1RC5 - JenaLib

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Title :   CRYSTAL STRUCTURE OF MG(II)-COMPLEX OF RNASE III ENDONUCLEASE DOMAIN FROM AQUIFEX AEOLICUS AT 2.30 ANGSTROM RESOLUTION

Authors :   J. Blaszczyk, J. Gan, X. Ji

Date :   03 Nov 03 (Deposition) - 30 Mar 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)

Keywords :   Ribonuclease, Rnase Iii, Double-Stranded Rna, Rna Interference, Endonuclease Domain, Endonucleolytic Cleavage, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Blaszczyk, J. Gan, J. E. Tropea, D. L. Court, D. S. Waugh, X. Ji
Noncatalytic Assembly Of Ribonuclease Iii With Double-Stranded Rna.
Structure V. 12 457 2004
PubMed-ID: 15016361 | Reference-DOI: 10.1016/J.STR.2004.02.004
(for further references see the PDB file header)

Molecule 1 - RIBONUCLEASE III
	Chains	:	A, B, C, D
	EC Number	:	3.1.26.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PKM803
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	N-TERMINAL ENDONUCLEASE DOMAIN (RESIDUES 1-147)
	Gene	:	RNC, AQ_946
	Organism Scientific	:	AQUIFEX AEOLICUS
	Organism Taxid	:	63363
	Synonym	:	RNASE III

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	MG	4	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (0, 0)

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

Biological Unit 2 (0, 0)

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

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:40 , ASP A:107 , GLU A:110 , HOH A:1004 , HOH A:1056 , HOH A:1136	BINDING SITE FOR RESIDUE MG A 761
2	AC2	SOFTWARE	GLU B:240 , ASP B:307 , GLU B:310 , HOH B:1007 , HOH B:1245 , HOH B:1319	BINDING SITE FOR RESIDUE MG B 762
3	AC3	SOFTWARE	GLU C:440 , ASP C:507 , GLU C:510 , HOH C:1008 , HOH C:1015 , HOH C:1039	BINDING SITE FOR RESIDUE MG C 763
4	AC4	SOFTWARE	GLU D:640 , ASP D:707 , GLU D:710 , HOH D:1123 , HOH D:1302	BINDING SITE FOR RESIDUE MG D 764

(no "SS Bond" information available for 1RC5)

(no "Cis Peptide Bond" information available for 1RC5)

(no "SAP(SNP)/Variant" information available for 1RC5)

Asymmetric Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RNASE_3_2	PS50142	Ribonuclease III family domain profile.	RNC_AQUAE	4-121	4	A:4-121 B:204-321 C:404-521 D:604-721
2	RNASE_3_1	PS00517	Ribonuclease III family signature.	RNC_AQUAE	37-45	4	A:37-45 B:237-245 C:437-445 D:637-645

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RNASE_3_2	PS50142	Ribonuclease III family domain profile.	RNC_AQUAE	4-121	2	A:4-121 B:204-321 - -
2	RNASE_3_1	PS00517	Ribonuclease III family signature.	RNC_AQUAE	37-45	2	A:37-45 B:237-245 - -

Biological Unit 2 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RNASE_3_2	PS50142	Ribonuclease III family domain profile.	RNC_AQUAE	4-121	2	- - C:404-521 D:604-721
2	RNASE_3_1	PS00517	Ribonuclease III family signature.	RNC_AQUAE	37-45	2	- - C:437-445 D:637-645

(no "Exon" information available for 1RC5)

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:148
 aligned with RNC_AQUAE | O67082 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:148
                             1                                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139        
            RNC_AQUAE     - -MKMLEQLEKKLGYTFKDKSLLEKALTHVSYSKKEHYETLEFLGDALVNFFIVDLLVQYSPNKREGFLSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINETIIGDVFEALWAAVYIDSGRDANFTRELFYKLFKEDILSAIKEGR 147
               SCOP domains d1rc5a_ A: RNase III endonuclease catalytic domain                                                                                                   SCOP domains
               CATH domains 1rc5A00 A:0-147  [code=1.10.1520.10, no name defined]                                                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh....hhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----RNASE_3_2  PDB: A:4-121 UniProt: 4-121                                                                                -------------------------- PROSITE (1)
                PROSITE (2) -------------------------------------RNASE_3_1------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rc5 A   0 GMKMLEQLEKKLGYTFKDKSLLEKALTHVSYSKKEHYETLEFLGDALVNFFIVDLLVQYSPNKREGFLSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINETIIGDVFEALWAAVYIDSGRDANFTRELFYKLFKEDILSAIKEGR 147
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139

Chain B from PDB  Type:PROTEIN  Length:149
 aligned with RNC_AQUAE | O67082 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:149
                             1                                                                                                                                                   
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139         
            RNC_AQUAE     - -MKMLEQLEKKLGYTFKDKSLLEKALTHVSYSKKEHYETLEFLGDALVNFFIVDLLVQYSPNKREGFLSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINETIIGDVFEALWAAVYIDSGRDANFTRELFYKLFKEDILSAIKEGRV 148
               SCOP domains d1rc5b_ B: RNase III endonuclease catalytic domain                                                                                                    SCOP domains
               CATH domains 1rc5B00 B:200-348  [code=1.10.1520.10, no name defined]                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhh....hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----RNASE_3_2  PDB: B:204-321 UniProt: 4-121                                                                              --------------------------- PROSITE (1)
                PROSITE (2) -------------------------------------RNASE_3_1------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rc5 B 200 GMKMLEQLEKKLGYTFKDKSLLEKALTHVSYSKKEHYETLEFLGDALVNFFIVDLLVQYSPNKREGFLSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINETIIGDVFEALWAAVYIDSGRDANFTRELFYKLFKEDILSAIKEGRH 348
                                   209       219       229       239       249       259       269       279       289       299       309       319       329       339

