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(-) Description

Title :  CRYSTAL STRUCTURE OF THE RNASE NT IN COMPLEX WITH 5'-GMP
 
Authors :  S. Kawano, Y. Kakuta, M. Kimura
Date :  17 Mar 04  (Deposition) - 26 Apr 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Ribonuclease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Kawano, Y. Kakuta, M. Kimura
Crystal Structure Of The Nicotiana Glutinosa Ribonuclease Nt In Complex With Nucleotide Monophosphates
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RNASE NGR3
    Chains: A
    EC Number: 3.1.27.1
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Plasmid: PPIC9K
    Expression System Strain: GS115
    Expression System Taxid: 4922
    Expression System Vector Type: PLASMID
    Organism Scientific: NICOTIANA GLUTINOSA
    Organism Taxid: 35889
    Synonym: RIBONUCLEASE NT, RNASE NT
    Tissue: LEAVES

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

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
1AC1SOFTWARETYR A:8 , TRP A:42 , PRO A:43 , ASN A:44 , TRP A:50 , LYS A:96 , HIS A:97 , 5GP A:296 , HOH A:317 , HOH A:382BINDING SITE FOR RESIDUE 5GP A 295
2AC2SOFTWAREGLN A:12 , TYR A:17 , HIS A:39 , TRP A:42 , PRO A:77 , SER A:78 , LEU A:79 , ALA A:80 , PHE A:89 , HIS A:92 , GLU A:93 , LYS A:96 , HIS A:97 , ASN A:127 , TYR A:170 , 5GP A:295 , HOH A:381 , HOH A:384BINDING SITE FOR RESIDUE 5GP A 296

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:18 -A:24
2A:25 -A:81
3A:54 -A:100
4A:159 -A:195
5A:175 -A:186

(-) Cis Peptide Bonds  (1, 1)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1VCZ)

(-) 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:204
 aligned with Q9SSV1_NICGU | Q9SSV1 from UniProtKB/TrEMBL  Length:236

    Alignment length:204
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223    
         Q9SSV1_NICGU    24 AQDFDFFYFVQQWPASYCDTRRSCCYPTTGKPDEDFSIHGLWPNYENGKWPQNCDRESSLDESEISDLISTMEKNWPSLACPSSDGVRFWSHEWLKHGTCSALGERAYFQAALDFRKKSNLLENLKNAEITPRNGEHYTLESIKKAIEEGVGHSPYIECNVDTQGNHQIYQVYLCVDKTATDFIDCPIFPHGRGCGSKIEFPPF 227
               SCOP domains d1vcza_ A: automated matches                                                                                                                                                                                 SCOP domains
               CATH domains 1vczA00 A:1-204 Ribonuclease Rh; Chain A                                                                                                                                                                     CATH domains
               Pfam domains ---Ribonuclease_T2-1vczA01 A:4-188                                                                                                                                                          ---------------- Pfam domains
         Sec.struct. author .....eeeeeeehhhhhh..................eeeeeeee................hhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeehhhhhhhhhhhhh...eeeeee.....eeeeeeeeeee.....ee.............eeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vcz A   1 AQDFDFFYFVQQWPASYCDTRRSCCYPTTGKPDEDFSIHGLWPNYENGKWPQNCDRESSLDESEISDLISTMEKNWPSLACPSSDGVRFWSHEWLKHGTCSALGERAYFQAALDFRKKSNLLENLKNAEITPRNGEHYTLESIKKAIEEGVGHSPYIECNVDTQGNHQIYQVYLCVDKTATDFIDCPIFPHGRGCGSKIEFPPF 204
                                    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  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Ribonuclease_T2] (11)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9SSV1_NICGU | Q9SSV1)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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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 Related Entries

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

UniProtKB/TrEMBL
        Q9SSV1_NICGU | Q9SSV1: 1vd1 1vd3

(-) Related Entries Specified in the PDB File

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