2PO0 - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE P. ABYSSI EXOSOME RNASE PH RING COMPLEXED WITH ADP IN DOUBLE CONFORMATION

Authors :   M. V. A. S. Navarro, B. G. Guimaraes

Date :   25 Apr 07 (Deposition) - 18 Mar 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (3x)

Keywords :   Rnase Ph, Hydrolase/Hydrolase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. V. A. S. Navarro, C. C. Oliveira, N. I. Zanchin, B. G. Guimaraes
Insights Into The Mechanism Of Progressive Rna Degradation By The Archaeal Exosome.
J. Biol. Chem. V. 283 14120 2008
PubMed-ID: 18353775 | Reference-DOI: 10.1074/JBC.M801005200
(for further references see the PDB file header)

Molecule 1 - PROBABLE EXOSOME COMPLEX EXONUCLEASE 1
	Chains	:	A
	EC Number	:	3.1.13.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET29
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	RRP41
	Organism Scientific	:	PYROCOCCUS ABYSSI
	Organism Taxid	:	29292

Molecule 2 - PROBABLE EXOSOME COMPLEX EXONUCLEASE 2
	Chains	:	B
	EC Number	:	3.1.13.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PAE
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	RRP42
	Organism Scientific	:	PYROCOCCUS ABYSSI
	Organism Taxid	:	29292

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (3x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	MPD	3	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL

Biological Unit 1 (2, 12)

No.	Name	Count	Type	Full Name
1	ADP	3	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	MPD	9	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	MET A:81 , ARG A:97 , ASP A:133 , ALA A:134 , GLY A:135 , THR A:136 , ARG A:137 , ASP A:180 , ASP A:186 , ASP A:204 , HOH A:301 , HOH A:302 , HOH A:303 , HOH A:339	BINDING SITE FOR RESIDUE ADP A 300
2	AC2	SOFTWARE	ASN A:181 , ALA A:185 , ASP A:204 , GLY A:205 , GLU B:116	BINDING SITE FOR RESIDUE MPD A 250
3	AC3	SOFTWARE	ASN B:203 , LEU B:205 , GLU B:246 , TYR B:249	BINDING SITE FOR RESIDUE MPD B 280
4	AC4	SOFTWARE	LEU B:162 , LYS B:191 , GLU B:227	BINDING SITE FOR RESIDUE MPD B 281

(no "SS Bond" information available for 2PO0)

Asymmetric Unit

No.	Residues
1	Asn A:14	-	Gly A:15
2	Tyr A:57	-	Gly A:58
3	Gly A:58	-	Pro A:59
4	His A:63	-	Pro A:64
5	Gln A:243	-	Glu A:244

(no "SAP(SNP)/Variant" information available for 2PO0)

(no "PROSITE Motif" information available for 2PO0)

(no "Exon" information available for 2PO0)

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:236
 aligned with RRP41_PYRAB | Q9V119 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:236
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238      
          RRP41_PYRAB     9 KLIDENGRRIDGRKKYELRPIKMEVGVLKNANGSAYIEWGKNKIIAAVYGPRELHPKHLQRPDRAILRVRYNMAPFSVEERKKPGPDRRSIEISKVIKGALEPALILEMFPRTAIDVFIEVLQADAGTRVAGITAASLALADAGIPMRDLVAACAAGKIEGEIVLDLNKEEDNYGEADVPVAIMPLKNDITLLQMDGYLTKDEFIEAVKLAIKGAKAVYQKQREALKEKYLKIAQE 244
               SCOP domains d2po0a1 A:9-153 automated matches                                                                                                                d2po0a2 A:154-244 automated matches                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee..ee...........eeeee.......eeeeeee..eeeeeeeeeeee............eeeeeeee.............hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeee...hhhhhhhhhhhhhhhhh........eeeeeeee..eeee..hhhhhhhh.eeeeeeeehhhheeeee..ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2po0 A   9 KLIDENGRRIDGRKKYELRPIKMEVGVLKNANGSAYIEWGKNKIIAAVYGPRELHPKHLQRPDRAILRVRYNMAPFSVEERKKPGPDRRSIEISKVIKGALEPALILEMFPRTAIDVFIEVLQADAGTRVAGITAASLALADAGIPMRDLVAACAAGKIEGEIVLDLNKEEDNYGEADVPVAIMPLKNDITLLQMDGYLTKDEFIEAVKLAIKGAKAVYQKQREALKEKYLKIAQE 244
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238

