1YZ9 | PR0150 - JenaLib

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Title :   CRYSTAL STRUCTURE OF RNASE III MUTANT E110Q FROM AQUIFEX AEOLICUS COMPLEXED WITH DOUBLE STRANDED RNA AT 2.1-ANGSTROM RESOLUTION

Authors :   J. Gan, J. E. Tropea, B. P. Austin, D. L. Court, D. S. Waugh, X. Ji

Date :   28 Feb 05 (Deposition) - 22 Nov 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym./Biol. Unit : A,B,C,D,E,F

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

Reference :   J. Gan, J. E. Tropea, B. P. Austin, D. L. Court, D. S. Waugh, X. Ji
Intermediate States Of Ribonuclease Iii In Complex With Double-Stranded Rna
Structure V. 13 1435 2005
PubMed-ID: 16216575 | Reference-DOI: 10.1016/J.STR.2005.06.014
(for further references see the PDB file header)

*Molecule 1 - 5'-R(CPGPAPAPCPUPUPCPGPCPG)-3'**
	Chains	:	C, D, E, F
	Engineered	:	YES
	Synthetic	:	YES

Molecule 2 - RIBONUCLEASE III
	Chains	:	A, B
	EC Number	:	3.1.26.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PHPK1409
	Expression System Strain	:	BL21(DE3)-RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	RNC
	Mutation	:	YES
	Organism Scientific	:	AQUIFEX AEOLICUS
	Organism Taxid	:	63363
	Synonym	:	RNASE III

		1	2	3	4	5	6
Asymmetric/Biological Unit	:	A	B	C	D	E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 7)

No.	Name	Count	Type	Full Name
1	SO4	7	Ligand/Ion	SULFATE ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:76 , GLU A:77 , LYS A:149 , HOH A:1026 , HOH A:1028	BINDING SITE FOR RESIDUE SO4 A 1001
2	AC2	SOFTWARE	HOH C:158 , HOH C:303 , C E:1 , HOH E:164	BINDING SITE FOR RESIDUE SO4 E 1002
3	AC3	SOFTWARE	C D:12 , HOH D:163 , HOH D:183	BINDING SITE FOR RESIDUE SO4 D 1003
4	AC4	SOFTWARE	ARG A:208 , GLU A:211 , HOH A:1054	BINDING SITE FOR RESIDUE SO4 A 1004
5	AC5	SOFTWARE	SER B:76 , GLU B:77 , LYS B:149 , HOH B:1077	BINDING SITE FOR RESIDUE SO4 B 1005
6	AC6	SOFTWARE	ARG A:163 , TRP A:164 , HOH A:1133	BINDING SITE FOR RESIDUE SO4 A 1006
7	AC7	SOFTWARE	ARG B:163 , TRP B:164	BINDING SITE FOR RESIDUE SO4 B 1007

(no "SS Bond" information available for 1YZ9)

(no "Cis Peptide Bond" information available for 1YZ9)

(no "SAP(SNP)/Variant" information available for 1YZ9)

Asymmetric/Biological Unit (3, 6)

	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:4-121
2	RNASE_3_1	PS00517	Ribonuclease III family signature.	RNC_AQUAE	37-45	2	A:37-45 B:37-45
3	DS_RBD	PS50137	Double stranded RNA-binding domain (dsRBD) profile.	RNC_AQUAE	151-219	2	A:151-219 B:151-219

(no "Exon" information available for 1YZ9)

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

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:220
 aligned with RNC_AQUAE | O67082 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220
            RNC_AQUAE     1 MKMLEQLEKKLGYTFKDKSLLEKALTHVSYSKKEHYETLEFLGDALVNFFIVDLLVQYSPNKREGFLSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINETIIGDVFEALWAAVYIDSGRDANFTRELFYKLFKEDILSAIKEGRVKKDYKTILQEITQKRWKERPEYRLISVEGPHHKKKFIVEAKIKEYRTLGEGKSKKEAEQRAAEELIKLLEES 220
               SCOP domains d1yz9a1 A:1-150 RNase III endonuclease catalytic domain                                                                                               d1yz9a2 A:151-220 RNase III, C-terminal domain                         SCOP domains
               CATH domains 1yz9A01 A:1-149  [code=1.10.1520.10, no name defined]                                                                                                1yz9A02 A:150-220  [code=3.30.160.20, no name defined]                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh....hhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh...eeeeeeee......eeeeeeee..eeeeeee.hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---RNASE_3_2  PDB: A:4-121 UniProt: 4-121                                                                                -----------------------------DS_RBD  PDB: A:151-219 UniProt: 151-219                              - PROSITE (1)
                PROSITE (2) ------------------------------------RNASE_3_1------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yz9 A   1 MKMLEQLEKKLGYTFKDKSLLEKALTHVSYSKKEHYETLEFLGDALVNFFIVDLLVQYSPNKREGFLSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINETIIGDVFQALWAAVYIDSGRDANFTRELFYKLFKEDILSAIKEGRVKKDYKTILQEITQKRWKERPEYRLISVEGPHHKKKFIVEAKIKEYRTLGEGKSKKEAEQRAAEELIKLLEES 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

