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(-) Description

Title :  CRYSTAL STRUCTURE OF JAPANESE PEAR S3-RNASE
 
Authors :  T. Matsuura, H. Sakai, S. Norioka
Date :  25 Jul 01  (Deposition) - 07 Nov 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Pyrus Pyrifolia, Japanese Pear, S-Rnase, Self-Incompatibility, T2 Family Ribonuclease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Matsuura, H. Sakai, M. Unno, K. Ida, M. Sato, F. Sakiyama, S. Norioka
Crystal Structure At 1. 5-A Resolution Of Pyrus Pyrifolia Pistil Ribonuclease Responsible For Gametophytic Self-Incompatibility.
J. Biol. Chem. V. 276 45261 2001
PubMed-ID: 11577107  |  Reference-DOI: 10.1074/JBC.M107617200

(-) Compounds

Molecule 1 - S3-RNASE
    Chains: A
    EC Number: 3.1.27.1
    Organism Scientific: PYRUS PYRIFOLIA
    Organism Taxid: 3767
    Synonym: RIBONUCLEASE S-3

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2MAN1Ligand/IonALPHA-D-MANNOSE
3NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
4XYP1Ligand/IonBETA-D-XYLOPYRANOSE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:116 , SER A:118 , ARG A:119 , NAG A:202 , HOH A:213 , HOH A:253 , HOH A:319 , HOH A:384 , HOH A:406BINDING SITE FOR RESIDUE NAG A 201
2AC2SOFTWARELEU A:29 , PRO A:128 , NAG A:201 , BMA A:203 , XYP A:205 , HOH A:329 , HOH A:384 , HOH A:405 , HOH A:421 , HOH A:430 , HOH A:455BINDING SITE FOR RESIDUE NAG A 202
3AC3SOFTWARENAG A:202 , MAN A:204 , XYP A:205 , HOH A:455BINDING SITE FOR RESIDUE BMA A 203
4AC4SOFTWAREBMA A:203 , XYP A:205BINDING SITE FOR RESIDUE MAN A 204
5AC5SOFTWARENAG A:202 , BMA A:203 , MAN A:204 , HOH A:455BINDING SITE FOR RESIDUE XYP A 205

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:15 -A:22
2A:48 -A:91
3A:155 -A:193
4A:170 -A:181

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Tyr A:93 -Pro A:94

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RNASE_T2_1PS00530 Ribonuclease T2 family histidine active site 1.RNS3_PYRPY52-59  1A:30-37

(-) Exons   (0, 0)

(no "Exon" information available for 1IQQ)

(-) 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:200
 aligned with RNS3_PYRPY | O80323 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:200
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222
           RNS3_PYRPY    23 YDYFQFTQQYQLAVCNSNRTLCKDPPDKLFTVHGLWPSNMVGPDPSKCPIKNIRKREKLLEHQLEIIWPNVFDRTKNNLFWDKEWMKHGSCGYPTIDNENHYFETVIKMYISKKQNVSRILSKAKIEPDGKKRALLDIENAIRNGADNKKPKLKCQKKGTTTELVEITLCSDKSGEHFIDCPHPFEPISPHYCPTNNIKY 222
               SCOP domains d1iqqa_ A: S3-RNase                                                                                                                                                                                      SCOP domains
               CATH domains 1iqqA00 A:1-200 Ribonuclease Rh; Chain A                                                                                                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeehhhh...............eeeeeeeee...................hhhhhhhhhh......hhhhhhhhhhhhhh.hhh.......hhhhhhhhhhhh......hhhhhhh........ee.hhhhhhhhh........eeeeeee..eeeeeeeeeee......ee..................ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------RNASE_T2------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iqq A   1 YDYFQFTQQYQLAVCNSNRTLCKDPPDKLFTVHGLWPSNMVGPDPSKCPIKNIRKREKLLEHQLEIIWPNVFDRTKNNLFWDKEWMKHGSCGYPTIDNENHYFETVIKMYISKKQNVSRILSKAKIEPDGKKRALLDIENAIRNGADNKKPKLKCQKKGTTTELVEITLCSDKSGEHFIDCPHPFEPISPHYCPTNNIKY 200
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
   Legend:   → Mismatch (orange background)
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  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
(-)
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 1IQQ)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RNS3_PYRPY | O80323)
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: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:0033897    ribonuclease T2 activity    Catalysis of the two-stage endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotides with 2',3'-cyclic phosphate intermediates.
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.

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