2C0B | PR0255 - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   CATALYTIC DOMAIN OF E. COLI RNASE E IN COMPLEX WITH 13-MER RNA

Authors :   M. J. Marcaida, A. J. Callaghan, W. G. Scott, B. F. Luisi

Date :   30 Aug 05 (Deposition) - 14 Oct 05 (Release) - 20 May 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.18

Chains :   Asym. Unit : L,R
Biol. Unit 1: L,R  (4x)

Keywords :   Hydrolase, Ribonuclease, Rna Turnover, Rna Processing, Endonuclease, Nuclease, Rna-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. J. Callaghan, M. J. Marcaida, J. A. Stead, K. J. Mcdowall, W. G. Scott B. F. Luisi
Structure Of E. Coli Rnase E Catalytic Domain And Implications For Rna Processing And Turnover
Nature V. 437 1187 2005
PubMed-ID: 16237448 | Reference-DOI: 10.1038/NATURE04084

Molecule 1 - RIBONUCLEASE E
	Chains	:	L
	EC Number	:	3.1.4.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Fragment	:	CATALYTIC DOMAIN, RESIDUES 1-510
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	RNASE E

*Molecule 2 - 5'-R(UPUPUPAPCPAPGPUPAPUPUPUPG)-3'**
	Chains	:	R
	Synthetic	:	YES

		1	2
Asymmetric Unit	:	L	R
Biological Unit 1 (4x)	:	L	R

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	MG	2	Ligand/Ion	MAGNESIUM ION
2	ZN	1	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP L:303 , ASP L:346 , HOH L:2023 , HOH L:2024 , HOH L:2028 , HOH L:2029 , HOH R:2002 , HOH R:2003	BINDING SITE FOR RESIDUE MG L1510
2	AC2	SOFTWARE	CYS L:404 , CYS L:407	BINDING SITE FOR RESIDUE ZN L1511
3	AC3	SOFTWARE	SER L:295	BINDING SITE FOR RESIDUE MG L1512

(no "SS Bond" information available for 2C0B)

(no "Cis Peptide Bond" information available for 2C0B)

(no "SAP(SNP)/Variant" information available for 2C0B)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	S1	PS50126	S1 domain profile.	RNE_ECOLI	39-119	1	L:39-119

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	S1	PS50126	S1 domain profile.	RNE_ECOLI	39-119	4	L:39-119

(no "Exon" information available for 2C0B)

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 L from PDB  Type:PROTEIN  Length:488
 aligned with RNE_ECOLI | P21513 from UniProtKB/Swiss-Prot  Length:1061

