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(-) Description

Title :  X-RAY STRUCTURE OF FULLY GLYCOSYLATED BIFUNCTIONAL NUCLEASE TBN1 FROM SOLANUM LYCOPERSICUM (TOMATO)
 
Authors :  T. Koval, A. Stepankova, P. Lipovova, T. Podzimek, J. Matousek, J. Dusk T. Skalova, J. Hasek, J. Dohnalek
Date :  29 Jun 11  (Deposition) - 04 Jul 12  (Release) - 20 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.16
Chains :  Asym./Biol. Unit :  A
Keywords :  Mainly Alpha Helical, Trinuclear Metal Centre, Bi-Functional, Endonuclease, 3'-Nucleotidase, Nucleic Acids, Mononucleotides, Cytosol Membrane Associated, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Koval', P. Lipovova, T. Podzimek, J. Matousek, J. Duskova, T. Skalova, A. Stepankova, J. Hasek, J. Dohnalek
Plant Multifunctional Nuclease Tbn1 With Unexpected Phospholipase Activity: Structural Study And Reaction-Mechanism Analysis.
Acta Crystallogr. , Sect. D V. 69 213 2013
PubMed-ID: 23385457  |  Reference-DOI: 10.1107/S0907444912043697

(-) Compounds

Molecule 1 - NUCLEASE
    Chains: A
    EC Number: 3.1.30.-
    Engineered: YES
    Expression System: NICOTIANA BENTHAMIANA
    Expression System Plasmid: PLV07
    Expression System Taxid: 4100
    Expression System Vector Type: PLASMID
    Fragment: MATURE ENZYME NUCLEASE, UNP RESIDUES 26-302
    Gene: TBN1
    Organism Common: TOMATO
    Organism Scientific: SOLANUM LYCOPERSICUM
    Organism Taxid: 4081
    Strain: CV. RUTGERS

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 16)

Asymmetric/Biological Unit (7, 16)
No.NameCountTypeFull Name
1BMA3Ligand/IonBETA-D-MANNOSE
2BTB1Ligand/Ion2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
3CL1Ligand/IonCHLORIDE ION
4MAN1Ligand/IonALPHA-D-MANNOSE
5NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
6SO41Ligand/IonSULFATE ION
7ZN3Ligand/IonZINC ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:26 , HIS A:31 , SER A:132 , ASP A:151 , ZN A:402 , HOH A:701BINDING SITE FOR RESIDUE ZN A 401
02AC2SOFTWAREASP A:70 , HIS A:85 , HIS A:147 , ASP A:151 , ZN A:401 , HOH A:701BINDING SITE FOR RESIDUE ZN A 402
03AC3SOFTWARESER A:132 , HIS A:157 , HIS A:181 , ASP A:185 , SO4 A:601BINDING SITE FOR RESIDUE ZN A 403
04AC4SOFTWARETRP A:80 , LEU A:84 , ASP A:110 , MET A:111 , ALA A:116 , ASN A:119 , PHE A:120 , GLN A:123 , NAG A:502BINDING SITE FOR RESIDUE NAG A 501
05AC5SOFTWARETRP A:80 , ARG A:135 , NAG A:501 , BMA A:503BINDING SITE FOR RESIDUE NAG A 502
06AC6SOFTWARENAG A:502 , HOH A:708 , HOH A:731BINDING SITE FOR RESIDUE BMA A 503
07AC7SOFTWARETRP A:68 , LYS A:79 , SER A:82 , ASN A:137 , GLU A:140 , NAG A:512 , HOH A:725 , HOH A:735BINDING SITE FOR RESIDUE NAG A 511
08AC8SOFTWAREPRO A:55 , TYR A:57 , LYS A:79 , LEU A:143 , NAG A:511 , BMA A:513 , CL A:602 , HOH A:735BINDING SITE FOR RESIDUE NAG A 512
09AC9SOFTWARENAG A:512 , MAN A:514BINDING SITE FOR RESIDUE BMA A 513
10BC1SOFTWAREBMA A:513BINDING SITE FOR RESIDUE MAN A 514
11BC2SOFTWARETYR A:197 , LEU A:204 , ASN A:211 , ILE A:216 , NAG A:522BINDING SITE FOR RESIDUE NAG A 521
12BC3SOFTWARETYR A:196 , NAG A:521 , BMA A:523BINDING SITE FOR RESIDUE NAG A 522
13BC4SOFTWARETYR A:196 , NAG A:522BINDING SITE FOR RESIDUE BMA A 523
14BC5SOFTWAREARG A:73 , HIS A:85 , PHE A:86 , SER A:132 , ARG A:134 , HIS A:157 , ASN A:167 , HIS A:181 , ZN A:403BINDING SITE FOR RESIDUE SO4 A 601
15BC6SOFTWARETRP A:68 , NAG A:512BINDING SITE FOR RESIDUE CL A 602
16BC7SOFTWAREASP A:97 , GLU A:99 , GLN A:118 , ASN A:229 , PHE A:231 , HOH A:807 , HOH A:821 , HOH A:826 , HOH A:827BINDING SITE FOR RESIDUE BTB A 603

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:35 -A:66
2A:94 -A:246
3A:102 -A:112
4A:227 -A:233

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3SNG)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3SNG)

(-) 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:267
 aligned with Q0KFV0_SOLLC | Q0KFV0 from UniProtKB/TrEMBL  Length:302

    Alignment length:267
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       
         Q0KFV0_SOLLC    26 WSKEGHVMTCRIAQGLLNDEAAHAVKMLLPEYVNGDLSALCVWPDQVRHWYKYKWTSPLHFIDTPDKACNFDYERDCHDQHGVKDMCVAGAIQNFTTQLSHYREGTSDRRYNMTEALLFLSHFMGDIHQPMHVGFTSDAGGNSIDLRWFRHKSNLHHVWDREIILTAAKDYYAKDINLLEEDIEGNFTDGIWSDDLASWRECGNVFSCVNKFATESINIACKWGYKGVEAGETLSDDYFNSRLPIVMKRVAQGGIRLAMLLNNVFGA 292
               SCOP domains d3snga_ A: automated matches                                                                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhhhhhhhhhh..........hhhhhh.........hhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhh..........eeee..eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.....hhhhhhh..hhhhhhhhhhhhhhhhhhhh.........eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sng A  26 WSKEGHVMTCRIAQGLLNDEAAHAVKMLLPEYVNGDLSALCVWPDQVRHWYKYKWTSPLHFIDTPDKACNFDYERDCHDQHGVKDMCVAGAIQNFTTQLSHYREGTSDRRYNMTEALLFLSHFMGDIHQPMHVGFTSDAGGNSIDLRWFRHKSNLHHVWDREIILTAAKDYYAKDINLLEEDIEGNFTDGIWSDDLASWRECGNVFSCVNKFATESINIACKWGYKGVEAGETLSDDYFNSRLPIVMKRVAQGGIRLAMLLNNVFGA 292
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3SNG)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q0KFV0_SOLLC | Q0KFV0)
molecular function
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0016788    hydrolase activity, acting on ester bonds    Catalysis of the hydrolysis of any ester bond.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
biological process
    GO:0006308    DNA catabolic process    The cellular DNA metabolic process resulting in the breakdown of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
    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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        Q0KFV0_SOLLC | Q0KFV0: 4dj4 4jdg

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