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Title :   A PROCESSED NON-CODING RNA REGULATES A BACTERIAL ANTIVIRAL SYSTEM

Authors :   T. R. Blower, X. Y. Pei, F. L. Short, P. C. Fineran, D. P. Humphreys, B. F. L G. P. C. Salmond

Date :   30 Apr 10 (Deposition) - 12 Jan 11 (Release) - 16 Feb 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.55

Chains :   Asym./Biol. Unit : A,G

Keywords :   Toxin-Rna Complex, Abortive Infection, Phage (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. R. Blower, X. Y. Pei, F. L. Short, P. C. Fineran, D. P. Humphreys, B. F. Luisi, G. P. C. Salmond
A Processed Noncoding Rna Regulates An Altruistic Bacterial Antiviral System.
Nat. Struct. Mol. Biol. V. 18 185 2011
PubMed-ID: 21240270 | Reference-DOI: 10.1038/NSMB.1981

Compounds

Molecule 1 - TOXN
	Atcc	:	BAA-673
	Chains	:	A
	EC Number	:	3.1.27.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PTYB1
	Expression System Strain	:	ER2566
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	PECTOBACTERIUM ATROSEPTICUM
	Organism Taxid	:	29471
	Other Details	:	ENVIRONMENTAL ISOLATED FROM SCOTLAND, U.K
	Strain	:	SCRI 1039

Molecule 2 - TOXI
	Atcc	:	BAA-673
	Cell Line	:	ER2566
	Chains	:	G
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PACYC184
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	BACTERIA ANTITOX, RESIDUES 1775-1814
	Organism Scientific	:	PECTOBACTERIUM ATROSEPTICUM
	Organism Taxid	:	29471
	Other Details	:	ENVIRONMENTAL ISOLATED FROM SCOTLAND, U.K
	Plasmid	:	PECA1039
	Strain	:	ECA SCRI 1039

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 11)

Sites (9, 9)

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:46 , GLU A:94 , ARG A:158	BINDING SITE FOR RESIDUE SO4 A1163
2	AC2	SOFTWARE	MET A:1 , LYS A:2 , HOH A:2056	BINDING SITE FOR RESIDUE SO4 A1164
3	AC3	SOFTWARE	ILE A:42 , GLN A:43 , HOH A:2022	BINDING SITE FOR RESIDUE SO4 A1165
4	AC4	SOFTWARE	HIS A:72 , GLY A:75	BINDING SITE FOR RESIDUE CO A1166
5	AC5	SOFTWARE	GLU A:73 , ASN A:74 , LYS A:116 , GLN A:119 , HOH A:2039	BINDING SITE FOR RESIDUE CO A1167
6	AC6	SOFTWARE	G G:26 , C G:27	BINDING SITE FOR RESIDUE SO4 G1032
7	AC7	SOFTWARE	A G:13 , C G:14 , U G:22	BINDING SITE FOR RESIDUE CO G1033
8	AC8	SOFTWARE	U G:16 , U G:18	BINDING SITE FOR RESIDUE CO G1034
9	AC9	SOFTWARE	G G:2	BINDING SITE FOR RESIDUE CO G1035

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

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Chain A from PDB  Type:PROTEIN  Length:162
 aligned with TOXN_PECAT | B8X8Z0 from UniProtKB/Swiss-Prot  Length:171

    Alignment length:162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  
           TOXN_PECAT     1 MKFYTISSKYIEYLKEFDDKVPNSEDPTYQNPKAFIGIVLEIQGHKYLAPLTSPKKWHNNVKESSLSCFKLHENGVPENQLGLINLKFMIPIIEAEVSLLDLGNMPNTPYKRMLYKQLQFIRANSDKIASKSDTLRNLVLQGKMQGTCNFSLLEEKYRDFGK 162
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeehhhhhhhhhhhh................eeeeeeee..eeeeeeee..hhhhhhh.......eeeee..eeeeeeeee.hhhhee.hhh.eee.hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2xdb A   1 MKFYTISSKYIEYLKEFDDKVPNSEDPTYQNPKAFIGIVLEIQGHKYLAPLTSPKKWHNNVKESSLSCFKLHENGVPENQLGLINLKFMIPIIEAEVSLLDLGNMPNTPYKRMLYKQLQFIRANSDKIASKSDTLRNLVLQGKMQGTCNFSLLEEKYRDFGK 162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160

Chain G from PDB  Type:RNA  Length:36
                                                                    
                 2xdb G  -3 AUUCAGGUGAUUUGCUACCUUUAAGUGCAGCUAGAa  32
                                     6        16        26     |
                                                              32-A23

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 (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (TOXN_PECAT | B8X8Z0)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	GO:0004521	endoribonuclease activity	Catalysis of the hydrolysis of ester linkages within ribonucleic acid 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.
biological process
	GO:0090502	RNA phosphodiester bond hydrolysis, endonucleolytic	The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
	GO:0051607	defense response to virus	Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
	GO:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
	GO:0006276	plasmid maintenance	The maintenance of the integrity of extrachromosomal plasmid DNA; includes processes that ensure plasmids are retained in the daughter cells after cell division.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.

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Description