEVVAAAGIKIVAPGIDDVMAGSPLRVVTDPEKVREEILSEIEDIKIDTDEAGVVVKADTLGSLEAVVKILRDMYVPIKVADIGDVSRRDVVNAGIALQEDRVYGAIIAFNVKVIPSAAQELKNSDIKLFQGNVIYRLMEEYEEWVRGIEEEKKKKWMEAIIKPASIRLIPKLVFRQSKPAIGGVEVLTGVIRQGYPLMNDDGETVGTVESMQDKGENLKSASRGQKVAMAIKDAVYGKTIHEGDTLYVDIPENHYHILKEQLSGDLTDEELDLMDKIAEIKRKKN 585
               SCOP domains d1g7ra4 A:1-      227 Initiation        factor IF2/eIF5b, N-terminal (G) domain                                                                                                                                                    d1g7ra1 A:228-328 Initiation factor IF2/eIF5b, domains 2 an        d 4                               d1g7ra3 A:329-459 Initiation factor IF2/eIF5b, domain 3                                                                            d1g7ra2 A:460-585 Initiation factor IF2/eIF5b, domains 2 and 4                                                                 SCOP domains
               CATH domains -1g7rA01 A:2      -225 P-loop co       ntaining nucleotide triphosphate hydrola  ses                                                                                                                                             1g7rA02 A:226-337 Translation factors                                                                           -------------1g7rA03 A:351-431  [code=3.40.50.10050, no name defined]                         ------------------------------1g7rA04 A:462-550 Translation factors                                                    ------------   -------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...eeeee.------hhhhhhhhhhhhh.-------....eeeeehhhhhhhh..hhhhhhhhhh..eeeee....--.....ee..ee...eeeeeee.....hhhhhhhhhhhhhh...eeeeeehhhhh.........hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..eeee.hhh.....eeeeee.......hhhhhhhhhhhhhhhhhhhh.ee......eeeeeeeeee..eeeeeeeeeee.eee...eeeee....eeeee..eeeee...--------.eeee.eee..eeeeee...........eeee..hhhhhhhhhhhhhhhhhh.......eeee.hhhhhhhhhhhhhhh.....eeee...hhhhhhhhhhhhh......eeeee....hhhhhhh......eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeeeeee....eeeeeeeeee.ee...eee.....eeeeeeeeee..eee.ee.....eeeeee............eeee..hhhhhhh.....---.hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1g7r A   1 mKIRSPIVSVLG------TTLLDHIRGSAVAS-------QHIGATEIPmDVIEGICGDFLKKFSIRETLPGLFFIDTPG--AFTTLRKRGGALADLAILIVDINEGFKPQTQEALNILRmYRTPFVVAANKIDRIHGWRVHEGRPFmETFSKQDIQVQQKLDTKVYELVGKLHEEGFESERFDRVTDFASQVSIIPISAITGEGIPELLTmLmGLAQQYLREQLKIEEDSPARGTILEVKEETGLGmTIDAVIYDGILRKDDTIAmmTSKDVISTRIRSLLKPRPL--------KFQKVDEVVAAAGIKIVAPGIDDVmAGSPLRVVTDPEKVREEILSEIEDIKIDTDEAGVVVKADTLGSLEAVVKILRDmYVPIKVADIGDVSRRDVVNAGIALQEDRVYGAIIAFNVKVIPSAAQELKNSDIKLFQGNVIYRLmEEYEEWVRGIEEEKKKKWmEAIIKPASIRLIPKLVFRQSKPAIGGVEVLTGVIRQGYPLmNDDGETVGTVESmQDKGENLKSASRGQKVAmAIKDAVYGKTIHEGDTLYVDIPENHYHILKEQL---LTDEELDLmDKIAEIKRKKN 585
                            |       10 |      20        30 |      40        50        60        70        |- |      90       100       110       120       130       140      |150       160       170       180       190       200       210| |    220       230       240      |250       260     ||270       280     |   -    |  300       310       320       330       340       350       360       370  |    380       390       400       410       420       430       440       450      |460       470       480       490       500       510|      520       530       540       550       560 |   | 570   |   580     
                            |         12     19           32      40       49-MSE                        79 82                                   120-MSE                    147-MSE                                                         211-MSE                             247-MSE            266-MSE             286      295                     319-MSE                                               373-MSE                                                          438-MSE            457-MSE                                  498-MSE      511-MSE           529-MSE                          562 566     574-MSE       
                            1-MSE                                                                                                                                                                                                             213-MSE                                               267-MSE
   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  (3, 4)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1G7R)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (IF2P_METTH | O26359)
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: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
        IF2P_METTH | O26359: 1g7s 1g7t 4v8z

(-) Related Entries Specified in the PDB File

1g7s 1g7t