2A11 - JenaLib

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Title :   CRYSTAL STRUCTURE OF NUCLEASE DOMAIN OF RIBONUCLASE III FROM MYCOBACTERIUM TUBERCULOSIS

Authors :   D. L. Akey, J. M. Berger, Mycobacterium Tuberculosis Structural Pr Project (Xmtb)

Date :   17 Jun 05 (Deposition) - 05 Jul 05 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Ribonuclease; Rnase Iii; Nuclease Domain; Structural Genomics, Psi, Protein Structure Initiative; Mycobacterium Tuberculosis Structural Proteomics Project (Xmtb), Transcription, Translation, Hydrolase, Transcription, Translation, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. L. Akey, J. M. Berger
Structure Of The Nuclease Domain Of Ribonuclease Iii From M Tuberculosis At 2. 1 A
Protein Sci. V. 14 2744 2005
PubMed-ID: 16155207 | Reference-DOI: 10.1110/PS.051665905

Molecule 1 - RIBONUCLEASE III
	Chains	:	A
	EC Number	:	3.1.26.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)PLYS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	NUCLEASE DOMAIN
	Gene	:	RNC
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	1773
	Synonym	:	RNASE III

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:44 , ASP A:120 , GLU A:123 , HOH A:1008 , HOH A:1009 , HOH A:1010	BINDING SITE FOR RESIDUE CA A 1001
2	AC2	SOFTWARE	HOH A:1004 , HOH A:1005 , HOH A:1006 , HOH A:1007	BINDING SITE FOR RESIDUE CA A 1002

(no "SS Bond" information available for 2A11)

(no "Cis Peptide Bond" information available for 2A11)

(no "SAP(SNP)/Variant" information available for 2A11)

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RNASE_3_2	PS50142	Ribonuclease III family domain profile.	RNC_MYCTO	19-134	1	A:19-134
1	RNASE_3_2	PS50142	Ribonuclease III family domain profile.	RNC_MYCTU	19-134	1	A:19-134
2	RNASE_3_1	PS00517	Ribonuclease III family signature.	RNC_MYCTO	41-49	1	A:41-49
2	RNASE_3_1	PS00517	Ribonuclease III family signature.	RNC_MYCTU	41-49	1	A:41-49

Biological Unit 1 (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RNASE_3_2	PS50142	Ribonuclease III family domain profile.	RNC_MYCTO	19-134	2	A:19-134
1	RNASE_3_2	PS50142	Ribonuclease III family domain profile.	RNC_MYCTU	19-134	2	A:19-134
2	RNASE_3_1	PS00517	Ribonuclease III family signature.	RNC_MYCTO	41-49	2	A:41-49
2	RNASE_3_1	PS00517	Ribonuclease III family signature.	RNC_MYCTU	41-49	2	A:41-49

(no "Exon" information available for 2A11)

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
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Chain A from PDB  Type:PROTEIN  Length:154
 aligned with RNC_MYCTO | P9WH02 from UniProtKB/Swiss-Prot  Length:240

    Alignment length:154
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151    
            RNC_MYCTO     2 IRSRQPLLDALGVDLPDELLSLALTHRSYAYENGGLPTNERLEFLGDAVLGLTITDALFHRHPDRSEGDLAKLRASVVNTQALADVARRLCAEGLGVHVLLGRGEANTGGADKSSILADGMESLLGAIYLQHGMEKAREVILRLFGPLLDAAPT 155
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2a11A00 A:2-155  [code=1.10.1520.10, no name defined]                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhh...hhhhhhhhh.hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -----------------RNASE_3_2  PDB: A:19-134 UniProt: 19-134                                                                            --------------------- PROSITE (2)
                PROSITE (3) ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) ---------------------------------------RNASE_3_1---------------------------------------------------------------------------------------------------------- PROSITE (4)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a11 A   2 IRSRQPLLDALGVDLPDELLSLALTHRSYAYENGGLPTNERLEFLGDAVLGLTITDALFHRHPDRSEGDLAKLRASVVNTQALADVARRLCAEGLGVHVLLGRGEANTGGADKSSILADGMESLLGAIYLQHGMEKAREVILRLFGPLLDAAPT 155
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151

Chain A from PDB  Type:PROTEIN  Length:154
 aligned with RNC_MYCTU | P9WH03 from UniProtKB/Swiss-Prot  Length:240

    Alignment length:154
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151    
            RNC_MYCTU     2 IRSRQPLLDALGVDLPDELLSLALTHRSYAYENGGLPTNERLEFLGDAVLGLTITDALFHRHPDRSEGDLAKLRASVVNTQALADVARRLCAEGLGVHVLLGRGEANTGGADKSSILADGMESLLGAIYLQHGMEKAREVILRLFGPLLDAAPT 155
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2a11A00 A:2-155  [code=1.10.1520.10, no name defined]                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhh...hhhhhhhhh.hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------RNASE_3_2  PDB: A:19-134 UniProt: 19-134                                                                            --------------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) ---------------------------------------RNASE_3_1---------------------------------------------------------------------------------------------------------- PROSITE (3)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a11 A   2 IRSRQPLLDALGVDLPDELLSLALTHRSYAYENGGLPTNERLEFLGDAVLGLTITDALFHRHPDRSEGDLAKLRASVVNTQALADVARRLCAEGLGVHVLLGRGEANTGGADKSSILADGMESLLGAIYLQHGMEKAREVILRLFGPLLDAAPT 155
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151

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 2A11)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Ribonuclease iii, N-terminal Endonuclease Domain; Chain A (11)

Homologous Superfamily: [code=1.10.1520.10, no name defined] (11)

Mycobacterium tuberculosis. Organism_taxid: 1773. (1)

2a11A00

A:2-155

(no "Pfam Domain" information available for 2A11)

Asymmetric Unit(hide GO term definitions)

Chain A (RNC_MYCTO | P9WH02)

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: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: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:0004525	ribonuclease III activity	Catalysis of the endonucleolytic cleavage of RNA with 5'-phosphomonoesters and 3'-OH termini; makes two staggered cuts in both strands of dsRNA, leaving a 3' overhang of 2 nt.
biological process
	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:0006397	mRNA processing	Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
	GO:0016075	rRNA catabolic process	The chemical reactions and pathways resulting in the breakdown of rRNA, ribosomal RNA, a structural constituent of ribosomes.
	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.

Chain A (RNC_MYCTU | P9WH03)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0003725	double-stranded RNA binding	Interacting selectively and non-covalently with double-stranded RNA.
	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: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:0004525	ribonuclease III activity	Catalysis of the endonucleolytic cleavage of RNA with 5'-phosphomonoesters and 3'-OH termini; makes two staggered cuts in both strands of dsRNA, leaving a 3' overhang of 2 nt.
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:0006396	RNA processing	Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
	GO:0040007	growth	The increase in size or mass of an entire organism, a part of an organism or a cell.
	GO:0006397	mRNA processing	Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
	GO:0016075	rRNA catabolic process	The chemical reactions and pathways resulting in the breakdown of rRNA, ribosomal RNA, a structural constituent of ribosomes.
	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.

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