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Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF RNASE III FROM AQUIFEX AEOLICUS COMPLEXED WITH DS-RNA AT 2.9-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 :   2.90

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

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 - 46-MER
	Chains	:	C
	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
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2NUE)

(no "Site" information available for 2NUE)

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

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

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

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 2NUE)

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
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221
            RNC_AQUAE     2 KMLEQLEKKLGYTFKDKSLLEKALTHVSYSKKEHYETLEFLGDALVNFFIVDLLVQYSPNKREGFLSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINETIIGDVFEALWAAVYIDSGRDANFTRELFYKLFKEDILSAIKEGRVKKDYKTILQEITQKRWKERPEYRLISVEGPHHKKKFIVEAKIKEYRTLGEGKSKKEAEQRAAEELIKLLEESE 221
               SCOP domains d2nuea1 A:2-150 RNase III endonuclease catalytic domain                                                                                              d2nuea2 A:151-221 RNase III, C-terminal domain                          SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh.....hhhhhhh...........hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh...eeeeeeee.hhhhheeeeeeee..eeeeeee.hhhhhhhhhhhhhhhhhh... 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
                 2nue A   2 KMLEQLEKKLGYTFKDKSLLEKALTHVSYSKKEHYETLEFLGDALVNFFIVDLLVQYSPNKREGFLSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINETIIGDVFEALWAAVYIDSGRDANFTRELFYKLFKEDILSAIKEGRVKKDYKTILQEITQKRWKERPEYRLISVEGPHHKKKFIVEAKIKEYRTLGEGKSKKEAEQRAAEELIKLLEESE 221
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221

Chain B 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 d2nueb1 B:1-150 RNase III endonuclease catalytic domain                                                                                               d2nueb2 B:151-220 RNase III, C-terminal domain                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------Ribonuclease_3-2nueB03 B:37-121                                                      ------------------------------dsrm-2nueB01 B:152-217                                            --- Pfam domains (1)
           Pfam domains (2) ------------------------------------Ribonuclease_3-2nueB04 B:37-121                                                      ------------------------------dsrm-2nueB02 B:152-217                                            --- Pfam domains (2)
         Sec.struct. author ....hhhhhhhh....hhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh..hhhhhh.......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhhhhhhh....hhhhhhhhhhhhhhh...eeeeeeee......eeeeeeee..eeeeeee.hhhhhhhhhhhhhhhhhh.. 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
                 2nue B   1 MKMLEQLEKKLGYTFKDKSLLEKALTHVSYSKKEHYETLEFLGDALVNFFIVDLLVQYSPNKREGFLSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINETIIGDVFEALWAAVYIDSGRDANFTRELFYKLFKEDILSAIKEGRVKKDYKTILQEITQKRWKERPEYRLISVEGPHHKKKFIVEAKIKEYRTLGEGKSKKEAEQRAAEELIKLLEES 220
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

Chain C from PDB  Type:RNA  Length:46
                                                                              
                 2nue C   1 GGGACAAGCGCAAGGUCAUUCGCAAGAGUGGCCUUGCGCUUGUCCC  46
                                    10        20        30        40

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 2NUE)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: DSRM (45)

Family: dsrm (27)

Aquifex aeolicus (7)

1a	dsrm-2nueB01	B:152-217
1b	dsrm-2nueB02	B:152-217

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

Family: Ribonuclease_3 (11)

Aquifex aeolicus (9)

2a	Ribonuclease_3-2nueB03	B:37-121
2b	Ribonuclease_3-2nueB04	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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	3.1.26.3
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	RNC_AQUAE \| O67082
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UniProtKB/Swiss-Prot
	RNC_AQUAE \| O67082	:	1i4s 1jfz 1rc5 1rc7 1yyk 1yyo 1yyw 1yz9 2ez6 2nuf 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
2nuf
2nug

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PROSITE Motifs (3, 6)

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SCOP Domains (2, 4)

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Pfam Domains (2, 4)

Gene Ontology (14, 14)

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