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(-) Description

Title :  CRYSTAL STRUCTURE OF RIBONUCLEASE MS (AS RIBONUCLEASE T1 HOMOLOGUE) COMPLEXED WITH A GUANYLYL-3',5'-CYTIDINE ANALOGUE
 
Authors :  T. Nonaka, K. T. Nakamura, Y. Mitsui
Date :  14 May 93  (Deposition) - 31 Oct 93  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase(Endoribonuclease) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Nonaka, K. T. Nakamura, S. Uesugi, M. Ikehara, M. Irie, Y. Mitsui
Crystal Structure Of Ribonuclease Ms (As A Ribonuclease T1 Homologue) Complexed With A Guanylyl-3', 5'-Cytidine Analogue.
Biochemistry V. 32 11825 1993
PubMed-ID: 8218254  |  Reference-DOI: 10.1021/BI00095A011
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBONUCLEASE MS
    Chains: A
    EC Number: 3.1.27.3
    Engineered: YES
    Organism Scientific: ASPERGILLUS PHOENICIS
    Organism Taxid: 5063

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1GPC1Ligand/Ion2'-FLUOROGUANYLYL-(3'-5')-PHOSPHOCYTIDINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:1 , TRP A:13 , TYR A:37 , HIS A:39 , GLU A:40 , TYR A:41 , HIS A:42 , ASP A:43 , TYR A:44 , GLU A:45 , GLU A:57 , PRO A:72 , GLY A:73 , ALA A:74 , ARG A:76 , HIS A:91 , GLY A:96 , ASP A:97 , PHE A:99 , CYS A:102 , HOH A:135BINDING SITE FOR RESIDUE GPC A 106

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:3 -A:11
2A:7 -A:102

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:37 -Pro A:38
2Gly A:53 -Thr A:54

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1RDS)

(-) 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:105
 aligned with RNMS_ASPPH | P00653 from UniProtKB/Swiss-Prot  Length:105

    Alignment length:105
                                    10        20        30        40        50        60        70        80        90       100     
           RNMS_ASPPH     1 ESCEYTCGSTCYWSSDVSAAKAKGYSLYESGDTIDDYPHGYHDYEGFDFPVSGTYYEYPIMSDYDVYTGGSPGADRVIFNGDDELAGVITHTGASGDDFVACSSS 105
               SCOP domains d1rdsa_ A: RNase Ms                                                                                       SCOP domains
               CATH domains 1rdsA00 A:1-105  [code=3.10.450.30, no name defined]                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eee.hhhhhhhhhhhhhhhhh........eee.............eeeeee..............eeeeee..eeeeeeee.........eeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 1rds A   1 ESCEYTCGSTCYWSSDVSAAKAKGYSLYESGDTIDDYPHEYHDYEGFDFPVSGTYYEYPIMSDYDVYTGGSPGADRVIFNGDDELAGVITHTGASGDDFVACSSS 105
                                    10        20        30        40        50        60        70        80        90       100
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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
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1RDS)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RNMS_ASPPH | P00653)
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:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0046589    ribonuclease T1 activity    Catalysis of the endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotides ending in 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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