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Title :   CRYSTAL STRUCTURE OF RNASE III FROM AQUIFEX AEOLICUS COMPLEXED WITH DS-RNA AT 1.7-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 :   1.70

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

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 - 5'-R(PAPAPGPGPUPCPAPUPUPCPG)-3'**
	Chains	:	C, D
	Engineered	:	YES
	Synthetic	:	YES

*Molecule 2 - 5'-R(PAPGPUPGPGPCPCPUPUPGPC)-3'**
	Chains	:	E, F
	Engineered	:	YES
	Synthetic	:	YES

Molecule 3 - 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	5	6
Asymmetric/Biological Unit	:	A	B	C	D	E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 19)

No.	Name	Count	Type	Full Name
1	MG	19	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (19, 19)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:44 , GLU A:110 , HOH A:518 , HOH A:519 , G D:12 , HOH D:517 , A E:17	BINDING SITE FOR RESIDUE MG A 501
02	AC2	SOFTWARE	GLU A:40 , GLU A:110 , MG A:503 , HOH A:519 , HOH A:520 , HOH A:531 , A E:17 , HOH E:506	BINDING SITE FOR RESIDUE MG A 502
03	AC3	SOFTWARE	ASP A:107 , MG A:502 , HOH A:521 , HOH A:522 , HOH A:523 , HOH E:506 , HOH E:507	BINDING SITE FOR RESIDUE MG A 503
04	AC4	SOFTWARE	GLU A:37 , GLU A:40 , HOH A:524 , HOH A:525 , HOH B:519 , G E:18 , HOH E:508	BINDING SITE FOR RESIDUE MG A 504
05	AC5	SOFTWARE	A E:17 , G E:18 , HOH E:509 , HOH E:510 , HOH E:511 , HOH E:512	BINDING SITE FOR RESIDUE MG E 505
06	AC6	SOFTWARE	HOH A:526 , HOH A:527 , HOH A:528 , HOH A:529 , HOH C:520 , HOH C:521	BINDING SITE FOR RESIDUE MG A 506
07	AC7	SOFTWARE	ASP B:44 , GLU B:110 , HOH B:520 , G C:12 , HOH C:522 , HOH C:523 , A F:17	BINDING SITE FOR RESIDUE MG B 507
08	AC8	SOFTWARE	GLU B:40 , GLU B:110 , HOH B:521 , HOH B:530 , HOH C:523 , A F:17 , HOH F:514	BINDING SITE FOR RESIDUE MG B 508
09	AC9	SOFTWARE	ASP B:107 , HOH B:521 , HOH B:522 , HOH B:523 , HOH B:524 , HOH B:530 , HOH F:515	BINDING SITE FOR RESIDUE MG B 509
10	BC1	SOFTWARE	HOH A:530 , GLU B:37 , GLU B:40 , HOH B:525 , HOH B:526 , HOH F:516	BINDING SITE FOR RESIDUE MG B 510
11	BC2	SOFTWARE	A F:17 , G F:18 , HOH F:517 , HOH F:518 , HOH F:519 , HOH F:520	BINDING SITE FOR RESIDUE MG F 511
12	BC3	SOFTWARE	HOH B:527 , HOH B:528 , HOH B:529 , HOH D:518 , HOH D:519 , HOH D:563	BINDING SITE FOR RESIDUE MG B 512
13	BC4	SOFTWARE	HOH E:522 , HOH F:542 , HOH F:543 , HOH F:544 , HOH F:545 , HOH F:552	BINDING SITE FOR RESIDUE MG F 513
14	BC5	SOFTWARE	HOH D:529 , HOH D:533 , HOH D:550 , HOH D:551 , HOH D:552	BINDING SITE FOR RESIDUE MG D 514
15	BC6	SOFTWARE	HOH C:535 , HOH C:538 , HOH C:559 , HOH C:563	BINDING SITE FOR RESIDUE MG C 515
16	BC7	SOFTWARE	HOH D:522 , HOH D:531 , HOH D:535 , HOH D:562 , HOH E:513 , HOH E:526	BINDING SITE FOR RESIDUE MG D 516
17	BC8	SOFTWARE	GLY A:12 , HOH A:534 , HOH A:620 , HOH A:632 , ARG B:194	BINDING SITE FOR RESIDUE MG A 517
18	BC9	SOFTWARE	HOH B:538 , HOH B:561 , HOH B:657	BINDING SITE FOR RESIDUE MG B 518
19	CC1	SOFTWAR	HOH C:526 , HOH C:530 , HOH C:540 , HOH C:546 , HOH C:562 , HOH F:551	BINDING SITE FOR RESIDUE MG C 519

