2C1W - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   THE STRUCTURE OF XENDOU: A SPLICING INDEPENDENT SNORNA PROCESSING ENDORIBONUCLEASE

Authors :   F. Renzi, E. Caffarelli, P. Laneve, I. Bozzoni, M. Brunori, B. Vallone

Date :   21 Sep 05 (Deposition) - 20 Jul 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)

Keywords :   Nuclease, Snorna, Endoribonuclease, Splicing Independent Processing (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. Renzi, E. Caffarelli, P. Laneve, I. Bozzoni, M. Brunori, B. Vallone
The Structure Of The Endoribonuclease Xendou: From Small Nucleolar Rna Processing To Severe Acute Respiratory Syndrome Coronavirus Replication.
Proc. Natl. Acad. Sci. Usa V. 103 12365 2006
PubMed-ID: 16895992 | Reference-DOI: 10.1073/PNAS.0602426103

Molecule 1 - ENDOU PROTEIN
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PQE30
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Variant	:	PLYSS
	Expression System Vector Type	:	PLASMID
	Organism Common	:	AFRICAN CLAWED FROG
	Organism Scientific	:	XENOPUS LAEVIS
	Organism Taxid	:	8355
	Synonym	:	XENDOU

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	PO4	3	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	PO4	1	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:149 , HIS A:162 , ASN A:270 , HIS A:272 , THR A:278 , HOH A:2161	BINDING SITE FOR RESIDUE PO4 A1290
2	AC2	SOFTWARE	ARG B:149 , HIS B:272 , GLY B:277 , THR B:278	BINDING SITE FOR RESIDUE PO4 B1290
3	AC3	SOFTWARE	ARG C:149 , HIS C:162 , ASN C:270 , HIS C:272 , GLY C:277 , THR C:278	BINDING SITE FOR RESIDUE PO4 C1288

(no "SS Bond" information available for 2C1W)

(no "Cis Peptide Bond" information available for 2C1W)

(no "SAP(SNP)/Variant" information available for 2C1W)

(no "PROSITE Motif" information available for 2C1W)

(no "Exon" information available for 2C1W)

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:273
 aligned with ENDUA_XENLA | Q8JFY9 from UniProtKB/Swiss-Prot  Length:292

    Alignment length:284
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285    
          ENDUA_XENLA     6 GQLNHELSKLFNELWDADQNRMKSGKDYRISLQGKAGYVPAGSNQARDSASFPLFQFVDEEKLKSRKTFATFISLLDNYEMDTGVAEVVTPEEIAENNNFLDAILETKVMKMAHDYLVRKNQAKPTRNDFKVQLYNIWFQLYSRAPGSRPDSCGFEHVFVGESKRGQEMMGLHNWVQFYLQEKRKNIDYKGYVARQNKSRPDEDDQVLNLQFNWKEMVKPVGSSFIGVSPEFEFALYTIVFLASQEKMSREVVRLEEYELQIVVNRHGRYIGTAYPVLLSTNNP 289
               SCOP domains d2c1wa1 A:6-289 EndoU                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh..........eee.........---------......eeeehhhhhh...hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh....--......hhhhhhh..............hhhhhhhhhhh..eeeeee..............eeeeeeee.......eeee...hhhhhhhhhhhhhhh....eeeeeeee..eeeeeeeeee..eeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c1w A   6 GQLNHELSKLFNELWDADQNRMKSGKDYRISLQGKAGYV---------SASFPLFQFVDEEKLKSRKTFATFISLLDNYEMDTGVAEVVTPEEIAENNNFLDAILETKVMKMAHDYLVRKNQAKPTRNDFKVQLYNIWFQLYSR--GSRPDSCGFEHVFVGESKRGQEMMGLHNWVQFYLQEKRKNIDYKGYVARQNKSRPDEDDQVLNLQFNWKEMVKPVGSSFIGVSPEFEFALYTIVFLASQEKMSREVVRLEEYELQIVVNRHGRYIGTAYPVLLSTNNP 289
                                    15        25        35        |-        55        65        75        85        95       105       115       125       135       145   |  |155       165       175       185       195       205       215       225       235       245       255       265       275       285    
                                                                 44        54                                                                                            149  |                                                                                                                                         
                                                                                                                                                                            152

Chain B from PDB  Type:PROTEIN  Length:276
 aligned with ENDUA_XENLA | Q8JFY9 from UniProtKB/Swiss-Prot  Length:292

