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(-) Description

Title :  CRYSTAL STRUCTURE OF TRANSLATION INITIATION FACTOR 5A FROM PYROCOCCUS HORIKOSHII
 
Authors :  M. Yao, A. Ohsawa, S. Kikukawa, I. Tanaka, M. Kimura
Date :  25 Sep 02  (Deposition) - 28 Jan 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Sh3-Like Barrel, Ob Fold, Biosynthetic Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Yao, A. Ohsawa, S. Kikukawa, I. Tanaka, M. Kimura
Crystal Structure Of Hyperthermophilic Archaeal Initiation Factor 5A: A Homologue Of Eukaryotic Initiation Factor 5A (Eif-5A)
J. Biochem. (Tokyo) V. 133 75 2003
PubMed-ID: 12761201  |  Reference-DOI: 10.1093/JB/MVG011

(-) Compounds

Molecule 1 - INITIATION FACTOR 5A
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-22B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PH1381
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 70601
    Strain: OT3
    Synonym: TRANSLATION INITIATION FACTOR 5A, HYPUSINE-CONTAINING PROTEIN

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1IZ6)

(-) Sites  (0, 0)

(no "Site" information available for 1IZ6)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1IZ6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1IZ6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1IZ6)

(-) PROSITE Motifs  (1, 3)

Asymmetric Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IF5A_HYPUSINEPS00302 Eukaryotic initiation factor 5A hypusine signature.IF5A_PYRHO35-42
 
 		  3A:35-42
B:35-42
C:35-42
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IF5A_HYPUSINEPS00302 Eukaryotic initiation factor 5A hypusine signature.IF5A_PYRHO35-42
 
 		  1A:35-42
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IF5A_HYPUSINEPS00302 Eukaryotic initiation factor 5A hypusine signature.IF5A_PYRHO35-42
 
 		  1-
B:35-42
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IF5A_HYPUSINEPS00302 Eukaryotic initiation factor 5A hypusine signature.IF5A_PYRHO35-42
 
 		  1-
-
C:35-42

(-) Exons   (0, 0)

(no "Exon" information available for 1IZ6)

(-) 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:136
 aligned with IF5A_PYRHO | O50089 from UniProtKB/Swiss-Prot  Length:138

    Alignment length:136
                                    11        21        31        41        51        61        71        81        91       101       111       121       131      
           IF5A_PYRHO     2 GDKTKVQVSKLKPGRYIIIDDEPCRIVNITVSSPGKHGSAKARIEAVGIFDGKVRSIVKPTSAEVDVPIIDKKTAQVIAITPDTVQIMDMETYETFEVPIDTGVADEIRDQLKEGINVEYWETLGRIKIMRIKGEG 137
               SCOP domains d1iz6a1 A:2-70 Eukaryotic initiation translation factor 5a (eIF5a)   d1iz6a2 A:71-137                                                    SCOP domains
               CATH domains 1iz6A01 A:2-70  [code=2.30.30.30, no name defined]                   1iz6A02 A:71-134 Nucleic acid-binding proteins                  --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.hhh....eeee..eeeeeeeeee.........eeeeeeee.....eeeeeee...eeeee..eeeeeeeeee...eeeee......eeeeehhhhhhhhhh.......eeeeeee..eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------IF5A_HYP----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iz6 A   2 GDKTKVQVSKLKPGRYIIIDDEPCRIVNITVSSPGKHGSAKARIEAVGIFDGKVRSIVKPTSAEVDVPIIDKKTAQVIAITPDTVQIMDMETYETFEVPIDTGVADEIRDQLKEGINVEYWETLGRIKIMRIKGEG 137
                                    11        21        31        41        51        61        71        81        91       101       111       121       131      


Chain B from PDB  Type:PROTEIN  Length:136
 aligned with IF5A_PYRHO | O50089 from UniProtKB/Swiss-Prot  Length:138

    Alignment length:136
                                    11        21        31        41        51        61        71        81        91       101       111       121       131      
           IF5A_PYRHO     2 GDKTKVQVSKLKPGRYIIIDDEPCRIVNITVSSPGKHGSAKARIEAVGIFDGKVRSIVKPTSAEVDVPIIDKKTAQVIAITPDTVQIMDMETYETFEVPIDTGVADEIRDQLKEGINVEYWETLGRIKIMRIKGEG 137
               SCOP domains d1iz6b1 B:2-70 Eukaryotic initiation translation factor 5a (eIF5a)   d1iz6b2 B:71-137                                                    SCOP domains
               CATH domains 1iz6B01 B:2-70  [code=2.30.30.30, no name defined]                   1iz6B02 B:71-134 Nucleic acid-binding proteins                  --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.hhh....eeee..eeeeeeeeeee........eeeeeeee.....eeeeeee...eeeee..eeeeeeeeee...eeeeee.....eeeee.....hhhhhh......eeeeeee..eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------IF5A_HYP----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iz6 B   2 GDKTKVQVSKLKPGRYIIIDDEPCRIVNITVSSPGKHGSAKARIEAVGIFDGKVRSIVKPTSAEVDVPIIDKKTAQVIAITPDTVQIMDMETYETFEVPIDTGVADEIRDQLKEGINVEYWETLGRIKIMRIKGEG 137
                                    11        21        31        41        51        61        71        81        91       101       111       121       131      


Chain C from PDB  Type:PROTEIN  Length:135
 aligned with IF5A_PYRHO | O50089 from UniProtKB/Swiss-Prot  Length:138

    Alignment length:135
                                    11        21        31        41        51        61        71        81        91       101       111       121       131     
           IF5A_PYRHO     2 GDKTKVQVSKLKPGRYIIIDDEPCRIVNITVSSPGKHGSAKARIEAVGIFDGKVRSIVKPTSAEVDVPIIDKKTAQVIAITPDTVQIMDMETYETFEVPIDTGVADEIRDQLKEGINVEYWETLGRIKIMRIKGE 136
               SCOP domains d1iz6c1 C:2-70 Eukaryotic initiation translation factor 5a (eIF5a)   d1iz6c2 C:71-136                                                   SCOP domains
               CATH domains 1iz6C01 C:2-70  [code=2.30.30.30, no name defined]                   1iz6C02 C:71-134 Nucleic acid-binding proteins                  -- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.hhh....eeee..eeeeeeeeeee........eeeeeeee.....eeeeeee...eeeee..eeeeeeeeee...eeeeee.....eeeee.....hhhhhh......eeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------IF5A_HYP---------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iz6 C   2 GDKTKVQVSKLKPGRYIIIDDEPCRIVNITVSSPGKHGSAKARIEAVGIFDGKVRSIVKPTSAEVDVPIIDKKTAQVIAITPDTVQIMDMETYETFEVPIDTGVADEIRDQLKEGINVEYWETLGRIKIMRIKGE 136
                                    11        21        31        41        51        61        71        81        91       101       111       121       131
   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, 6)

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

(-) CATH Domains  (2, 6)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1IZ6)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (IF5A_PYRHO | O50089)
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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