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(-) Description

Title :  X-RAY STRUCTURE OF MUTANT N211D OF 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 :  01 Feb 12  (Deposition) - 07 Nov 12  (Release) - 20 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Mainly Alpha Helical, Trinuclear Metal Centre, Bi-Functional, Nuclease, 3'-Nucleotidase, 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, B
    Engineered: YES
    Expression System: NICOTIANA BENTHAMIANA
    Expression System Plasmid: PLV07
    Expression System Taxid: 4100
    Expression System Vector Type: PLASMID CLONE 3062
    Gene: TBN1
    Mutation: YES
    Organism Common: TOMATO
    Organism Scientific: SOLANUM LYCOPERSICUM
    Organism Taxid: 4081
    Strain: CV. RUTGERS

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 25)

Asymmetric/Biological Unit (6, 25)
No.NameCountTypeFull Name
1BMA3Ligand/IonBETA-D-MANNOSE
2CL2Ligand/IonCHLORIDE ION
3MAN5Ligand/IonALPHA-D-MANNOSE
4NA1Ligand/IonSODIUM ION
5NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
6ZN6Ligand/IonZINC ION

(-) Sites  (25, 25)

Asymmetric Unit (25, 25)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:26 , HIS A:31 , 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:701 , HOH A:703BINDING SITE FOR RESIDUE ZN A 402
03AC3SOFTWAREHIS A:157 , HIS A:181 , ASP A:185 , HOH A:702BINDING SITE FOR RESIDUE ZN A 403
04AC4SOFTWARETRP A:80 , LEU A:84 , ASP A:110 , ASN A:119 , GLN A:123 , ARG A:135 , TYR A:136 , NAG A:502BINDING SITE FOR RESIDUE NAG A 501
05AC5SOFTWAREMET A:111 , NAG A:501BINDING SITE FOR RESIDUE NAG A 502
06AC6SOFTWARETRP A:68 , TYR A:78 , ASN A:137 , GLU A:140 , NAG A:512 , HOH A:773 , LYS B:79BINDING SITE FOR RESIDUE NAG A 511
07AC7SOFTWAREPRO A:55 , TYR A:57 , NAG A:511 , BMA A:513 , CL A:601 , HOH A:714 , LYS B:79BINDING SITE FOR RESIDUE NAG A 512
08AC8SOFTWARENAG A:512 , MAN A:514 , MAN A:515 , HOH A:738BINDING SITE FOR RESIDUE BMA A 513
09AC9SOFTWAREBMA A:513 , HOH A:749BINDING SITE FOR RESIDUE MAN A 514
10BC1SOFTWARETYR A:57 , BMA A:513BINDING SITE FOR RESIDUE MAN A 515
11BC2SOFTWARETRP A:68 , NAG A:512 , HOH A:728BINDING SITE FOR RESIDUE CL A 601
12BC3SOFTWARETRP B:26 , HIS B:31 , ASP B:151 , ZN B:402 , HOH B:701BINDING SITE FOR RESIDUE ZN B 401
13BC4SOFTWAREASP B:70 , HIS B:85 , HIS B:147 , ASP B:151 , ZN B:401 , HOH B:701 , HOH B:703BINDING SITE FOR RESIDUE ZN B 402
14BC5SOFTWAREASP A:133 , HIS B:157 , HIS B:181 , ASP B:185 , HOH B:702BINDING SITE FOR RESIDUE ZN B 403
15BC6SOFTWARETRP B:80 , LEU B:84 , ASP B:110 , MET B:111 , ALA B:116 , ASN B:119 , PHE B:120 , GLN B:123 , TYR B:136 , NAG B:502BINDING SITE FOR RESIDUE NAG B 501
16BC7SOFTWARETRP B:80 , MET B:111 , NAG B:501 , BMA B:503BINDING SITE FOR RESIDUE NAG B 502
17BC8SOFTWARENAG B:502 , MAN B:504 , HOH B:740BINDING SITE FOR RESIDUE BMA B 503
18BC9SOFTWAREBMA B:503 , HOH B:739 , HOH B:763BINDING SITE FOR RESIDUE MAN B 504
19CC1SOFTWARELYS A:79 , SER A:82 , TRP B:68 , TYR B:78 , ASN B:137 , GLU B:140 , NAG B:512BINDING SITE FOR RESIDUE NAG B 511
20CC2SOFTWARELYS A:79 , PRO B:55 , TYR B:57 , NAG B:511 , BMA B:513 , CL B:601 , HOH B:722BINDING SITE FOR RESIDUE NAG B 512
21CC3SOFTWARENAG B:512 , MAN B:514 , MAN B:515BINDING SITE FOR RESIDUE BMA B 513
22CC4SOFTWAREASP A:44 , HIS A:48 , BMA B:513 , HOH B:752BINDING SITE FOR RESIDUE MAN B 514
23CC5SOFTWAREBMA B:513BINDING SITE FOR RESIDUE MAN B 515
24CC6SOFTWARETRP B:68 , NAG B:512BINDING SITE FOR RESIDUE CL B 601
25CC7SOFTWAREARG B:100 , HIS B:103 , HOH B:736 , HOH B:741 , HOH B:743BINDING SITE FOR RESIDUE NA B 602

