1RTU - JenaLib

Asym./Biol. Unit

Asym./Biol. Unit - sites

collapse

expand

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Description

Title :   USTILAGO SPHAEROGENA RIBONUCLEASE U2

Authors :   S. Noguchi, Y. Satow, T. Uchida, C. Sasaki, T. Matsuzaki

Date :   12 May 95 (Deposition) - 08 Nov 96 (Release) - 27 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym./Biol. Unit : A

Keywords :   Hydrolase, Endoribonuclease, Beta-Isomerized Aspartate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Noguchi, Y. Satow, T. Uchida, C. Sasaki, T. Matsuzaki
Crystal Structure Of Ustilago Sphaerogena Ribonuclease U2 A 1. 8 A Resolution.
Biochemistry V. 34 15583 1995
PubMed-ID: 7492561 | Reference-DOI: 10.1021/BI00047A025

Compounds

Molecule 1 - RIBONUCLEASE U2
	Atcc	:	12421
	Chains	:	A
	Organism Scientific	:	USTILAGO SPHAEROGENA
	Organism Taxid	:	5271

Structural Features

Chains, Units

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (2, 2)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	IAS	1	Mod. Amino Acid	BETA-L-ASPARTIC ACID
2	SO4	1	Ligand/Ion	SULFATE ION

Sites (2, 2)

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:39 , HIS A:41 , GLU A:62 , ARG A:85 , HIS A:101 , PHE A:110 , HOH A:396	BINDING SITE FOR RESIDUE SO4 A 201
2	CAT	UNKNOWN	TYR A:39 , HIS A:41 , GLU A:62 , ARG A:85 , HIS A:101	CATALYTIC SITE.

SS Bonds (3, 3)

Asymmetric/Biological Unit

No.	Residues
1	A:1	-	A:54
2	A:9	-	A:113
3	A:55	-	A:96

Cis Peptide Bonds (3, 3)

Asymmetric/Biological Unit

No.	Residues
1	Tyr A:39	-	Pro A:40
2	Gly A:58	-	Pro A:59
3	Gly A:69	-	Pro A:70

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 1RTU)

PROSITE Motifs (0, 0)

(no "PROSITE Motif" information available for 1RTU)

Exons (0, 0)

(no "Exon" information available for 1RTU)

Sequences/Alignments

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:114
 aligned with RNU2_USTSP | P00654 from UniProtKB/Swiss-Prot  Length:114

    Alignment length:114
                                    10        20        30        40        50        60        70        80        90       100       110    
           RNU2_USTSP     1 CDIPQSTNCGGNVYSNDDINTAIQGALDDVANGDRPDNYPHQYYDEASEDITLCCGSGPWSEFPLVYNGPYYSSRDNYVSPGPDRVIYQTNTGEFCATVTHTGAASYDGFTQCS 114
               SCOP domains d1rtua_ A: RNase U2                                                                                                SCOP domains
               CATH domains 1rtuA00 A:1-114  [code=3.10.450.30, no name defined]                                                               CATH domains
               Pfam domains ---Ribonuclease-1rtuA01 A:4-113                                                                                  - Pfam domains
         Sec.struct. author .....eeee..eeeehhhhhhhhhhhhhhhhh...hhh..eee................eeeee...................eeeeee.....eeeeee.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 1rtu A   1 CDIPQSTNCGGNVYSNDDINTAIQGALDDVANGDRPDNYPHQYYxEASEDITLCCGSGPWSEFPLVYNGPYYSSRDNYVSPGPDRVIYQTNTGEFCATVTHTGAASYDGFTQCS 114
                                    10        20        30        40    |   50        60        70        80        90       100       110    
                                                                       45-IAS

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Microbial ribonucleases (174)

Superfamily: Microbial ribonucleases (174)

Family: Fungal ribonucleases (79)

Protein domain: RNase U2 (5)

Ustilago sphaerogena [TaxId: 5271] (5)

d1rtua_

CATH Domains (1, 1)

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: Nuclear Transport Factor 2; Chain: A, (517)

Homologous Superfamily: [code=3.10.450.30, no name defined] (159)

Ustilago sphaerogena. Organism_taxid: 5271. (1)

1rtuA00

A:1-114

Pfam Domains (1, 1)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Ribonuclease] (57)

Family: Ribonuclease (57)

Ustilago sphaerogena (Smut fungus) (1)

Ribonuclease-1rtuA01

A:4-113

Gene Ontology (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (RNU2_USTSP | P00654)

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: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:0033899	ribonuclease U2 activity	Catalysis of the two-stage endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotides ending in Ap or Gp with 2',3'-cyclic phosphate intermediates.
	GO:0004540	ribonuclease activity	Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
biological process
	GO:0090501	RNA phosphodiester bond hydrolysis	The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
	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.

Visualization

Interactive Views

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		IAS	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		CAT	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Gly A:58 - Pro A:59	[ RasMol ]
		Gly A:69 - Pro A:70	[ RasMol ]
		Tyr A:39 - Pro A:40	[ RasMol ]

Still Images

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	1rtu
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	RNU2_USTSP \| P00654
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Analysis Tools

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	RNU2_USTSP \| P00654
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	RNU2_USTSP \| P00654	:	3agn 3ago 3ahs 3ahw

Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1RTU)