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(-) Description

Title :  ARCHEAL RELEASE FACTOR ARF1
 
Authors :  J. L. Karlsen, M. Kjeldgaard
Date :  16 Jan 12  (Deposition) - 20 Mar 13  (Release) - 20 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. L. Karlsen, M. Kjeldgaard
Archeal Release Factor Arf1 Contains A Metal Binding Domain
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PEPTIDE CHAIN RELEASE FACTOR SUBUNIT 1
    Chains: A
    EC Number: 3.6.5.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Variant: CODONPLUS RIL
    Expression System Vector: PET19B
    Expression System Vector Type: PLASMID
    Organism Scientific: HALOBACTERIUM SALINARUM
    Organism Taxid: 478009
    Strain: R1
    Synonym: TRANSLATION TERMINATION FACTOR ARF1, RELEASE FACTOR 1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1ZN1Ligand/IonZINC ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:335 , ASN A:337 , HIS A:339 , CYS A:356 , CYS A:359BINDING SITE FOR RESIDUE ZN A 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4AF1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4AF1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4AF1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4AF1)

(-) Exons   (0, 0)

(no "Exon" information available for 4AF1)

(-) 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:410
 aligned with RF1_HALS3 | B0R748 from UniProtKB/Swiss-Prot  Length:416

    Alignment length:410
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416
            RF1_HALS3     7 VPSEDRRKYEFRKVIEELKDYEGSGTQLVTIYIPPDKQISDVVAHVTQEHSEASNIKSKQTRTNVQDALTSIKDRLRYYDTFPPDNGMVVFSGAVDSGGGRTDMVTEVLESPPQPIESFRYHCDSAFLTEPLAEMLGDKGLYGLIVLDRRESNVGWLKGKRVQPVKSAESLVPGKQRKGGQSAQRFARLRLEAIDNFYQEVAGMADDLFVPKRHEIDGILVGGPSPTKDEFLDGDYLHHELQDKVLGKFDVSYTDESGLSDLVDAGQAALAEADLMDDKSDMEEFFEELNGGKLATYGFEQTRRNLIMGSVDRLLVSEDLREDVVIYECPNDHEEYETIDRRNTSPEHTCSDCGEEATEVDREDAIDHLMSIADQRGTETHFISTDFEKGEQLLTAFGGYAGILRYSTGV 416
               SCOP domains d4af1a1 A:7-144 automated matches                                                                                                         d4af1a2 A:145-277 automated matches                                                                                                  d4af1a3 A:278-416 automated matches                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh.......eeeeee....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh........eeeeeeeee.....eeeeeeeee.........eeeee................eeeeeee...eeeeeeee..eeeeeeeee................hhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeehhhhhhhhhhh...hhhhhh.eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeehhhhhhhhhhh..eeeeeee....eeeeeee.......eeeee.................eeeeeeehhhhhhhhhhhh..eeeee...hhhhhhhhhh...eeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4af1 A   7 VPSEDRRKYEFRKVIEELKDYEGSGTQLVTIYIPPDKQISDVVAHVTQEHSEASNIKSKQTRTNVQDALTSIKDRLRYYDTFPPDNGMVVFSGAVDSGGGRTDMVTEVLESPPQPIESFRYHCDSAFLTEPLAEMLGDKGLYGLIVLDRRESNVGWLKGKRVQPVKSAESLVPGKQRKGGQSAQRFARLRLEAIDNFYQEVAGMADDLFVPKRHEIDGILVGGPSPTKDEFLDGDYLHHELQDKVLGKFDVSYTDESGLSDLVDAGQAALAEADLMDDKSDMEEFFEELNGGKLATYGFEQTRRNLIMGSVDRLLVSEDLREDVVIYECPNDHEEYETIDRRNTSPEHTCSDCGEEATEVDREDAIDHLMSIADQRGTETHFISTDFEKGEQLLTAFGGYAGILRYSTGV 416
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416


Chain A from PDB  Type:PROTEIN  Length:410
 aligned with RF1_HALSA | Q9HNF0 from UniProtKB/Swiss-Prot  Length:416

    Alignment length:410
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416
            RF1_HALSA     7 VPSEDRRKYEFRKVIEELKDYEGSGTQLVTIYIPPDKQISDVVAHVTQEHSEASNIKSKQTRTNVQDALTSIKDRLRYYDTFPPDNGMVVFSGAVDSGGGRTDMVTEVLESPPQPIESFRYHCDSAFLTEPLAEMLGDKGLYGLIVLDRRESNVGWLKGKRVQPVKSAESLVPGKQRKGGQSAQRFARLRLEAIDNFYQEVAGMADDLFVPKRHEIDGILVGGPSPTKDEFLDGDYLHHELQDKVLGKFDVSYTDESGLSDLVDAGQAALAEADLMDDKSDMEEFFEELNGGKLATYGFEQTRRNLIMGSVDRLLVSEDLREDVVIYECPNDHEEYETIDRRNTSPEHTCSDCGEEATEVDREDAIDHLMSIADQRGTETHFISTDFEKGEQLLTAFGGYAGILRYSTGV 416
               SCOP domains d4af1a1 A:7-144 automated matches                                                                                                         d4af1a2 A:145-277 automated matches                                                                                                  d4af1a3 A:278-416 automated matches                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh.......eeeeee....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh........eeeeeeeee.....eeeeeeeee.........eeeee................eeeeeee...eeeeeeee..eeeeeeeee................hhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeehhhhhhhhhhh...hhhhhh.eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeehhhhhhhhhhh..eeeeeee....eeeeeee.......eeeee.................eeeeeeehhhhhhhhhhhh..eeeee...hhhhhhhhhh...eeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4af1 A   7 VPSEDRRKYEFRKVIEELKDYEGSGTQLVTIYIPPDKQISDVVAHVTQEHSEASNIKSKQTRTNVQDALTSIKDRLRYYDTFPPDNGMVVFSGAVDSGGGRTDMVTEVLESPPQPIESFRYHCDSAFLTEPLAEMLGDKGLYGLIVLDRRESNVGWLKGKRVQPVKSAESLVPGKQRKGGQSAQRFARLRLEAIDNFYQEVAGMADDLFVPKRHEIDGILVGGPSPTKDEFLDGDYLHHELQDKVLGKFDVSYTDESGLSDLVDAGQAALAEADLMDDKSDMEEFFEELNGGKLATYGFEQTRRNLIMGSVDRLLVSEDLREDVVIYECPNDHEEYETIDRRNTSPEHTCSDCGEEATEVDREDAIDHLMSIADQRGTETHFISTDFEKGEQLLTAFGGYAGILRYSTGV 416
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416
   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, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4AF1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4AF1)

(-) Gene Ontology  (4, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RF1_HALS3 | B0R748)
molecular function
    GO:0016149    translation release factor activity, codon specific    A translation release factor that is specific for one or more particular termination codons; acts at the ribosomal A-site and require polypeptidyl-tRNA at the P-site.
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:0006415    translational termination    The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code).
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain A   (RF1_HALSA | Q9HNF0)
molecular function
    GO:0016149    translation release factor activity, codon specific    A translation release factor that is specific for one or more particular termination codons; acts at the ribosomal A-site and require polypeptidyl-tRNA at the P-site.
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:0006415    translational termination    The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code).
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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 Related Entries

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