    Alignment length:284
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285    
          ENDUA_XENLA     6 GQLNHELSKLFNELWDADQNRMKSGKDYRISLQGKAGYVPAGSNQARDSASFPLFQFVDEEKLKSRKTFATFISLLDNYEMDTGVAEVVTPEEIAENNNFLDAILETKVMKMAHDYLVRKNQAKPTRNDFKVQLYNIWFQLYSRAPGSRPDSCGFEHVFVGESKRGQEMMGLHNWVQFYLQEKRKNIDYKGYVARQNKSRPDEDDQVLNLQFNWKEMVKPVGSSFIGVSPEFEFALYTIVFLASQEKMSREVVRLEEYELQIVVNRHGRYIGTAYPVLLSTNNP 289
               SCOP domains d2c1wb_ B: automated matches                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh..........eee..........--------......eeeehhhhhh...hhhhhhhhhhhh..........hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.............hhhhhhh..............hhhhhhhhhhh..eeeeee..............eeeeeeee..ee...eeee...hhhhhhhhhhhhhhh....eeeeeeee..eeeeeeeeee..eeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c1w B   6 GQLNHELSKLFNELWDADQNRMKSGKDYRISLQGKAGYVP--------SASFPLFQFVDEEKLKSRKTFATFISLLDNYEMDTGVAEVVTPEEIAENNNFLDAILETKVMKMAHDYLVRKNQAKPTRNDFKVQLYNIWFQLYSRAPGSRPDSCGFEHVFVGESKRGQEMMGLHNWVQFYLQEKRKNIDYKGYVARQNKSRPDEDDQVLNLQFNWKEMVKPVGSSFIGVSPEFEFALYTIVFLASQEKMSREVVRLEEYELQIVVNRHGRYIGTAYPVLLSTNNP 289
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285    
                                                                  45       54

Chain C from PDB  Type:PROTEIN  Length:271
 aligned with ENDUA_XENLA | Q8JFY9 from UniProtKB/Swiss-Prot  Length:292

    Alignment length:282
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285  
          ENDUA_XENLA     6 GQLNHELSKLFNELWDADQNRMKSGKDYRISLQGKAGYVPAGSNQARDSASFPLFQFVDEEKLKSRKTFATFISLLDNYEMDTGVAEVVTPEEIAENNNFLDAILETKVMKMAHDYLVRKNQAKPTRNDFKVQLYNIWFQLYSRAPGSRPDSCGFEHVFVGESKRGQEMMGLHNWVQFYLQEKRKNIDYKGYVARQNKSRPDEDDQVLNLQFNWKEMVKPVGSSFIGVSPEFEFALYTIVFLASQEKMSREVVRLEEYELQIVVNRHGRYIGTAYPVLLSTN 287
               SCOP domains d2c1wc_ C: automated matches                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh..........eee.........-----------....eeeehhhhhhh..hhhhhhhhhhhh..........hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.............hhhhhhh..............hhhhhhhhhhh..eeeeee..............eeeeeeee.......eeee...hhhhhhhhhhhhhhh....eeeeeeee..eeeeeeeeee..eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2c1w C   6 GQLNHELSKLFNELWDADQNRMKSGKDYRISLQGKAGYV-----------SFPLFQFVDEEKLKSRKTFATFISLLDNYEMDTGVAEVVTPEEIAENNNFLDAILETKVMKMAHDYLVRKNQAKPTRNDFKVQLYNIWFQLYSRAPGSRPDSCGFEHVFVGESKRGQEMMGLHNWVQFYLQEKRKNIDYKGYVARQNKSRPDEDDQVLNLQFNWKEMVKPVGSSFIGVSPEFEFALYTIVFLASQEKMSREVVRLEEYELQIVVNRHGRYIGTAYPVLLSTN 287
                                    15        25        35        |-         -|       65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285  
                                                                 44          56

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: EndoU-like (7)

Superfamily: EndoU-like (7)

Family: Eukaryotic EndoU ribonuclease (2)

Protein domain: automated matches (1)

African clawed frog (Xenopus laevis) [TaxId: 8355] (1)

1a	d2c1wb_	B:
1b	d2c1wc_	C:

Protein domain: EndoU (1)

African clawed frog (Xenopus laevis) [TaxId: 8355] (1)

d2c1wa1

A:6-289

(no "CATH Domain" information available for 2C1W)

(no "Pfam Domain" information available for 2C1W)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (ENDUA_XENLA | Q8JFY9)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	GO:0004521	endoribonuclease activity	Catalysis of the hydrolysis of ester linkages within ribonucleic acid 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:0016788	hydrolase activity, acting on ester bonds	Catalysis of the hydrolysis of any ester bond.
	GO:0030145	manganese ion binding	Interacting selectively and non-covalently with manganese (Mn) ions.
	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.
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:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
	GO:0043144	snoRNA processing	Any process involved in the conversion of a primary small nucleolar RNA (snoRNA) transcript into a mature snoRNA.
cellular component
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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2c09	THE CRYSTAL STRUCTURE OF XENDOU, A SPLICING INDEPENDENT SNORNA PROCESSING ENDORIBONUCLEASE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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