Chain B from PDB  Type:PROTEIN  Length:218
 aligned with RNC_AQUAE | O67082 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:218
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212        
            RNC_AQUAE     3 MLEQLEKKLGYTFKDKSLLEKALTHVSYSKKEHYETLEFLGDALVNFFIVDLLVQYSPNKREGFLSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINETIIGDVFEALWAAVYIDSGRDANFTRELFYKLFKEDILSAIKEGRVKKDYKTILQEITQKRWKERPEYRLISVEGPHHKKKFIVEAKIKEYRTLGEGKSKKEAEQRAAEELIKLLEES 220
               SCOP domains d1yz9b1 B:3-150 RNase III endonuclease catalytic domain                                                                                             d1yz9b2 B:151-220 RNase III, C-terminal domain                         SCOP domains
               CATH domains 1yz9B01 B:3-149  [code=1.10.1520.10, no name defined]                                                                                              1yz9B02 B:150-220  [code=3.30.160.20, no name defined]                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh....hhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh...eeeeeeee.hhhhheeeeeeee..eeeeeee.hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -RNASE_3_2  PDB: B:4-121 UniProt: 4-121                                                                                -----------------------------DS_RBD  PDB: B:151-219 UniProt: 151-219                              - PROSITE (1)
                PROSITE (2) ----------------------------------RNASE_3_1------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yz9 B   3 MLEQLEKKLGYTFKDKSLLEKALTHVSYSKKEHYETLEFLGDALVNFFIVDLLVQYSPNKREGFLSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINETIIGDVFQALWAAVYIDSGRDANFTRELFYKLFKEDILSAIKEGRVKKDYKTILQEITQKRWKERPEYRLISVEGPHHKKKFIVEAKIKEYRTLGEGKSKKEAEQRAAEELIKLLEES 220
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212

Chain C from PDB  Type:RNA  Length:11
                                           
                 1yz9 C   1 CGAACUUCGCG  11
                                    10

Chain D from PDB  Type:RNA  Length:11
                                           
                 1yz9 D  12 CGAACUUCGCG  22
                                    21

Chain E from PDB  Type:RNA  Length:11
                                           
                 1yz9 E   1 CGAACUUCGCG  11
                                    10

Chain F from PDB  Type:RNA  Length:11
                                           
                 1yz9 F  12 CGAACUUCGCG  22
                                    21

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/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Double Stranded RNA Binding Domain (204)

Homologous Superfamily: [code=3.30.160.20, no name defined] (122)

[unclassified] (7)

1a	1yz9A02	A:150-220
1b	1yz9B02	B:150-220

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)

[unclassified] (5)

2a	1yz9B01	B:3-149
2b	1yz9A01	A:1-149

(no "Pfam Domain" information available for 1YZ9)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1yz9)

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	1yz9
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	RNC_AQUAE \| O67082
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	3.1.26.3
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UniProtKB/Swiss-Prot
	RNC_AQUAE \| O67082	:	1i4s 1jfz 1rc5 1rc7 1yyk 1yyo 1yyw 2ez6 2nue 2nuf 2nug 4m2z 4m30

1i4s	THE CRYSTAL STRUCTURE OF RNASE III ENDONUCLEASE DOMAIN FROM AQUIFEX AEOLICUS
1jfz	CRYSTAL STRUCTURE OF A MN(II)COMPLEX OF RNASE III ENDONUCLEASE DOMAIN FROM AQUIFEX AEOLICUS
1o0w	THE CRYSTAL STRUCTURE OF RNASE III FROM THERMOTOGA MARITIMA
1rc5	THE CRYSTAL STRUCTURE OF A MG(II) COMPLEX OF RNASE III ENDONUCLEASE DOMAIN FROM AQUIFEX AEOLICUS
1rc7	CRYSTAL STRUCTURE OF RNASE III MUTANT E110K FROM AQUIFEX AEOLICUS COMPLEXED WITH DOUBLE-STRANDED RNA
1yyk	WILD TYPE AT 2.5-ANGSTROM RESOLUTION
1yyo	THE SAME PROTEIN WITH MUTANT E110K
1yyw	WILD TYPE AT 2.8-ANGSTROM RESOLUTION

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 6)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 4)

CATH Domains (2, 4)

Pfam Domains (0, 0)

Gene Ontology (14, 14)

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