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(-) Description

Title :  STRUCTURE OF PUTATIVE DEOXYRIBONUCLEASE TATDN1 ISOFORM A
 
Authors :  J. R. C. Muniz, R. Cocking, S. Puranik, T. Krojer, J. Raynor, M. Vollmar, F. Von Delft, C. H. Arrowsmith, A. M. Edwards, J. Weigelt, C. Bountra, K. L. Kavanagh, U. Oppermann
Date :  30 Jun 10  (Deposition) - 14 Jul 10  (Release) - 05 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.19
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Nuclease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. R. C. Muniz, R. Cocking, S. Puranik, T. Krojer, J. Raynor, M. Vollmar F. Von Delft, C. H. Arrowsmith, A. M. Edwards, J. Weigelt, C. Bountra, W. W. Yue, K. L. Kavanagh, U. Oppermann
Structure Of Putative Deoxyribonuclease Tatdn1 Isoform A
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE DEOXYRIBONUCLEASE TATDN1
    Chains: A
    EC Number: 3.1.21.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: R3-PL
    Expression System Vector: PNIC-CTHF
    Fragment: RESIDUES 5-295
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HEPATOCARCINOMA HIGH EXPRESSION PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2NA1Ligand/IonSODIUM ION
3NI1Ligand/IonNICKEL (II) ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:230 , HIS A:232 , SER A:235BINDING SITE FOR RESIDUE NA A1297
2AC2SOFTWAREHIS A:252BINDING SITE FOR RESIDUE NI A1298
3AC3SOFTWAREGLU A:112 , HIS A:149 , ARG A:151 , HIS A:174 , SER A:175 , ASP A:222 , HOH A:2213 , HOH A:2346 , HOH A:2433 , HOH A:2530 , HOH A:2531BINDING SITE FOR RESIDUE EDO A1299

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:198 -A:226

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:111 -Glu A:112
2Ala A:223 -Pro A:224

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2XIO)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TATD_3PS01091 TatD deoxyribonuclease family signature 3.TATD1_HUMAN208-224  1A:208-224

(-) Exons   (0, 0)

(no "Exon" information available for 2XIO)

(-) 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:293
 aligned with TATD1_HUMAN | Q6P1N9 from UniProtKB/Swiss-Prot  Length:297

    Alignment length:294
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293    
          TATD1_HUMAN     4 FKFIDIGINLTDPMFRGIYRGVQKHQDDLQDVIGRAVEIGVKKFMITGGNLQDSKDALHLAQTNGMFFSTVGCHPTRCGEFEKNNPDLYLKELLNLAENNKGKVVAIGECGLDFDRLQFCPKDTQLKYFEKQFELSEQTKLPMFLHCRNSHAEFLDIMKRNRDRCVGGVVHSFDGTKEAAAALIDLDLYIGFNGCSLKTEANLEVLKSIPSEKLMIETDAPWCGVKSTHAGSKYIRTAFPTKKKWESGHCLKDRNEPCHIIQILEIMSAVRDEDPLELANTLYNNTIKVFFPGI 297
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ---TatD_DNase-2xioA01 A:7-294                                                                                                                                                                                                                                                                      --- Pfam domains
         Sec.struct. author ..eeeeee...hhhhh.ee..ee....hhhhhhhhhhhhheeeeee...hhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeeee.......hhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhh..eee.....hhhhhhhhhhh..eeeehhhhh.hhhhhhhhhh.hhh.eee..............hhhhh.....ee.......ee....hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.-. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TATD_3           ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2xio A   4 MKFIDIGINLTDPMFRGIYRGVQKHQDDLQDVIGRAVEIGVKKFMITGGNLQDSKDALHLAQTNGMFFSTVGCHPTRCGEFEKNNPDLYLKELLNLAENNKGKVVAIGECGLDFDRLQFCPKDTQLKYFEKQFELSEQTKLPMFLHCRNSHAEFLDITKRNRDRCVGGVVHSFDGTKEAAAALIDLDLYIGFNGCSLKTEANLEVLKSIPSEKLMIETDAPWCGVKSTHAGSKYIRTAFPTKKKWESGHCLKDRNEPCHIIQILEIMSAVRDEDPLELANTLYNNTIKVFFP-V 296
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293 | |
                                                                                                                                                                                                                                                                                                                             295 |
                                                                                                                                                                                                                                                                                                                               296
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2XIO)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2XIO)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Amidohydrolase (126)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TATD1_HUMAN | Q6P1N9)
molecular function
    GO:0004536    deoxyribonuclease activity    Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid.
    GO:0016888    endodeoxyribonuclease activity, producing 5'-phosphomonoesters    Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acids by creating internal breaks to yield 5'-phosphomonoesters.
    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: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:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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.
cellular component
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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