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(-) Description

Title :  CRYSTAL STRUCTURE OF ENDONUCLEASE IV FROM THERMUS THERMOPHILUS HB8
 
Authors :  R. Asano, H. Ishikawa, S. Nakane, S. Baba, N. Nakagawa, S. Kuramitsu, R. Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  20 Nov 09  (Deposition) - 01 Dec 10  (Release) - 02 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.58
Chains :  Asym./Biol. Unit :  A
Keywords :  Dna Repair, Base Excision Repair, Ber, Tim Barrel, Endonuclease, Hydrolase, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Asano, H. Ishikawa, S. Nakane, N. Nakagawa, S. Kuramitsu, R. Masui
An Additional C-Terminal Loop In Endonuclease Iv, An Apurinic/Apyrimidinic Endonuclease, Controls Binding Affinity To Dna
Acta Crystallogr. , Sect. D V. 67 149 2011
PubMed-ID: 21358045  |  Reference-DOI: 10.1107/S0907444910052479

(-) Compounds

Molecule 1 - ENDONUCLEASE IV
    Chains: A
    EC Number: 3.1.21.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: TTHA0834
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8
    Synonym: ENDOIV

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1MN1Ligand/IonMANGANESE (II) ION
2PO41Ligand/IonPHOSPHATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:172 , ASP A:217 , HIS A:219 , PO4 A:272 , HOH A:333BINDING SITE FOR RESIDUE MN A 271
2AC2SOFTWAREHIS A:69 , GLU A:139 , HIS A:172 , HIS A:219 , GLU A:248 , MN A:271 , HOH A:291 , HOH A:325 , HOH A:381BINDING SITE FOR RESIDUE PO4 A 272

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3AAM)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Arg A:133 -Pro A:134

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3AAM)

(-) 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:269
 aligned with Q5SK18_THET8 | Q5SK18 from UniProtKB/TrEMBL  Length:270

    Alignment length:269
                                    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         
         Q5SK18_THET8     2 PRYGFHLSIAGKKGVAGAVEEATALGLTAFQIFAKSPRSWRPRALSPAEVEAFRALREASGGLPAVIHASYLVNLGAEGELWEKSVASLADDLEKAALLGVEYVVVHPGSGRPERVKEGALKALRLAGVRSRPVLLVENTAGGGEKVGARFEELAWLVADTPLQVCLDTCHAYAAGYDVAEDPLGVLDALDRAVGLERVPVVHLNDSVGGLGSRVDHHAHLLQGKIGEGLKRVFLDPRLKDRVFILETPRGPEEDAWNLRVFRAWLEEA 270
               SCOP domains d3aama_ A: automated matches                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.......hhhhhhhhhhhhhh...eeee............hhhhhhhhhhhhhhh....eeee...........hhhhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhh.....eeeee...........hhhhhhhhhh....eeeeehhhhhhhh.....hhhhhhhhhhhhhhhhhh.eee..ee..........ee........hhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3aam A   2 PRYGFHLSIAGKKGVAGAVEEATALGLTAFQIFAKSPRSWRPRALSPAEVEAFRALREASGGLPAVIHASYLVNLGAEGELWEKSVASLADDLEKAALLGVEYVVVHPGSGRPERVKEGALKALRLAGVRSRPVLLVENTAGGGEKVGARFEELAWLVADTPLQVCLDTCHAYAAGYDVAEDPLGVLDALDRAVGLERVPVVHLNDSVGGLGSRVDHHAHLLQGKIGEGLKRVFLDPRLKDRVFILETPRGPEEDAWNLRVFRAWLEEA 270
                                    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
   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 3AAM)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q5SK18_THET8 | Q5SK18)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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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 Related Entries

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(-) Related Entries Specified in the PDB File

3aal THE SAME PROTEIN FROM GEOBACILLUS KAUSTOPHILUS RELATED ID: TTP001000834.1 RELATED DB: TARGETDB