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Title :   CRYSTAL STRUCTURE OF RNASE III FROM AQUIFEX AEOLICUS COMPLEXED WITH DS-RNA AT 2.5-ANGSTROM RESOLUTION

Authors :   J. H. Gan, G. Shaw, J. E. Tropea, D. S. Waugh, D. L. Court, X. Ji

Date :   09 Nov 06 (Deposition) - 20 Nov 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

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

Reference :   J. Gan, G. Shaw, J. E. Tropea, D. S. Waugh, D. L. Court, X. Ji
A Stepwise Model For Double-Stranded Rna Processing By Ribonuclease Iii.
Mol. Microbiol. V. 67 143 2007
PubMed-ID: 18047582 | Reference-DOI: 10.1111/J.1365-2958.2007.06032.X
(for further references see the PDB file header)

Molecule 1 - 28-MER
	Chains	:	C, D
	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
	Organism Scientific	:	AQUIFEX AEOLICUS
	Organism Taxid	:	63363
	Synonym	:	RNASE III

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 8)

No.	Name	Count	Type	Full Name
1	MG	8	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:44 , GLU A:110	BINDING SITE FOR RESIDUE MG A 222
2	AC2	SOFTWARE	C C:1 , A C:2 , HOH C:223	BINDING SITE FOR RESIDUE MG C 202
3	AC3	SOFTWARE	GLU A:40 , ASP A:107 , GLU A:110	BINDING SITE FOR RESIDUE MG A 223
4	AC4	SOFTWARE	GLU A:40 , HOH A:276 , HOH A:277 , HOH A:278 , HOH A:279 , C C:1 , A C:2	BINDING SITE FOR RESIDUE MG A 224
5	AC5	SOFTWARE	ASP B:44 , GLU B:110 , HOH B:248 , C D:1	BINDING SITE FOR RESIDUE MG B 222
6	AC6	SOFTWARE	C D:1 , A D:2 , HOH D:210	BINDING SITE FOR RESIDUE MG D 206
7	AC7	SOFTWARE	GLU B:40 , ASP B:107 , GLU B:110 , HOH B:232 , HOH B:248	BINDING SITE FOR RESIDUE MG B 223
8	AC8	SOFTWARE	GLU B:40 , C D:1 , A D:2	BINDING SITE FOR RESIDUE MG D 208

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

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

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

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 2NUF)

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:219
 aligned with RNC_AQUAE | O67082 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:219
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211         
            RNC_AQUAE     2 KMLEQLEKKLGYTFKDKSLLEKALTHVSYSKKEHYETLEFLGDALVNFFIVDLLVQYSPNKREGFLSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINETIIGDVFEALWAAVYIDSGRDANFTRELFYKLFKEDILSAIKEGRVKKDYKTILQEITQKRWKERPEYRLISVEGPHHKKKFIVEAKIKEYRTLGEGKSKKEAEQRAAEELIKLLEES 220
               SCOP domains d2nufa1 A:2-150 RNase III endonuclease catalytic domain                                                                                              d2nufa2 A:151-220 RNase III, C-terminal domain                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh....hhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh....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
                 2nuf A   2 KMLEQLEKKLGYTFKDKSLLEKALTHVSYSKKEHYETLEFLGDALVNFFIVDLLVQYSPNKREGFLSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINETIIGDVFEALWAAVYIDSGRDANFTRELFYKLFKEDILSAIKEGRVKKDYKTILQEITQKRWKERPEYRLISVEGPHHKKKFIVEAKIKEYRTLGEGKSKKEAEQRAAEELIKLLEES 220
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211

Chain B from PDB  Type:PROTEIN  Length:219
 aligned with RNC_AQUAE | O67082 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:219
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211         
            RNC_AQUAE     2 KMLEQLEKKLGYTFKDKSLLEKALTHVSYSKKEHYETLEFLGDALVNFFIVDLLVQYSPNKREGFLSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINETIIGDVFEALWAAVYIDSGRDANFTRELFYKLFKEDILSAIKEGRVKKDYKTILQEITQKRWKERPEYRLISVEGPHHKKKFIVEAKIKEYRTLGEGKSKKEAEQRAAEELIKLLEES 220
               SCOP domains d2nufb1 B:2-150 RNase III endonuclease catalytic domain                                                                                              d2nufb2 B:151-220 RNase III, C-terminal domain                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------Ribonuclease_3-2nufB03 B:37-121                                                      ------------------------------dsrm-2nufB01 B:152-217                                            --- Pfam domains (1)
           Pfam domains (2) -----------------------------------Ribonuclease_3-2nufB04 B:37-121                                                      ------------------------------dsrm-2nufB02 B:152-217                                            --- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhh....hhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh....eeeeeeee......eeeeeeee..eeeeeee.hhhhhhhhhhhhhhhhhhh. 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
                 2nuf B   2 KMLEQLEKKLGYTFKDKSLLEKALTHVSYSKKEHYETLEFLGDALVNFFIVDLLVQYSPNKREGFLSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINETIIGDVFEALWAAVYIDSGRDANFTRELFYKLFKEDILSAIKEGRVKKDYKTILQEITQKRWKERPEYRLISVEGPHHKKKFIVEAKIKEYRTLGEGKSKKEAEQRAAEELIKLLEES 220
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211

Chain C from PDB  Type:RNA  Length:28
                                                            
                 2nuf C   1 CAAGGUCAUUCGCAAGAGUGGCCUUGCG  28
                                    10        20

Chain D from PDB  Type:RNA  Length:28
                                                            
                 2nuf D   1 CAAGGUCAUUCGCAAGAGUGGCCUUGCG  28
                                    10        20

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 "CATH Domain" information available for 2NUF)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: DSRM (45)

Family: dsrm (27)

Aquifex aeolicus (7)

1a	dsrm-2nufB01	B:152-217
1b	dsrm-2nufB02	B:152-217

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

Family: Ribonuclease_3 (11)

Aquifex aeolicus (9)

2a	Ribonuclease_3-2nufB03	B:37-121
2b	Ribonuclease_3-2nufB04	B:37-121

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 2nuf)

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

1rc7	CRYSTAL STRUCTURE OF RNASE III MUTANT E110K FROM AQUIFEX AEOLICUS COMPLEXED WITH DS-RNA (5'-GGCGCGCGCC-3')
1yyo	CRYSTAL STRUCTURE OF RNASE III FROM AQUIFEX AEOLICUS COMPLEXED WITH DS-RNA (5'-CGCGAAUUCGCG-3') AT 2.5-ANGSTROM RESOLUTION
1yyw	CRYSTAL STRUCTURE OF RNASE III FROM AQUIFEX AEOLICUS COMPLEXED WITH DS-RNA (5'-AAAUAUAUAUUU-3') AT 2.8-ANGSTROM RESOLUTION
1yz9	CRYSTAL STRUCTURE OF RNASE III MUTANT E110Q FROM AQUIFEX AEOLICUS COMPLEXED WITH DS-RNA (5'-CGAACUUCGCG-3') AT 2.1- ANGSTROM RESOLUTION
2ez6	CRYSTAL STRUCTURE OF RNASE III MUTANT D44N FROM AQUIFEX AEOLICUS COMPLEXED WITH PRODUCTS AT 2.05-ANGSTROM RESOLUTION
2nue
2nug

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 8)

Sites (8, 8)

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 (0, 0)

Pfam Domains (2, 4)

Gene Ontology (14, 14)

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