1JFZ - JenaLib

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Title :   CRYSTAL STRUCTURE OF MN(II)-COMPLEX OF RNASE III ENDONUCLEASE DOMAIN FROM AQUIFEX AEOLICUS AT 2.10 ANGSTROM RESOLUTION

Authors :   J. Blaszczyk, X. Ji

Date :   22 Jun 01 (Deposition) - 19 Dec 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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. E. Tropea, M. Bubunenko, K. M. Routzahn, D. S. Waugh, D. L. Court, X. Ji
Crystallographic And Modeling Studies Of Rnase Iii Suggest A Mechanism For Double-Stranded Rna Cleavage.
Structure V. 9 1225 2001
PubMed-ID: 11738048 | Reference-DOI: 10.1016/S0969-2126(01)00685-2
(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
	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	MN	4	Ligand/Ion	MANGANESE (II) ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	MN	-1	Ligand/Ion	MANGANESE (II) ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	MN	-1	Ligand/Ion	MANGANESE (II) 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:1137	BINDING SITE FOR RESIDUE MN A 761
2	AC2	SOFTWARE	GLU B:240 , ASP B:307 , GLU B:310 , HOH B:1007 , HOH B:1246 , HOH B:1325	BINDING SITE FOR RESIDUE MN 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 MN C 763
4	AC4	SOFTWARE	GLU D:640 , ASP D:707 , GLU D:710 , HOH D:1124 , HOH D:1308 , HOH D:1311	BINDING SITE FOR RESIDUE MN D 764

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

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

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

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 1JFZ)

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 d1jfza_ A: RNase III endonuclease catalytic domain                                                                                                   SCOP domains
               CATH domains 1jfzA00 A:0-147  [code=1.10.1520.10, no name defined]                                                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh....hhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhh....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
                 1jfz 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 d1jfzb_ B: RNase III endonuclease catalytic domain                                                                                                    SCOP domains
               CATH domains 1jfzB00 B:200-348  [code=1.10.1520.10, no name defined]                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhh....hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh..hhhhhh.......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
                 1jfz 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 d1jfzc_ C: RNase III endonuclease catalytic domain                                                                                                    SCOP domains
               CATH domains 1jfzC00 C:400-548  [code=1.10.1520.10, no name defined]                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh....hhhhhhhhhh.........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
                 1jfz 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 d1jfzd_ D: RNase III endonuclease catalytic domain                                                                                                   SCOP domains
               CATH domains 1jfzD00 D:600-747  [code=1.10.1520.10, no name defined]                                                                                              CATH domains
           Pfam domains (1) -------------------------------------Ribonuclease_3-1jfzD01 D:637-721                                                     -------------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------Ribonuclease_3-1jfzD02 D:637-721                                                     -------------------------- Pfam domains (2)
           Pfam domains (3) -------------------------------------Ribonuclease_3-1jfzD03 D:637-721                                                     -------------------------- Pfam domains (3)
           Pfam domains (4) -------------------------------------Ribonuclease_3-1jfzD04 D:637-721                                                     -------------------------- Pfam domains (4)
         Sec.struct. author ......hhhhhhh....hhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh... 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
                 1jfz 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	d1jfza_	A:
1b	d1jfzd_	D:
1c	d1jfzb_	B:
1d	d1jfzc_	C:

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. (2)

1a	1jfzA00	A:0-147
1b	1jfzD00	D:600-747
1c	1jfzB00	B:200-348
1d	1jfzC00	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_3-1jfzD01	D:637-721
1b	Ribonuclease_3-1jfzD02	D:637-721
1c	Ribonuclease_3-1jfzD03	D:637-721
1d	Ribonuclease_3-1jfzD04	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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	RNC_AQUAE \| O67082	:	1i4s 1rc5 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
1stu	1STU IS THE NMR SOLUTION STRUCTURE OF A DOUBLE-STRANDED RNA -BINDING DOMAIN FROM DROSOPHILA STAUFEN PROTEIN

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