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(-) Description

Title :  CRYSTAL STRUCTURE OF RIBOSOME RECYCLING FACTOR FROM MYCOBACTERIUM TUBERCULOSIS
 
Authors :  K. Saikrishnan, S. K. Kalapala, U. Varshney, M. Vijayan
Date :  28 Sep 04  (Deposition) - 22 Feb 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym./Biol. Unit :  A
Keywords :  Translation Factor, Triple-Helix Bundle, Protein Synthesis, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Saikrishnan, S. K. Kalapala, U. Varshney, M. Vijayan
X-Ray Structural Studies Of Mycobacterium Tuberculosis Rrf And A Comparative Study Of Rrfs Of Known Structure. Molecular Plasticity And Biological Implications
J. Mol. Biol. V. 345 29 2005
PubMed-ID: 15567408  |  Reference-DOI: 10.1016/J.JMB.2004.10.034
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBOSOME RECYCLING FACTOR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET11
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Synonym: RIBOSOME RELEASING FACTOR, RRF

 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
1CD1Ligand/IonCADMIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:10 , GLU A:14 , HOH A:257BINDING SITE FOR RESIDUE CD A 186

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1WQF)

(-) 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:183
 aligned with RRF_MYCTO | P9WGY0 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:183
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181   
            RRF_MYCTO     2 IDEALFDAEEKMEKAVAVARDDLSTIRTGRANPGMFSRITIDYYGAATPITQLASINVPEARLVVIKPYEANQLRAIETAIRNSDLGVNPTNDGALIRVAVPQLTEERRRELVKQAKHKGEEAKVSVRNIRRKAMEELHRIRKEGEAGEDEVGRAEKDLDKTTHQYVTQIDELVKHKEGELLE 184
               SCOP domains d1wqfa1 A:2-184 Ribosome recycling factor, RRF                                                                                                                                          SCOP domains
               CATH domains 1wqfA01 A:2-30,A:106-184     1wqfA02 A:31-105  [code=3.30.1360.40, no name defined]                     1wqfA01 A:2-30,A:106-184  [code=1.10.132.20, no name defined]                   CATH domains
               Pfam domains -----------------RRF-1wqfA01 A:19-183                                                                                                                                                 - Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhh.eeee..eeee....eeee.....eeeeee....hhhhhhhhhhhh....eeee....eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wqf A   2 IDEALFDAEEKMEKAVAVARDDLSTIRTGRANPGMFSRITIDYYGAATPITQLASINVPEARLVVIKPYEANQLRAIETAIRNSDLGVNPTNDGALIRVAVPQLTEERRRELVKQAKHKGEEAKVSVRNIRRKAMEELHRIRKEGEAGEDEVGRAEKDLDKTTHQYVTQIDELVKHKEGELLE 184
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181   


Chain A from PDB  Type:PROTEIN  Length:183
 aligned with RRF_MYCTU | P9WGY1 from UniProtKB/Swiss-Prot  Length:185

    Alignment length:183
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181   
            RRF_MYCTU     2 IDEALFDAEEKMEKAVAVARDDLSTIRTGRANPGMFSRITIDYYGAATPITQLASINVPEARLVVIKPYEANQLRAIETAIRNSDLGVNPTNDGALIRVAVPQLTEERRRELVKQAKHKGEEAKVSVRNIRRKAMEELHRIRKEGEAGEDEVGRAEKDLDKTTHQYVTQIDELVKHKEGELLE 184
               SCOP domains d1wqfa1 A:2-184 Ribosome recycling factor, RRF                                                                                                                                          SCOP domains
               CATH domains 1wqfA01 A:2-30,A:106-184     1wqfA02 A:31-105  [code=3.30.1360.40, no name defined]                     1wqfA01 A:2-30,A:106-184  [code=1.10.132.20, no name defined]                   CATH domains
               Pfam domains -----------------RRF-1wqfA01 A:19-183                                                                                                                                                 - Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhh.eeee..eeee....eeee.....eeeeee....hhhhhhhhhhhh....eeee....eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wqf A   2 IDEALFDAEEKMEKAVAVARDDLSTIRTGRANPGMFSRITIDYYGAATPITQLASINVPEARLVVIKPYEANQLRAIETAIRNSDLGVNPTNDGALIRVAVPQLTEERRRELVKQAKHKGEEAKVSVRNIRRKAMEELHRIRKEGEAGEDEVGRAEKDLDKTTHQYVTQIDELVKHKEGELLE 184
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181
   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  (1, 1)

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

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: RRF] (3)

(-) Gene Ontology  (10, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RRF_MYCTO | P9WGY0)
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   (RRF_MYCTU | P9WGY1)
molecular function
    GO:0043023    ribosomal large subunit binding    Interacting selectively and non-covalently with any part of the larger ribosomal subunit.
    GO:0008079    translation termination factor activity    Functions in the termination of translation.
biological process
    GO:0002184    cytoplasmic translational termination    The process resulting in the release of a polypeptide chain from the ribosome in the cytoplasm, usually in response to a termination codon.
    GO:0040007    growth    The increase in size or mass of an entire organism, a part of an organism or a cell.
    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:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RRF_MYCTO | P9WGY0: 1wqg 1wqh 4kaw 4kb2 4kb4 4kc6 4kdd
        RRF_MYCTU | P9WGY1: 1wqg 1wqh 4kaw 4kb2 4kb4 4kc6 4kdd

(-) Related Entries Specified in the PDB File

1wqg THE SAME PROTEIN AT 2.15 ANGSTROM
1wqh THE SAME PROTEIN AT 2.90 ANGSTROM