Chain B from PDB  Type:PROTEIN  Length:267
 aligned with RRP42_PYRAB | Q9V118 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:267
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       
          RRP42_PYRAB     8 AGIMRDHIINLLKEGKRIDDRGFEDYRPIEIEVGVIEKAEGSALVKLGSTQVLVGIKTSLGEPFPDTPNMGVMTTNVELVPLASPTFEPGPPDERAIELARVIDRGIRESKALNLEKMVIVPGKIVRVVFIDVHVLDHDGNLMDAIGIAAIAALLNARVPKVRYNEETGEVETLDETEPLPVEKIPVPVTFAKIGNILVVDPSLDEELVMDGKITITTDETGHISAVQKSEGGAFKLEEVMYAVETAFKKAEEIRKLILEAVEKAKQ 274
               SCOP domains d2po0b1 B:8-187 automated matches                                                                                                                                                   d2po0b2 B:188-274 automated matches                                                     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..............eeeee.......eeeeeee..eeeeeeeeeeee..........eeeeeeee.............hhhhhhhhhhhhhhhhhhh..hhhh.eee...eeeeeeeeeeeee...hhhhhhhhhhhhhhhhheeeeeee......eeeeeeeee.......eeeeeeee..eeee..hhhhhhhh.eeeeeee.....eeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2po0 B   8 AGIMRDHIINLLKEGKRIDDRGFEDYRPIEIEVGVIEKAEGSALVKLGSTQVLVGIKTSLGEPFPDTPNMGVMTTNVELVPLASPTFEPGPPDERAIELARVIDRGIRESKALNLEKMVIVPGKIVRVVFIDVHVLDHDGNLMDAIGIAAIAALLNARVPKVRYNEETGEVETLDETEPLPVEKIPVPVTFAKIGNILVVDPSLDEELVMDGKITITTDETGHISAVQKSEGGAFKLEEVMYAVETAFKKAEEIRKLILEAVEKAKQ 274
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267

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(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Ribonuclease PH domain 2-like (52)

Superfamily: Ribonuclease PH domain 2-like (52)

Family: automated matches (11)

Protein domain: automated matches (11)

Pyrococcus abyssi [TaxId: 29292] (4)

1a	d2po0a2	A:154-244
1b	d2po0b2	B:188-274

Fold: Ribosomal protein S5 domain 2-like (306)

Superfamily: Ribosomal protein S5 domain 2-like (306)

Family: automated matches (39)

Protein domain: automated matches (39)

Pyrococcus abyssi [TaxId: 29292] (4)

2a	d2po0a1	A:9-153
2b	d2po0b1	B:8-187

(no "CATH Domain" information available for 2PO0)

(no "Pfam Domain" information available for 2PO0)

Asymmetric Unit(hide GO term definitions)

Chain A (RRP41_PYRAB | Q9V119)

molecular function
	GO:0000175	3'-5'-exoribonuclease activity	Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of an RNA molecule.
	GO:0004527	exonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
	GO:0016896	exoribonuclease activity, producing 5'-phosphomonoesters	Catalysis of the hydrolysis of ester linkages within ribonucleic acids by removing nucleotide residues from the 3' or 5' end to yield 5' phosphomonoesters.
	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:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
biological process
	GO:0006401	RNA catabolic process	The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
	GO:0090503	RNA phosphodiester bond hydrolysis, exonucleolytic	The chemical reactions and pathways involving the hydrolysis of terminal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0000178	exosome (RNase complex)	A ribonuclease complex that has 3-prime to 5-prime exoribonuclease activity and possibly endoribonuclease activity, producing 5-prime-phosphomonoesters. Participates in a multitude of cellular RNA processing and degradation events preventing nuclear export and/or translation of aberrant RNAs. Restricted to processing linear and circular single-stranded RNAs (ssRNA) only. RNAs with complex secondary structures may have to be unwound or pre-processed by co-factors prior to entering the complex, esp if the 3-prime end is structured.

Chain B (RRP42_PYRAB | Q9V118)

biological process
	GO:0006401	RNA catabolic process	The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0000178	exosome (RNase complex)	A ribonuclease complex that has 3-prime to 5-prime exoribonuclease activity and possibly endoribonuclease activity, producing 5-prime-phosphomonoesters. Participates in a multitude of cellular RNA processing and degradation events preventing nuclear export and/or translation of aberrant RNAs. Restricted to processing linear and circular single-stranded RNAs (ssRNA) only. RNAs with complex secondary structures may have to be unwound or pre-processed by co-factors prior to entering the complex, esp if the 3-prime end is structured.

Asymmetric Unit
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	Cis Peptide Bonds
		Asn A:14 - Gly A:15	[ RasMol ]
		Gln A:243 - Glu A:244	[ RasMol ]
		Gly A:58 - Pro A:59	[ RasMol ]
		His A:63 - Pro A:64	[ RasMol ]
		Tyr A:57 - Gly A:58	[ RasMol ]

Biological Unit
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	2po0
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	RRP41_PYRAB \| Q9V119
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	RRP42_PYRAB \| Q9V118
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	3.1.13.-
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UniProtKB/Swiss-Prot
	RRP41_PYRAB \| Q9V119	:	2pnz 2po1 2po2
	RRP42_PYRAB \| Q9V118	:	2pnz 2po1 2po2

2pnz	CRYSTAL STRUCTURE OF THE P. ABYSSI EXOSOME RNASE PH RING COMPLEXED WITH UDP AND GMP
2po1	CRYSTAL STRUCTURE OF THE P. ABYSSI EXOSOME RNASE PH RING COMPLEXED WITH A SINGLE STRANDED 10-MER POLY(A) RNA
2po2	CRYSTAL STRUCTURE OF THE P. ABYSSI EXOSOME RNASE PH RING COMPLEXED WITH CDP

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (5, 5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 4)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (10, 13)

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