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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CARBOXY-TERMINAL RIBONUCLEASE DOMAIN OF COLICIN E5
 
Authors :  S. Yajima, S. Inoue, T. Ogawa, T. Nonaka, K. Ohsawa, H. Masaki
Date :  03 Apr 06  (Deposition) - 23 Jan 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha/Beta Protein, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Yajima, S. Inoue, T. Ogawa, T. Nonaka, K. Ohsawa, H. Masaki
Structural Basis For Sequence-Dependent Recognition Of Colicin E5 Trnase By Mimicking The Mrna-Trna Interaction
Nucleic Acids Res. V. 34 6074 2006
PubMed-ID: 17099236  |  Reference-DOI: 10.1093/NAR/GKL729
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COLICIN-E5
    Chains: A
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBR328
    Expression System Strain: RR1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL RIBONUCLEASE DOMAIN, RESIDUES 2-116
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: FRAGMENT

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
13PD1Ligand/Ion2-AMINO-9-(2-DEOXY-3-O-PHOSPHONOPENTOFURANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE
2UM31Ligand/Ion2'-DEOXYURIDINE 3'-MONOPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:25 , GLN A:29 , ARG A:33 , PHE A:53 , LYS A:55 , GLN A:93 , TRP A:102 , VAL A:103 , SER A:106 , ARG A:107 , GLN A:109 , UM3 A:118 , HOH A:122 , HOH A:167BINDING SITE FOR RESIDUE 3PD A 117
2AC2SOFTWARESER A:52 , PHE A:53 , ASP A:54 , LYS A:55 , ARG A:56 , SER A:57 , LYS A:60 , VAL A:83 , THR A:92 , GLN A:93 , ASP A:105 , ARG A:107 , GLN A:109 , 3PD A:117 , HOH A:165 , HOH A:177BINDING SITE FOR RESIDUE UM3 A 118

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DJH)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro A:62 -Pro A:63

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DJH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2DJH)

(-) Exons   (0, 0)

(no "Exon" information available for 2DJH)

(-) 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:96
 aligned with CEA5_ECOLX | P18000 from UniProtKB/Swiss-Prot  Length:180

    Alignment length:96
                                    89        99       109       119       129       139       149       159       169      
           CEA5_ECOLX    80 KIPGLKIDQKIRGQMPERGWTEDDIKNTVSNGATGTSFDKRSPKKTPPDYLGRNDPATVYGSPGKYVVVNDRTGEVTQISDKTDPGWVDDSRIQWG 175
               SCOP domains d2djha_ A: automated matches                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhhhhh.....hhhhhhhhhhh...eeeee..hhhhh........eeeeeeee..eeeeee.....eeee..............ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 2djh A  16 KIPGLKIDQKIRGQMPERGWTEDDIKNTVSNGATGTSFDKRSPKKTPPDYLGRNDPATVYGSPGKYVVVNDRTGEVTQISDKTDPGWVDDSRIQWG 111
                                    25        35        45        55        65        75        85        95       105
   Legend:   → Mismatch (orange background)
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  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  (0, 0)

(no "CATH Domain" information available for 2DJH)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DJH)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CEA5_ECOLX | P18000)
molecular function
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0004540    ribonuclease activity    Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
biological process
    GO:0090501    RNA phosphodiester bond hydrolysis    The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
    GO:0019835    cytolysis    The rupture of cell membranes and the loss of cytoplasm.
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CEA5_ECOLX | P18000: 2a8k 2dfx 2fhz 3ao9 3vj7

(-) Related Entries Specified in the PDB File

2dfx THE SAME PROTEIN COMPLEXED WITH THE INHIBITOR PROTEIN