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(-) Description

Title :  CRYSTAL STRUCTURE OF ENDONUCLEASE IV (BA4508) FROM BACILLUS ANTHRACIS AT 2.57A RESOLUTION.
 
Authors :  M. J. Fogg, V. M. Levdikov, E. V. Blagova, J. A. Brannigan, A. J. Wilkinso K. S. Wilson, Structural Proteomics In Europe (Spine)
Date :  08 Oct 04  (Deposition) - 04 Oct 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.57
Chains :  Asym./Biol. Unit :  A
Keywords :  Endonuclease Iv, Nfo, Dna Replication, Dna Recombination, Dna Repair, Spine, Structural Genomics, Structural Proteomics In Europe, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. J. Fogg, V. M. Levdikov, E. V. Blagova, J. A. Brannigan, A. J. Wilkinson, K. S. Wilson
Crystal Structure Of Endonuclease Iv (Ba4508) From Bacillus Anthracis At 2. 57A Resolution.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ENDONUCLEASE IV
    Chains: A
    EC Number: 3.1.21.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-YSBLIC
    Expression System Strain: B834
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NFO
    Organism Scientific: BACILLUS ANTHRACIS
    Organism Taxid: 1392
    Synonym: ENDODEOXYRIBONUCLEASE IV

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
2ZN3Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:69 , HIS A:111 , GLU A:146 , ZN A:303 , SO4 A:305 , HOH A:313BINDING SITE FOR RESIDUE ZN A 301
2AC2SOFTWAREHIS A:183 , ASP A:228 , HIS A:230 , SO4 A:305BINDING SITE FOR RESIDUE ZN A 302
3AC3SOFTWAREGLU A:146 , ASP A:180 , HIS A:183 , HIS A:215 , GLU A:260 , ZN A:301 , SO4 A:305 , HOH A:313BINDING SITE FOR RESIDUE ZN A 303
4AC4SOFTWAREASP A:228 , ARG A:229 , HIS A:230 , HOH A:415BINDING SITE FOR RESIDUE SO4 A 304
5AC5SOFTWAREHIS A:111 , GLU A:146 , ASP A:180 , HIS A:183 , ASP A:228 , HIS A:230 , GLU A:260 , ZN A:301 , ZN A:302 , ZN A:303 , HOH A:313 , HOH A:415 , HOH A:458BINDING SITE FOR RESIDUE SO4 A 305

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1XP3)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gly A:12 -Lys A:13
2Glu A:266 -Asp A:267
3Lys A:269 -Asp A:270
4Asp A:270 -Lys A:271

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1XP3)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AP_NUCLEASE_F2_1PS00729 AP endonucleases family 2 signature 1.END4_BACAN69-77  1A:69-77
2AP_NUCLEASE_F2_2PS00730 AP endonucleases family 2 signature 2.END4_BACAN176-183  1A:176-183
3AP_NUCLEASE_F2_3PS00731 AP endonucleases family 2 signature 3.END4_BACAN214-230  1A:214-230

(-) Exons   (0, 0)

(no "Exon" information available for 1XP3)

(-) 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:297
 aligned with END4_BACAN | Q81LV1 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:297
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       
           END4_BACAN     2 LKIGSHVSMSGKKMLLAASEEAVSYGATTFMIYTGAPQNTRRKPIEELNIEAGRKHMEQNGIEEIIVHAPYIINVGNTTKPETFQLGVDFLRMEIERTSALGVAKQIVLHPGAHVGAGADAGIQQIIKGLNEVLTPDQTVNIALETMAGKGTECGRSFEEIAKIIDGVKYNEKLSVCFDTCHTHDAGYDIVNNFDGVLNEFDKIVGIDRLQVLHINDSKNVRGAGKDRHENIGFGHIGYKALHHIVHHPQLTHVPKILETPYVGEDKKDKKPPYKLEIEMLKNGTFDEGLLEKIKAQ 298
               SCOP domains d1xp3a1 A:2-298 Endonuclease IV                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee........hhhhhhhhhhh.....eee...........hhhhhhhhhhhhhhhhh....eeee...........hhhhhhhhhhhhhhhhhhhhhh....eeee..ee....hhhhhhhhhhhhhhhhh......eeeee.......ee..hhhhhhhhhhhh.hhh.eeeeeehhhhhhh..hhhhhhhhhhhhhhhhhhhh.eeeeee.ee..........ee.......hhhhhhhhhhhhhhh...eee..............hhhhhhhhhhhh....hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------AP_NUCLEA--------------------------------------------------------------------------------------------------AP_NUCLE------------------------------AP_NUCLEASE_F2_3 -------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xp3 A   2 LKIGSHVSMSGKKMLLAASEEAVSYGATTFMIYTGAPQNTRRKPIEELNIEAGRKHMEQNGIEEIIIHAPYIINVGNTTKPETFQLGVDFLRMEIERTSALGVAKQIVLHPGAHVGAGADAGIQQIIKGLNEVLTPDQTVNIALETMAGKGTECGRSFEEIAKIIDGVKYNEKLSVCFDTCHTHDAGYDIVNNFDGVLNEFDKIVGIDRLQVLHINDSKNVRGAGKDRHENIGFGHIGYKALHHIVHHPQLTHVPKILETPYVGEDKKDKKPPYKLEIEMLKNGTFDEGLLEKIKAQ 298
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291
   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) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1XP3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1XP3)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (END4_BACAN | Q81LV1)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0008833    deoxyribonuclease IV (phage-T4-induced) activity    Catalysis of the endonucleolytic cleavage to 5'-phosphooligonucleotide end-products.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    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: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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    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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