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(-) Description

Title :  HIGH RESOLUTION CRYSTAL STRUCTURE OF DNA APURINIC/APYRIMIDINIC (AP) ENDONUCLEASE IV NFO FROM THERMATOGA MARITIMA
 
Authors :  D. S. Shin, D. J. Hosfield, A. S. Arvai, S. E. Tsutakawa, J. A. Tainer
Date :  20 Oct 12  (Deposition) - 23 Jan 13  (Release) - 10 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  0.92
Chains :  Asym./Biol. Unit :  A
Keywords :  Endonuclease 4, Endodeoxyribonuclease Iv, Endo Iv, Nfo, Metalloprotein, Dna Damage, Dna Repair, Base Excision Repair, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. E. Tsutakawa, D. S. Shin, C. D. Mol, T. Izumi, A. S. Arvai, A. K. Mantha B. Szczesny, I. N. Ivanov, D. J. Hosfield, B. Maiti, M. E. Pique, K. A. Frankel, K. Hitomi, R. P. Cunningham, S. Mitra, J. A. Tainer
Conserved Structural Chemistry For Incision Activity In Structurally Non-Homologous Apurinic/Apyrimidinic Endonuclease Ape1 And Endonuclease Iv Dna Repair Enzymes.
J. Biol. Chem. V. 288 8445 2013
PubMed-ID: 23355472  |  Reference-DOI: 10.1074/JBC.M112.422774

(-) Compounds

Molecule 1 - PROBABLE ENDONUCLEASE 4
    Chains: A
    EC Number: 3.1.21.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: NFO, TM_0362
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 243274
    Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099
    Synonym: ENDODEOXYRIBONUCLEASE IV, ENDONUCLEASE IV

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 10)

Asymmetric/Biological Unit (6, 10)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2MG1Ligand/IonMAGNESIUM ION
3MN2Ligand/IonMANGANESE (II) ION
4SO41Ligand/IonSULFATE ION
5TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
6ZN3Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:69 , HIS A:109 , GLU A:144 , MN A:304 , ZN A:305 , HOH A:786BINDING SITE FOR RESIDUE ZN A 301
02AC2SOFTWAREHIS A:181 , ASP A:228 , HIS A:230 , TRS A:307 , EDO A:308BINDING SITE FOR RESIDUE MN A 302
03AC3SOFTWAREHIS A:181 , ASP A:228 , HIS A:230 , TRS A:307 , EDO A:308BINDING SITE FOR RESIDUE ZN A 303
04AC4SOFTWAREGLU A:144 , ASP A:178 , HIS A:181 , HIS A:215 , GLU A:260 , ZN A:301 , TRS A:307 , EDO A:308 , HOH A:786BINDING SITE FOR RESIDUE MN A 304
05AC5SOFTWAREGLU A:144 , ASP A:178 , HIS A:215 , GLU A:260 , ZN A:301 , HOH A:786BINDING SITE FOR RESIDUE ZN A 305
06AC6SOFTWAREHOH A:613 , HOH A:717 , HOH A:754 , HOH A:780 , HOH A:824 , HOH A:826BINDING SITE FOR RESIDUE MG A 306
07AC7SOFTWARETYR A:72 , HIS A:109 , HIS A:181 , ASP A:228 , HIS A:230 , MN A:302 , ZN A:303 , MN A:304 , HOH A:614 , HOH A:688 , HOH A:701 , HOH A:711 , HOH A:786 , HOH A:823BINDING SITE FOR RESIDUE TRS A 307
08AC8SOFTWARETYR A:72 , HIS A:181 , ASP A:228 , HIS A:230 , MN A:302 , ZN A:303 , MN A:304 , HOH A:614 , HOH A:786 , HOH A:823BINDING SITE FOR RESIDUE EDO A 308
09AC9SOFTWAREARG A:127 , ASP A:188 , THR A:190 , HOH A:411BINDING SITE FOR RESIDUE EDO A 309
10BC1SOFTWAREGLU A:47 , LYS A:51 , ARG A:54 , LYS A:220 , HOH A:722 , HOH A:747 , HOH A:750 , HOH A:810BINDING SITE FOR RESIDUE SO4 A 310

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4HNO)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HNO)

(-) 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    
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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:285
                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4hnoa_ A: automated matches                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.....hhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhh..hhh.eeee..........hhhhhhhhhhhhhhhhhhhhhhh..eeee..ee....hhhhhhhhhhhhhhhhhh.....eeeee.......ee..hhhhhhhhhhhh.hhh.eeeeeehhhhhhh.....hhhhhhhhhhhhhhhhhhh.eeeeee.ee..........ee......hhhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hno A   1 MIKIGAHMPISKGFDRVPQDTVNIGGNSFQIFPHNARSWSAKLPSDEAATKFKREMKKHGIDWENAFCHSGYLINLASPKDDIWQKSVELLKKEVEICRKLGIRYLNIHPGSHLGTGEEEGIDRIVRGLNEVLNNTEGVVILLENVSQKGGNIGYKLEQLKKIRDLVDQRDRVAITYDTCHGFDSGYDITKKEGVEALLNEIESLFGLERLKMIHLNDSKYPLGAAKDRHERIGSGFIGEEGFAVFFSFKEIQEVPWILETPGGNEEHAEDIKKVFEIIEKFGIE 285
                                    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       270       280
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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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)

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        END4_THEMA | Q9WYJ7: 2x7v 2x7w

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