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

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

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

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:151-218 B:151-219

(no "Exon" information available for 2NUG)

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:216
 aligned with RNC_AQUAE | O67082 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:216
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212      
            RNC_AQUAE     3 MLEQLEKKLGYTFKDKSLLEKALTHVSYSKKEHYETLEFLGDALVNFFIVDLLVQYSPNKREGFLSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINETIIGDVFEALWAAVYIDSGRDANFTRELFYKLFKEDILSAIKEGRVKKDYKTILQEITQKRWKERPEYRLISVEGPHHKKKFIVEAKIKEYRTLGEGKSKKEAEQRAAEELIKLLE 218
               SCOP domains d2nuga1 A:3-150 RNase III endonuclease catalytic domain                                                                                             d2nuga2 A:151-218 RNase III, C-terminal domain                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhh....hhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.....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:151-218 UniProt: 151-219                              PROSITE (1)
                PROSITE (2) ----------------------------------RNASE_3_1----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2nug A   3 MLEQLEKKLGYTFKDKSLLEKALTHVSYSKKEHYETLEFLGDALVNFFIVDLLVQYSPNKREGFLSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINETIIGDVFEALWAAVYIDSGRDANFTRELFYKLFKEDILSAIKEGRVKKDYKTILQEITQKRWKERPEYRLISVEGPHHKKKFIVEAKIKEYRTLGEGKSKKEAEQRAAEELIKLLE 218
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212

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 d2nugb1 B:3-150 RNase III endonuclease catalytic domain                                                                                             d2nugb2 B:151-220 RNase III, C-terminal domain                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------------Ribonuclease_3-2nugB03 B:37-121                                                      ------------------------------dsrm-2nugB01 B:152-217                                            --- Pfam domains (1)
           Pfam domains (2) ----------------------------------Ribonuclease_3-2nugB04 B:37-121                                                      ------------------------------dsrm-2nugB02 B:152-217                                            --- Pfam domains (2)
         Sec.struct. author hhhhhhhhhh....hhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh...eeeeeeee.hhhhheeeeeeee..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
                 2nug B   3 MLEQLEKKLGYTFKDKSLLEKALTHVSYSKKEHYETLEFLGDALVNFFIVDLLVQYSPNKREGFLSPLKAYLISEEFFNLLAQKLELHKFIRIKRGKINETIIGDVFEALWAAVYIDSGRDANFTRELFYKLFKEDILSAIKEGRVKKDYKTILQEITQKRWKERPEYRLISVEGPHHKKKFIVEAKIKEYRTLGEGKSKKEAEQRAAEELIKLLEES 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
                                           
                 2nug C   2 AAGGUCAUUCG  12
                                    11

Chain D from PDB  Type:RNA  Length:11
                                           
                 2nug D   2 AAGGUCAUUCG  12
                                    11

Chain E from PDB  Type:RNA  Length:11
                                           
                 2nug E  17 AGUGGCCUUGC  27
                                    26

Chain F from PDB  Type:RNA  Length:11
                                           
                 2nug F  17 AGUGGCCUUGC  27
                                    26

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 2NUG)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: DSRM (45)

Family: dsrm (27)

Aquifex aeolicus (7)

1a	dsrm-2nugB01	B:152-217
1b	dsrm-2nugB02	B:152-217

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

Family: Ribonuclease_3 (11)

Aquifex aeolicus (9)

2a	Ribonuclease_3-2nugB03	B:37-121
2b	Ribonuclease_3-2nugB04	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 2nug)

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	2nug
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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 2nuf 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
2nuf

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 19)

Sites (19, 19)

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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