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:35 -A:66
2A:94 -A:246
3A:102 -A:112
4A:227 -A:233
5B:35 -B:66
6B:94 -B:246
7B:102 -B:112
8B:227 -B:233

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4DJ4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4DJ4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4DJ4)

(-) Exons   (0, 0)

(no "Exon" information available for 4DJ4)

(-) 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:266
 aligned with Q0KFV0_SOLLC | Q0KFV0 from UniProtKB/TrEMBL  Length:302

    Alignment length:266
                                    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 WSKEGHVMTCRIAQGLLNDEAAHAVKMLLPEYVNGDLSALCVWPDQVRHWYKYKWTSPLHFIDTPDKACNFDYERDCHDQHGVKDMCVAGAIQNFTTQLSHYREGTSDRRYNMTEALLFLSHFMGDIHQPMHVGFTSDAGGNSIDLRWFRHKSNLHHVWDREIILTAAKDYYAKDINLLEEDIEGNFTDGIWSDDLASWRECGNVFSCVNKFATESINIACKWGYKGVEAGETLSDDYFNSRLPIVMKRVAQGGIRLAMLLNNVFG 291
               SCOP domains d4dj4a_ A: automated matches                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhh.........hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh..........eeee..eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.....hhhhhhh..hhhhhhhhhhhhhhhhhhhh.........eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dj4 A  26 WSKEGHVMTCRIAQGLLNDEAAHAVKMLLPEYVNGDLSALCVWPDQVRHWYKYKWTSPLHFIDTPDKACNFDYERDCHDQHGVKDMCVAGAIQNFTTQLSHYREGTSDRRYNMTEALLFLSHFMGDIHQPMHVGFTSDAGGNSIDLRWFRHKSNLHHVWDREIILTAAKDYYAKDINLLEEDIEGDFTDGIWSDDLASWRECGNVFSCVNKFATESINIACKWGYKGVEAGETLSDDYFNSRLPIVMKRVAQGGIRLAMLLNNVFG 291
                                    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      


Chain B from PDB  Type:PROTEIN  Length:251
 aligned with Q0KFV0_SOLLC | Q0KFV0 from UniProtKB/TrEMBL  Length:302

    Alignment length:265
                                    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 WSKEGHVMTCRIAQGLLNDEAAHAVKMLLPEYVNGDLSALCVWPDQVRHWYKYKWTSPLHFIDTPDKACNFDYERDCHDQHGVKDMCVAGAIQNFTTQLSHYREGTSDRRYNMTEALLFLSHFMGDIHQPMHVGFTSDAGGNSIDLRWFRHKSNLHHVWDREIILTAAKDYYAKDINLLEEDIEGNFTDGIWSDDLASWRECGNVFSCVNKFATESINIACKWGYKGVEAGETLSDDYFNSRLPIVMKRVAQGGIRLAMLLNNVF 290
               SCOP domains d4dj4b_ B: automated matches                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhh.........hhhhhhhhhhhhhhh.....----.hhhhhhhhhhhhhhhhhhhhhhh..........eeee..eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh...----------...hhhhhhhhhhhhhhhhhhhhh........eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dj4 B  26 WSKEGHVMTCRIAQGLLNDEAAHAVKMLLPEYVNGDLSALCVWPDQVRHWYKYKWTSPLHFIDTPDKACNFDYERDCHDQHGVKDMCVAGAIQNFTTQLSHYREGT----YNMTEALLFLSHFMGDIHQPMHVGFTSDAGGNSIDLRWFRHKSNLHHVWDREIILTAAKDYYAKDINLLEEDIEGDFTDG----------ECGNVFSCVNKFATESINIACKWGYKGVEAGETLSDDYFNSRLPIVMKRVAQGGIRLAMLLNNVF 290
                                    35        45        55        65        75        85        95       105       115       125     |   -|      145       155       165       175       185       195       205       215         -|      235       245       255       265       275       285     
                                                                                                                                   131  136                                                                            215        226
   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, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4DJ4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4DJ4)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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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  4dj4
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  Q0KFV0_SOLLC | Q0KFV0
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 Related Entries

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

UniProtKB/TrEMBL
        Q0KFV0_SOLLC | Q0KFV0: 3sng 4jdg

(-) Related Entries Specified in the PDB File

3sng FULLY GLYCOSYLATED WILD TYPE