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(-) Description

Title :  CRSYTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF SEQUENCE-SPECIFIC RIBONUCLEASE
 
Authors :  S. Inoue, S. Fushinobu, T. Ogawa, M. Hidaka, H. Masaki, S. Yajima
Date :  22 Sep 10  (Deposition) - 28 Sep 11  (Release) - 06 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ribonuclease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Inoue-Ito, S. Yajima, S. Fushinobu, S. Nakamura, T. Ogawa, M. Hidaka, H. Masaki
Identification Of The Catalytic Residues Of Sequence-Specific And Histidine-Free Ribonuclease Colicin E
J. Biochem. V. 152 365 2012
PubMed-ID: 22815490  |  Reference-DOI: 10.1093/JB/MVS077

(-) Compounds

Molecule 1 - COLICIN-E5
    Chains: A, B
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL RIBONUCLEASE DOMAIN (CRD)
    Gene: COL
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1CD4Ligand/IonCADMIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:32 , HOH A:180 , GLU B:32 , HOH B:122 , HOH B:143BINDING SITE FOR RESIDUE CD A 117
2AC2SOFTWARETHR A:98 , HOH A:173 , HOH A:174 , CD B:117 , HOH B:170BINDING SITE FOR RESIDUE CD A 118
3AC3SOFTWAREGLU A:32 , HOH A:138BINDING SITE FOR RESIDUE CD A 119
4AC4SOFTWAREGLU A:32 , THR A:98 , CD A:118 , HOH A:174 , GLU B:32 , HOH B:170BINDING SITE FOR RESIDUE CD B 117

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3AO9)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Ile A:17 -Pro A:18
2Gly A:19 -Leu A:20
3Pro A:62 -Pro A:63

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3AO9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3AO9)

(-) Exons   (0, 0)

(no "Exon" information available for 3AO9)

(-) 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:97
 aligned with CEA5_ECOLX | P18000 from UniProtKB/Swiss-Prot  Length:180

    Alignment length:97
                                    90       100       110       120       130       140       150       160       170       
           CEA5_ECOLX    81 IPGLKIDQKIRGQMPERGWTEDDIKNTVSNGATGTSFDKRSPKKTPPDYLGRNDPATVYGSPGKYVVVNDRTGEVTQISDKTDPGWVDDSRIQWGNK 177
               SCOP domains d3ao9a_ A: Colicin E5                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhh.hhhhhhhhhhhheeeeeeeeehhhhh......eeeeeeeeee..eeeeee.....eeee..............ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 3ao9 A  17 IPGLKIDQKIRGQMPERGWTEDDIKNTVSNGATGTSFDKRSPKKTPPDYLGRNDPATVYGSPGKYVVVNDRTGEVTQISDKTDPGWVDDSRIQWGNK 113
                                    26        36        46        56        66        76        86        96       106       


Chain B from PDB  Type:PROTEIN  Length:86
 aligned with CEA5_ECOLX | P18000 from UniProtKB/Swiss-Prot  Length:180

    Alignment length:96
                                    92       102       112       122       132       142       152       162       172      
           CEA5_ECOLX    83 GLKIDQKIRGQMPERGWTEDDIKNTVSNGATGTSFDKRSPKKTPPDYLGRNDPATVYGSPGKYVVVNDRTGEVTQISDKTDPGWVDDSRIQWGNKN 178
               SCOP domains d3ao9b_ B: Colicin E5                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhh..hhhhhhhhhhh...eeeeee..----------.eeeeeeeee..eeeeee.....eeee..............ee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 3ao9 B  19 GLKIDQKIRGQMPERGWTEDDIKNTVSNGATGTSFDKRS----------RNDPATVYGSPGKYVVVNDRTGEVTQISDKTDPGWVDDSRIQWGNKN 114
                                    28        38        48        |-        68        78        88        98       108      
                                                                 57         68
   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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3AO9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3AO9)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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 2djh 2fhz 3vj7

(-) Related Entries Specified in the PDB File

2djh THE SAME PROTEIN COMPLEXED WITH A SUBSTRATE.