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(-) Description

Title :  STRUCTURAL AND MUTATIONAL STUDIES OF THE CATALYTIC DOMAIN OF COLICIN E5A TRNA-SPECIFIC RIBONUCLEASE
 
Authors :  Y. L. Lin, Y. Elias, R. H. Huang
Date :  08 Jul 05  (Deposition) - 20 Sep 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Ribonuclease, Toxin, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. L. Lin, Y. Elias, R. H. Huang
Structural And Mutational Studies Of The Catalytic Domain Of Colicin E5: A Trna-Specific Ribonuclease
Biochemistry V. 44 10494 2005
PubMed-ID: 16060658  |  Reference-DOI: 10.1021/BI050749S
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COLICIN E5
    Chains: A, B, C, D
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PLM1-COLE5
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: COL
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:24 , HOH A:405 , GLU D:24 , THR D:90 , HOH D:405 , HOH D:432 , HOH D:436BINDING SITE FOR RESIDUE CA A 401
2AC2SOFTWAREGLU A:24 , THR A:90 , HOH A:408 , HOH A:414 , HOH A:426 , GLU D:24 , HOH D:409BINDING SITE FOR RESIDUE CA D 402
3AC3SOFTWAREGLU B:24 , THR B:90 , HOH B:413 , HOH B:417 , GLU C:24 , HOH C:410BINDING SITE FOR RESIDUE CA C 403
4AC4SOFTWAREGLU B:24 , HOH B:410 , GLU C:24 , THR C:90 , HOH C:407 , HOH C:432BINDING SITE FOR RESIDUE CA B 404

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2A8K)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Pro A:54 -Pro A:55
2Pro B:54 -Pro B:55
3Pro C:54 -Pro C:55
4Pro D:54 -Pro D:55

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2A8K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2A8K)

(-) Exons   (0, 0)

(no "Exon" information available for 2A8K)

(-) 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:94
 aligned with CEA5_ECOLX | P18000 from UniProtKB/Swiss-Prot  Length:180

    Alignment length:94
                                    93       103       113       123       133       143       153       163       173    
           CEA5_ECOLX    84 LKIDQKIRGQMPERGWTEDDIKNTVSNGATGTSFDKRSPKKTPPDYLGRNDPATVYGSPGKYVVVNDRTGEVTQISDKTDPGWVDDSRIQWGNK 177
               SCOP domains d2a8ka1 A:12-105 Colicin E5                                                                    SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh.hhhhhhhhhhh.eeeeeeeeehhhhh......eeeeeeeeee..eeeeee.....eeee..............ee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                 2a8k A  12 LKIDQKIRGQMPERGWTEDDIKNTVSNGATGTSFDKRSPKKTPPDYLGRNDPATVYGSPGKYVVVNDRTGEVTQISDKTDPGWVDDSRIQWGNK 105
                                    21        31        41        51        61        71        81        91       101    


Chain B from PDB  Type:PROTEIN  Length:94
 aligned with CEA5_ECOLX | P18000 from UniProtKB/Swiss-Prot  Length:180

    Alignment length:94
                                    93       103       113       123       133       143       153       163       173    
           CEA5_ECOLX    84 LKIDQKIRGQMPERGWTEDDIKNTVSNGATGTSFDKRSPKKTPPDYLGRNDPATVYGSPGKYVVVNDRTGEVTQISDKTDPGWVDDSRIQWGNK 177
               SCOP domains d2a8kb_ B: Colicin E5                                                                          SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh.hhhhhhhhhhh.eeeeeeeeehhhhh......eeeeeeeeee..eeeeee.....eeee..............ee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                 2a8k B  12 LKIDQKIRGQMPERGWTEDDIKNTVSNGATGTSFDKRSPKKTPPDYLGRNDPATVYGSPGKYVVVNDRTGEVTQISDKTDPGWVDDSRIQWGNK 105
                                    21        31        41        51        61        71        81        91       101    


Chain C from PDB  Type:PROTEIN  Length:94
 aligned with CEA5_ECOLX | P18000 from UniProtKB/Swiss-Prot  Length:180

    Alignment length:94
                                    93       103       113       123       133       143       153       163       173    
           CEA5_ECOLX    84 LKIDQKIRGQMPERGWTEDDIKNTVSNGATGTSFDKRSPKKTPPDYLGRNDPATVYGSPGKYVVVNDRTGEVTQISDKTDPGWVDDSRIQWGNK 177
               SCOP domains d2a8kc_ C: Colicin E5                                                                          SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh.hhhhhhhhhhh...eeeeeee...........eeeeeeeeee..eeeeee.....eeee..............ee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                 2a8k C  12 LKIDQKIRGQMPERGWTEDDIKNTVSNGATGTSFDKRSPKKTPPDYLGRNDPATVYGSPGKYVVVNDRTGEVTQISDKTDPGWVDDSRIQWGNK 105
                                    21        31        41        51        61        71        81        91       101    


Chain D from PDB  Type:PROTEIN  Length:94
 aligned with CEA5_ECOLX | P18000 from UniProtKB/Swiss-Prot  Length:180

    Alignment length:94
                                    93       103       113       123       133       143       153       163       173    
           CEA5_ECOLX    84 LKIDQKIRGQMPERGWTEDDIKNTVSNGATGTSFDKRSPKKTPPDYLGRNDPATVYGSPGKYVVVNDRTGEVTQISDKTDPGWVDDSRIQWGNK 177
               SCOP domains d2a8kd_ D: Colicin E5                                                                          SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh.hhhhhhhhhhh...eeeeeee...........eeeeeeeeee..eeeeee.....eeee..............ee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                 2a8k D  12 LKIDQKIRGQMPERGWTEDDIKNTVSNGATGTSFDKRSPKKTPPDYLGRNDPATVYGSPGKYVVVNDRTGEVTQISDKTDPGWVDDSRIQWGNK 105
                                    21        31        41        51        61        71        81        91       101
   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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2A8K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2A8K)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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

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        CEA5_ECOLX | P18000: 2dfx 2djh 2fhz 3ao9 3vj7

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