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(-) Description

Title :  INITIATION FACTOR 5A FROM ARCHEBACTERIUM PYROBACULUM AEROPHILUM
 
Authors :  T. S. Peat, J. Newman, G. S. Waldo, J. Berendzen, T. C. Terwilliger
Date :  05 Jul 98  (Deposition) - 04 Nov 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Translation Initiation Factor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. S. Peat, J. Newman, G. S. Waldo, J. Berendzen, T. C. Terwilliger
Structure Of Translation Initiation Factor 5A From Pyrobaculum Aerophilum At 1. 75 A Resolution.
Structure V. 6 1207 1998
PubMed-ID: 9753699  |  Reference-DOI: 10.1016/S0969-2126(98)00120-8
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRANSLATION INITIATION FACTOR 5A
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector: PET
    Expression System Vector Type: PET
    Mutation: YES
    Organism Scientific: PYROBACULUM AEROPHILUM
    Organism Taxid: 13773
    Other Details: MSE HAS REPLACED MET, AS SELENO-METHIONINE WAS INCORPORATED INTO THE PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 16)
No.NameCountTypeFull Name
1MSE16Mod. Amino AcidSELENOMETHIONINE

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 Sequence-Structure Mapping

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(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IF5A_HYPUSINEPS00302 Eukaryotic initiation factor 5A hypusine signature.IF5A_PYRAE40-47  1A:40-47
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IF5A_HYPUSINEPS00302 Eukaryotic initiation factor 5A hypusine signature.IF5A_PYRAE40-47  4A:40-47

(-) Exons   (0, 0)

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(-) Sequences/Alignments

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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:136
 aligned with IF5A_PYRAE | P56635 from UniProtKB/Swiss-Prot  Length:138

    Alignment length:136
                                                                                                                                                                138 
                                    13        23        33        43        53        63        73        83        93       103       113       123       133    | 
           IF5A_PYRAE     4 KWVMSTKYVEAGELKEGSYVVIDGEPCRVVEIEKSKTGKHGSAKARIVAVGVFDGGKRTLSLPVDAQVEVPIIEKFTAQILSVSGDVIQLMDMRDYKTIEVPMKYVEEEAKGRLAPGAEVEVWQILDRYKIIRVK-   -
               SCOP domains d1bkba1 A:4-74 Eukaryotic initiation translation factor 5a (eIF5a)     d1bkba2 A:75-139                                                  SCOP domains
               CATH domains 1bkbA01 A:4-74  [code=2.30.30.30, no name defined]                     1bkbA02 A:75-139 Nucleic acid-binding proteins                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeehhh.....eeee..eeeeeeeeeee........eeeeeeee.....eeeeeee...eeee...eeeeee........eee........eee......hhhhhh.....eeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------IF5A_HYP-------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bkb A   4 KWVmSTKYVEAGELKEGSYVVIDGEPCRVVEIEKSKTGKHGSAKARIVAVGVFDGGKRTLSLPVDAQVEVPIIEKFTAQILSVSGDVIQLmDmRDYKTIEVPmKYVEEEAKGRLAPGAEVEVWQILDRYKIIRVKG 139
                               |    13        23        33        43        53        63        73        83        93| |    103  |    113       123       133      
                               |                                                                                     94-MSE     106-MSE                             
                               7-MSE                                                                                   96-MSE
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 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (IF5A_PYRAE | P56635)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0043022    ribosome binding    Interacting selectively and non-covalently with any part of a ribosome.
    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:0045901    positive regulation of translational elongation    Any process that activates or increases the frequency, rate or extent of translational elongation.
    GO:0045905    positive regulation of translational termination    Any process that activates or increases the frequency, rate or extent of translational termination.
    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:0006452    translational frameshifting    A mechanism whereby different proteins may result from a single mRNA molecule, due to a change in the parsing of three nucleotides per codon relative to an initiating AUG codon.
    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.

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