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(-) Description

Title :  CRYSTAL STRUCTURE OF USTILAGO SPHAEROGENA RIBONUCLEASE U2 COMPLEXED WITH ADENOSINE 3'-MONOPHOSPHATE
 
Authors :  S. Noguchi
Date :  03 Apr 10  (Deposition) - 07 Jul 10  (Release) - 04 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  0.96
Chains :  Asym./Biol. Unit :  A
Keywords :  Purine-Specific Endo-Ribonuclease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Noguchi
Isomerization Mechanism Of Aspartate To Isoaspartate Implie By Structures Of Ustilago Sphaerogena Ribonuclease U2 Complexed With Adenosine 3'-Monophosphate
Acta Crystallogr. , Sect. D V. 66 843 2010
PubMed-ID: 20606265  |  Reference-DOI: 10.1107/S0907444910019621

(-) Compounds

Molecule 1 - RIBONUCLEASE U2
    ChainsA
    EC Number3.1.27.4
    Organism CommonSMUT FUNGUS
    Organism ScientificUSTILAGO SPHAEROGENA
    Organism Taxid5271
    SynonymRNASE U2

 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.NameCountTypeFull Name
13AM1Ligand/Ion[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-4-HYDROXY-2-(HYDROXYMETHYL)OXOLAN-3-YL] DIHYDROGEN PHOSPHATE
2CA1Ligand/IonCALCIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:39 , HIS A:41 , GLN A:42 , TYR A:43 , TYR A:44 , GLU A:46 , GLU A:49 , GLU A:62 , ARG A:85 , HIS A:101 , ASP A:108 , PHE A:110 , HOH A:180 , HOH A:238 , HOH A:240 , HOH A:246 , HOH A:247BINDING SITE FOR RESIDUE 3AM A 115
2AC2SOFTWAREASP A:50 , GLN A:112 , HOH A:163 , HOH A:164 , HOH A:165 , HOH A:166 , HOH A:279BINDING SITE FOR RESIDUE CA A 116

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:1 -A:54
2A:9 -A:113
3A:55 -A:96

(-) Cis Peptide Bonds  (3, 3)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3AGN)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3AGN)

(-) Exons   (0, 0)

(no "Exon" information available for 3AGN)

(-) 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 d3agna_ A: RNase U2                                                                                                SCOP domains
               CATH domains 3agnA00 A:1-114  [code=3.10.450.30, no name defined]                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeee..eeeehhhhhhhhhhhhhhhhh..hhhhh.eee..hhhhh.........eeeee...................eeeeee.....eeeeee..........ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 3agn A   1 CDIPQSTNCGGNVYSNDDINTAIQGALDDVANGDRPDNYPHQYYDEASEDITLCCGSGPWSEFPLVYNGPYYSSRDNYVSPGPDRVIYQTNTGEFCATVTHTGAASYDGFTQCS 114
                                    10        20        30        40        50        60        70        80        90       100       110    

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  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

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3AGN)

(-) 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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        RNU2_USTSP | P006541rtu 3ago 3ahs 3ahw

(-) Related Entries Specified in the PDB File

1rtu THE SAME PROTEIN, ASP45 OF WHICH IS ISOMERIZED TO ISOASPARTATE
3ago CRYSTAL STRUCTURE OF USTILAGO SPHAEROGENA RIBONUCLEASE U2 COMPLEXED WITH ADENOSINE 3'-MONOPHOSPHATE