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(-) Description

Title :  A NOVEL DOMAIN IN HUMAN EXOG CONVERTS APOPTOTIC ENDONUCLEASE TO DNA-REPAIR ENZYME
 
Authors :  M. R. Szymanski, W. Y. Yin
Date :  27 Aug 16  (Deposition) - 17 May 17  (Release) - 17 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.81
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Mitochondria, Exonuclease, Dna-Repair, Complex, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. R. Szymanski, W. Yu, A. M. Gmyrek, M. A. White, I. J. Molineux, J. C. Lee, Y. W. Yin
A Domain In Human Exog Converts Apoptotic Endonuclease To Dna-Repair Exonuclease.
Nat Commun V. 8 14959 2017
PubMed-ID: 28466855  |  Reference-DOI: 10.1038/NCOMMS14959

(-) Compounds

Molecule 1 - NUCLEASE EXOG, MITOCHONDRIAL
    Chains: A, B
    EC Number: 3.1.30.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 59-368
    Gene: EXOG, ENDOGL1, ENDOGL2, ENGL
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ENDONUCLEASE G-LIKE 1,ENDO G-LIKE 1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2SO44Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:109 , GLY A:145 , ARG A:314 , HOH A:513 , HOH A:515 , HOH A:548 , HOH A:575 , HOH A:629 , HOH B:528binding site for residue SO4 A 401
2AC2SOFTWAREPHE A:114 , SER A:137 , ARG A:138 , HOH A:533 , LYS B:357 , GLU B:358binding site for residue SO4 A 402
3AC3SOFTWAREASN A:171 , HOH A:528 , HOH A:543 , HOH A:563 , HOH A:583 , HOH A:639binding site for residue MG A 403
4AC4SOFTWAREHOH A:527 , ARG B:109 , ALA B:144 , GLY B:145 , ARG B:314 , HOH B:521 , HOH B:537 , HOH B:553 , HOH B:559binding site for residue SO4 B 401
5AC5SOFTWARELYS A:357 , GLU A:358 , ARG B:138 , PHE B:168 , HOH B:525 , HOH B:531 , HOH B:620binding site for residue SO4 B 402
6AC6SOFTWAREASN B:171 , HOH B:510 , HOH B:532 , HOH B:570 , HOH B:588 , HOH B:646binding site for residue MG B 403

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:294 -A:299
2B:294 -B:299

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5T40)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5T40)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5T40)

(-) Exons   (0, 0)

(no "Exon" information available for 5T40)

(-) 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:299
                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............ee...eeeeee....eeeeeeeee.........hhhhh........hhhhh.hhhhhh....eeee..hhhhhh.hhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhh....eeeeeeeee..eee.....eeeeeeee....ee...eeeeeeeee.........eeeeeeee........hhhh.eehhhhhhhhhh.............eehhhhh.....hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5t40 A  60 AVLEQFGFPLTGTEARCYTNHALSYDQAKRVPRWVLEHISKSKIMGDADRKHCKFKPDPNIPPTFSAFNEDYVGSGWSRGHMAPAGNNKFSSKAMAETFYLSNIVPQDFDNNSGYWNRIEMYCRELTERFEDVWVVSGPLTLPQTRGDGKKIVSYQVIGEDNVAVPSHLYKVILARRSSVSTEPLALGAFVVPNEAIGFQPQLTEFQVSLQDLEKLSGLVFFPHLDRTSDIRNICSVDTCKLLDFQEFTLYLSTRKIEGARSVLRLEKIMENLKNAEIEPDDYFMSRYEKKLEELKAKE 358
                                    69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349         


Chain B from PDB  Type:PROTEIN  Length:300
                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhh........ee...eeeeee....eeeeeeeee.........hhhhh........hhhhh.hhhhhh....eeee..hhhhhh.hhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee..eee.....eeeeeeee....ee...eeeeeeeee.........eeeeeeee........hhhh.eehhhhhhhhhh.............eehhhhh.....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5t40 B  59 KAVLEQFGFPLTGTEARCYTNHALSYDQAKRVPRWVLEHISKSKIMGDADRKHCKFKPDPNIPPTFSAFNEDYVGSGWSRGHMAPAGNNKFSSKAMAETFYLSNIVPQDFDNNSGYWNRIEMYCRELTERFEDVWVVSGPLTLPQTRGDGKKIVSYQVIGEDNVAVPSHLYKVILARRSSVSTEPLALGAFVVPNEAIGFQPQLTEFQVSLQDLEKLSGLVFFPHLDRTSDIRNICSVDTCKLLDFQEFTLYLSTRKIEGARSVLRLEKIMENLKNAEIEPDDYFMSRYEKKLEELKAKE 358
                                    68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358
   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  (0, 0)

(no "SCOP Domain" information available for 5T40)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5T40)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5T40)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

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  5t40
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 Related Entries

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

UniProtKB/Swiss-Prot
        EXOG_HUMAN | Q9Y2C4: 4a1n 5t3v 5t4i 5t5c

(-) Related Entries Specified in the PDB File

5t3v 5t4i 5t5c