Chain C from PDB  Type:PROTEIN  Length:149
 aligned with RNC_AQUAE | O67082 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:149
                             1                                                                                                                                                   
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139         
            RNC_AQUAE     - -MKMLEQLEKKLGYTFKDKSLLEKALTHVSYSKKEHYETLEFLGDALVNFFIVDLLVQYSPNKREGFLSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINETIIGDVFEALWAAVYIDSGRDANFTRELFYKLFKEDILSAIKEGRV 148
               SCOP domains d1rc5c_ C: RNase III endonuclease catalytic domain                                                                                                    SCOP domains
               CATH domains 1rc5C00 C:400-548  [code=1.10.1520.10, no name defined]                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh....hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----RNASE_3_2  PDB: C:404-521 UniProt: 4-121                                                                              --------------------------- PROSITE (1)
                PROSITE (2) -------------------------------------RNASE_3_1------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rc5 C 400 GMKMLEQLEKKLGYTFKDKSLLEKALTHVSYSKKEHYETLEFLGDALVNFFIVDLLVQYSPNKREGFLSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINETIIGDVFEALWAAVYIDSGRDANFTRELFYKLFKEDILSAIKEGRH 548
                                   409       419       429       439       449       459       469       479       489       499       509       519       529       539

Chain D from PDB  Type:PROTEIN  Length:148
 aligned with RNC_AQUAE | O67082 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:148
                             1                                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139        
            RNC_AQUAE     - -MKMLEQLEKKLGYTFKDKSLLEKALTHVSYSKKEHYETLEFLGDALVNFFIVDLLVQYSPNKREGFLSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINETIIGDVFEALWAAVYIDSGRDANFTRELFYKLFKEDILSAIKEGR 147
               SCOP domains d1rc5d_ D: RNase III endonuclease catalytic domain                                                                                                   SCOP domains
               CATH domains 1rc5D00 D:600-747  [code=1.10.1520.10, no name defined]                                                                                              CATH domains
           Pfam domains (1) -------------------------------------Ribonuclease_3-1rc5D01 D:637-721                                                     -------------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------Ribonuclease_3-1rc5D02 D:637-721                                                     -------------------------- Pfam domains (2)
           Pfam domains (3) -------------------------------------Ribonuclease_3-1rc5D03 D:637-721                                                     -------------------------- Pfam domains (3)
           Pfam domains (4) -------------------------------------Ribonuclease_3-1rc5D04 D:637-721                                                     -------------------------- Pfam domains (4)
         Sec.struct. author ......hhhhhhh....hhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----RNASE_3_2  PDB: D:604-721 UniProt: 4-121                                                                              -------------------------- PROSITE (1)
                PROSITE (2) -------------------------------------RNASE_3_1------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rc5 D 600 GMKMLEQLEKKLGYTFKDKSLLEKALTHVSYSKKEHYETLEFLGDALVNFFIVDLLVQYSPNKREGFLSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINETIIGDVFEALWAAVYIDSGRDANFTRELFYKLFKEDILSAIKEGR 747
                                   609       619       629       639       649       659       669       679       689       699       709       719       729       739

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: RNase III domain-like (16)

Superfamily: RNase III domain-like (16)

Family: RNase III catalytic domain-like (14)

Protein domain: RNase III endonuclease catalytic domain (13)

Aquifex aeolicus [TaxId: 63363] (12)

1a	d1rc5a_	A:
1b	d1rc5b_	B:
1c	d1rc5c_	C:
1d	d1rc5d_	D:

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)

Aquifex aeolicus. Organism_taxid: 63363. (1)

1a	1rc5A00	A:0-147
1b	1rc5D00	D:600-747
1c	1rc5B00	B:200-348
1d	1rc5C00	C:400-548

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Ribonuclease_3] (11)

Family: Ribonuclease_3 (11)

Aquifex aeolicus (9)

1a	Ribonuclease_3-1rc5D01	D:637-721
1b	Ribonuclease_3-1rc5D02	D:637-721
1c	Ribonuclease_3-1rc5D03	D:637-721
1d	Ribonuclease_3-1rc5D04	D:637-721

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (RNC_AQUAE | O67082)

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: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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	1rc5
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	RNC_AQUAE \| O67082	:	1i4s 1jfz 1rc7 1yyk 1yyo 1yyw 1yz9 2ez6 2nue 2nuf 2nug 4m2z 4m30

1di2	1DI2 IS THE CRYSTAL STRUCTURE OF A DOUBLE-STRANDED RNA- BINDING DOMAIN FROM XENOPUS LAEVIS COMPLEXED WITH DOUBLE- STRANDED RNA
1i4s	1I4S IS THE CRYSTAL STRUCTURE OF UNLIGATED RNASE III ENDONUCLEASE DOMAIN FROM AQUIFEX AEOLICUS
1jfz	1JFZ IS THE CRYSTAL STRUCTURE OF A MN(II)-COMPLEX OF RNASE III ENDONUCLEASE DOMAIN FROM AQUIFEX AEOLICUS
1o0w	1O0W IS THE CRYSTAL STRUCTURE OF UNLIGATED RIBONUCLEASE III FROM THERMOTOGA MARITIMA
1rc7	CRYSTAL STRUCTURE OF RNASE III MUTANT E110K FROM AQUIFEX AEOLICUS COMPLEXED WITH DS-RNA AT 2.15 ANGSTROM RESOLUTION
1stu	1STU IS THE NMR SOLUTION STRUCTURE OF A DOUBLE-STRANDED RNA -BINDING DOMAIN FROM DROSOPHILA STAUFEN PROTEIN

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