    Alignment length:516
                                   1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
                                   | 3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503      
            RNE_ECOLI     - -------MKRMLINATQQEELRVALVDGQRLYDLDIESPGHEQKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNKGAALTTFISLAGSYLVLMPNNPRAGGISRRIEGDDRTELKEALASLELPEGMGLIVRTAGVGKSAEALQWDLSFRLKHWEAIKKAAESRPAPFLIHQESNVIVRAFRDYLRQDIGEILIDNPKVLELARQHIAALGRPDFSSKIKLYTGEIPLFSHYQIESQIESAFQREVRLPSGGSIVIDSTEALTAIDINSARATRGGDIEETAFNTNLEAADEIARQLRLRDLGGLIVIDFIDMTPVRHQRAVENRLREAVRQDRARIQISHISRFGLLEMSRQRLSPSLGESSHHVCPRCSGTGTVRDNESLSLSILRLIEEEALKENTQEVHAIVPVPIASYLLNEKRSAVNAIETRQDGVRCVIVPNDQMETPHYHVLRVRKGEETPTLSYMLPKLHEEA 509
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeeee......eeeeeee..eeeeeeee..--......eeeee.....----..............hhhhh......-------..hhhhhh....eeeeeeee........eee....ee...eee..............------hhhhhhhh....----.ee..hhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeee...hhhhhhhhhh....eeeeee.hhhhhhhhhhhhhh..hhhhhh.eee.....hhhhhh.hhhhhhhh...eee.....eeeeee....eeeeee...-----hhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhhhh......ee........eeeeee.....hhhhhh..............hhhhhhhhhhhhhhhhhhh..eeeeeeeeehhhhhhhh..hhhhhhhhhhhh...eeeeeee........eeeeee.......hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------S1  PDB: L:39-119 UniProt: 39-119                                                ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2c0b L  -6 AHIEGRHMKRMLINATQQEELRVALVDGQRLYDLDIESP--EQKKANIYKGKITRIE----AAFVDYGAERHGFLPLKEIAREYFP-------RPNIKDVLREGQEVIVQIDKEERGNKGAALTTFISLAGSYLVLMPNNPRAGGISRRI------ELKEALASLELP----LIVRTAGVGKSAEALQWDLSFRLKHWEAIKKAAESRPAPFLIHQESNVIVRAFRDYLRQDIGEILIDNPKVLELARQHIAALGRPDFSSKIKLYTGEIPLFSHYQIESQIESAFQREVRLPSGGSIVIDSTEALTAIDINSAR-----DIEETAFNTNLEAADEIARQLRLRDLGGLIVIDFIDMTPVRHQRAVENRLREAVRQDRARIQISHISRFGLLEMSRQRLSPSLGESSHHVCPRCSGTGTVRDNESLSLSILRLIEEEALKENTQEVHAIVPVPIASYLLNEKRSAVNAIETRQDGVRCVIVPNDQMETPHYHVLRVRKGEETPTLSYMLPKLHEEA 509
                                     3        13        23        |- |      43      |  - |      63        73     |   -   |    93       103       113       123       133       143      |153       | -  |    173       183       193       203       213       223       233       243       253       263       273       283       293       303    |    -|      323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503      
                                                                 32 35             50   55                      79      87                                                     143    150        161  166                                                                                                                                           308   314

Chain R from PDB  Type:DNA/RNA  Length:11
                                           
                 2c0b R   1 UUUACAGUAUU  11
                                    10

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 '\|'

(no "SCOP Domain" information available for 2C0B)

(no "CATH Domain" information available for 2C0B)

(no "Pfam Domain" information available for 2C0B)

Asymmetric Unit(hide GO term definitions)

Chain L (RNE_ECOLI | P21513)

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:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0008995	ribonuclease E activity	Catalysis of the cleavage of single-stranded RNA that is monophosphorylated at its 5'-end; cleavage occurs predominantly at 5 nucleotides from the 5'-end and in A + U-rich regions, and is blocked by the presence of a 5'-triphosphate group.
	GO:0004540	ribonuclease activity	Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0006401	RNA catabolic process	The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
	GO:0090501	RNA phosphodiester bond hydrolysis	The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
	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:0006396	RNA processing	Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
	GO:0006402	mRNA catabolic process	The chemical reactions and pathways resulting in the breakdown of mRNA, messenger RNA, which is responsible for carrying the coded genetic 'message', transcribed from DNA, to sites of protein assembly at the ribosomes.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
	GO:0000967	rRNA 5'-end processing	Any process involved in forming the mature 5' end of an rRNA molecule.
	GO:0006364	rRNA processing	Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
	GO:0008033	tRNA processing	The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0009898	cytoplasmic side of plasma membrane	The leaflet the plasma membrane that faces the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2c0b)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	2c0b
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	3.1.4.-
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UniProtKB/Swiss-Prot
	RNE_ECOLI \| P21513	:	1slj 1smx 1sn8 2bx2 2c4r 2fym 2vmk 2vrt 3gcm 3gme 3h1c 3h8a 5f6c

1slj	SOLUTION STRUCTURE OF THE S1 DOMAIN OF RNASE E FROM E. COLI
1smx	CRYSTAL STRUCTURE OF THE S1 DOMAIN OF RNASE E FROM E. COLI(NATIVE)
1sn8	CRYSTAL STRUCTURE OF THE S1 DOMAIN OF RNASE E FROM E. COLI(PB DERIVATIVE)
2bx2	CATALYTIC DOMAIN OF E. COLI RNASE E

Description

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Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

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Gene Ontology (25, 25)

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