3VJ7 - JenaLib

Title :   CRYSTAL STRUCTURE OF THE CARBOXY-TERMINAL RIBONUCLEASE DOMAIN OF COLICIN E5 R33Q MUTANT

Authors :   S. Yajima, S. Inoue, S. Fushinobu, T. Ogawa, M. Hidaka, H. Masaki

Date :   13 Oct 11 (Deposition) - 02 Nov 11 (Release) - 06 Feb 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym./Biol. Unit : A

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

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:25 , GLN A:29 , 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:117 , HOH A:125 , HOH A:146	BINDING SITE FOR RESIDUE 3PD A 1
2	AC2	SOFTWARE	3PD A:1 , LYS A:25 , SER 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 , HOH A:138	BINDING SITE FOR RESIDUE UM3 A 117

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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

    Alignment length:94
                                    91       101       111       121       131       141       151       161       171    
           CEA5_ECOLX    82 PGLKIDQKIRGQMPERGWTEDDIKNTVSNGATGTSFDKRSPKKTPPDYLGRNDPATVYGSPGKYVVVNDRTGEVTQISDKTDPGWVDDSRIQWG 175
               SCOP domains d3vj7a_ A: Colicin E5                                                                          SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhh.hhhhhhhhhhh.eeeeeee..hhhhh........eeeeeeee..eeeeee.....eeee..............ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                 3vj7 A  18 PGLKIDQKIRGQMPEQGWTEDDIKNTVSNGATGTSFDKRSPKKTPPDYLGRNDPATVYGSPGKYVVVNDRTGEVTQISDKTDPGWVDDSRIQWG 111
                                    27        37        47        57        67        77        87        97       107

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)

CATH Domains (0, 0)

Pfam Domains (0, 0)

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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