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(-) Description

Title :  CRYSTAL STRUCTURE OF THE NICOTIANA GLUTINOSA RIBONUCLEASE NW
 
Authors :  S. Kawano, Y. Kakuta, M. Kimura
Date :  05 Aug 02  (Deposition) - 05 Aug 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase, Ribonuclease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Kawano, Y. Kakuta, M. Kimura
Guanine Binding Site Of The Nicotiana Glutinosa Ribonuclease Nw Revealed By X-Ray Crystallography
Biochemistry V. 41 15195 2002
PubMed-ID: 12484757  |  Reference-DOI: 10.1021/BI026247L
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBONUCLEASE
    Chains: A, B
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Plasmid: PPIC9K
    Expression System Taxid: 4922
    Expression System Vector Type: PLASMID
    Organism Scientific: NICOTIANA GLUTINOSA
    Organism Taxid: 35889
    Synonym: RIBONUCLEASE M5

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
15GP2Ligand/IonGUANOSINE-5'-MONOPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:12 , TYR A:17 , HIS A:39 , TRP A:42 , THR A:78 , LEU A:79 , ALA A:80 , PHE A:89 , HIS A:92 , GLU A:93 , LYS A:96 , HIS A:97 , HOH A:1443 , HOH A:1472 , HOH A:1482BINDING SITE FOR RESIDUE 5GP A 1295
2AC2SOFTWAREGLN B:12 , TYR B:17 , HIS B:39 , TRP B:42 , THR B:78 , LEU B:79 , ALA B:80 , PHE B:89 , HIS B:92 , GLU B:93 , LYS B:96 , HIS B:97 , TYR B:171 , HOH B:1443 , HOH B:1465 , HOH B:1489BINDING SITE FOR RESIDUE 5GP B 1296

(-) SS Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1A:18 -A:24
2A:25 -A:81
3A:54 -A:100
4A:160 -A:195
5A:176 -A:187
6B:18 -B:24
7B:25 -B:81
8B:54 -B:100
9B:160 -B:195
10B:176 -B:187

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Cys A:81 -Pro A:82
2Cys B:81 -Pro B:82

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1IYB)

(-) 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:208
 aligned with Q7XZV5_NICGU | Q7XZV5 from UniProtKB/TrEMBL  Length:229

    Alignment length:208
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221        
         Q7XZV5_NICGU    22 VLTAAQDFDFFYFVQQWPGSYCDTKQSCCYPKTGKPASDFGIHGLWPNNNDGSYPSNCDSNSPYDQSQVSDLISRMQQNWPTLACPSGTGSAFWSHEWEKHGTCAENVFDQHGYFKKALDLKNQINLLEILQGAGINPDGGFYSLNSIKNAIRSAIGYAPGIECNVDESGNSQLYQIYICVDGSGSNLIECPIFPRGKCGSSIEFPTF 229
               SCOP domains d1iyba_ A: RNase NW                                                                                                                                                                                              SCOP domains
               CATH domains 1iybA00 A:-3-204 Ribonuclease Rh; Chain A                                                                                                                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeehhhhhh..................eeeeeeee................hhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.......eeehhhhhhhhhhhhh...eeeeee.....eeeeeeeeeee...................eee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iyb A  -3 YVEFAQDFDFFYFVQQWPGSYCDTKQSCCYPKTGKPASDFGIHGLWPNNNDGSYPSNCDSNSPYDQSQVSDLISRMQQNWPTLACPSGTGSAFWSHEWEKHGTCAENVFDQHGYFKKALDLKNQINLLEILQGAGIHPDGGFYSLNSIKNAIRSAIGYAPGIECNVDESGNSQLYQIYICVDGSGSNLIECPIFPRGKCGSSIEFPTF 204
                                     6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196        


Chain B from PDB  Type:PROTEIN  Length:208
 aligned with Q7XZV5_NICGU | Q7XZV5 from UniProtKB/TrEMBL  Length:229

    Alignment length:208
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221        
         Q7XZV5_NICGU    22 VLTAAQDFDFFYFVQQWPGSYCDTKQSCCYPKTGKPASDFGIHGLWPNNNDGSYPSNCDSNSPYDQSQVSDLISRMQQNWPTLACPSGTGSAFWSHEWEKHGTCAENVFDQHGYFKKALDLKNQINLLEILQGAGINPDGGFYSLNSIKNAIRSAIGYAPGIECNVDESGNSQLYQIYICVDGSGSNLIECPIFPRGKCGSSIEFPTF 229
               SCOP domains d1iybb_ B: RNase NW                                                                                                                                                                                              SCOP domains
               CATH domains 1iybB00 B:-3-204 Ribonuclease Rh; Chain A                                                                                                                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeehhhhhh..................eeeeeeee................hhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.......eeehhhhhhhhhhhhh...eeeeee.....eeeeeeeeeee...................eee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1iyb B  -3 YVEFAQDFDFFYFVQQWPGSYCDTKQSCCYPKTGKPASDFGIHGLWPNNNDGSYPSNCDSNSPYDQSQVSDLISRMQQNWPTLACPSGTGSAFWSHEWEKHGTCAENVFDQHGYFKKALDLKNQINLLEILQGAGIHPDGGFYSLNSIKNAIRSAIGYAPGIECNVDESGNSQLYQIYICVDGSGSNLIECPIFPRGKCGSSIEFPTF 204
                                     6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196
   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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q7XZV5_NICGU | Q7XZV5)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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.

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