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(-) Description

Title :  CRYSTAL STRUCTURE OF TATD DEOXYRIBONUCLEASE FROM ESCHERICHIA COLI K12 AT 2.0 A RESOLUTION
 
Authors :  V. N. Malashkevich, D. F. Xiang, F. M. Raushel, S. C. Almo, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  02 Nov 04  (Deposition) - 25 Jan 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Tatd, Tim Barrael, Deoxyribonuclease, Zinc Ion, Structural Genomics, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. N. Malashkevich, D. F. Xiang, F. M. Raushel, S. C. Almo
Crystal Structure Of Tatd Dnase From Escherichia Coli At 2. 0 A Resolution
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DEOXYRIBONUCLEASE TATD
    Chains: A
    EC Number: 3.1.21.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI K12
    Expression System Strain: K12
    Expression System Taxid: 83333
    Gene: TATD, MTTC
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: DNASE TATD

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1ZN1Ligand/IonZINC ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:152 , CYS A:153 , GLU A:201 , HOH A:505BINDING SITE FOR RESIDUE ZN A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1XWY)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:90 -Glu A:91
2Ala A:204 -Pro A:205

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TATD_2PS01090 TatD deoxyribonuclease family signature 2.TATD_ECOLI123-133  1A:123-133
2TATD_3PS01091 TatD deoxyribonuclease family signature 3.TATD_ECOLI189-205  1A:189-205

(-) Exons   (0, 0)

(no "Exon" information available for 1XWY)

(-) 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:260
 aligned with TATD_ECOLI | P27859 from UniProtKB/Swiss-Prot  Length:260

    Alignment length:260
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260
           TATD_ECOLI     1 MFDIGVNLTSSQFAKDRDDVVACAFDAGVNGLLITGTNLRESQQAQKLARQYSSCWSTAGVHPHDSSQWQAATEEAIIELAAQPEVVAIGECGLDFNRNFSTPEEQERAFVAQLRIAADLNMPVFMHCRDAHERFMTLLEPWLDKLPGAVLHCFTGTREEMQACVAHGIYIGITGWVCDERRGLELRELLPLIPAEKLLIETDAPYLLPRDLTPKPSSRRNEPAHLPHILQRIAHWRGEDAAWLAATTDANVKTLFGIAF 260
               SCOP domains d1xwya1 A:1-260 Deoxyribonuclease TatD (MttC)                                                                                                                                                                                                                        SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -TatD_DNase-1xwyA01 A:2-257                                                                                                                                                                                                                                      --- Pfam domains
         Sec.struct. author .eeeee...hhhhh.hhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhhhh...eeeeeeeeee......hhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhh..eee.....hhhhhhhhhhh..eeeehhhhhh...hhhhhhhhhhhhhh.eee.....................hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------TATD_2     -------------------------------------------------------TATD_3           ------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xwy A   1 MFDIGVNLTSSQFAKDRDDVVACAFDAGVNGLLITGTNLRESQQAQKLARQYSSCWSTAGVHPHDSSQWQAATEEAIIELAAQPEVVAIGECGLDFNRNFSTPEEQERAFVAQLRIAADLNMPVFMHCRDAHERFMTLLEPWLDKLPGAVLHCFTGTREEMQACVAHGIYIGITGWVCDERRGLELRELLPLIPAEKLLIETDAPYLLPRDLTPKPSSRRNEPAHLPHILQRIAHWRGEDAAWLAATTDANVKTLFGIAF 260
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260
   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: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1XWY)

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TATD_ECOLI | P27859)
molecular function
    GO:0008408    3'-5' exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end.
    GO:0000175    3'-5'-exoribonuclease activity    Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of an RNA molecule.
    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:0004527    exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
    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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    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:0008310    single-stranded DNA 3'-5' exodeoxyribonuclease activity    Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of a single-stranded DNA molecule.
biological process
    GO:0000738    DNA catabolic process, exonucleolytic    The chemical reactions and pathways resulting in the breakdown of DNA, involving the hydrolysis of terminal 3',5'-phosphodiester bonds in one or two strands of deoxyribonucleotides.
    GO:0090501    RNA phosphodiester bond hydrolysis    The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
    GO:0090503    RNA phosphodiester bond hydrolysis, exonucleolytic    The chemical reactions and pathways involving the hydrolysis of terminal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0042542    response to hydrogen peroxide    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hydrogen peroxide (H2O2) stimulus.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TATD_ECOLI | P27859: 4p5u 4pe8

(-) Related Entries Specified in the PDB File

1j6o CRYSTAL STRUCTURE OF TATD-RELATED DEOXYRIBONUCLEASE 2 (TM0667) FROM THERMOTOGA MARITIMA AT 1.8 A RESOLUTION RELATED ID: NYSGXRC-T2213 RELATED DB: TARGETDB