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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN NEIL1(P2G R242K) BOUND TO DUPLEX DNA CONTAINING THYMINE GLYCOL
 
Authors :  C. Zhu, L. Lu, J. Zhang, Z. Yue, J. Song, S. Zong, M. Liu, O. Stovicek, Y. Ga
Date :  17 Mar 16  (Deposition) - 06 Jul 16  (Release) - 03 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Biol. Unit 3:  E,F  (1x)
Keywords :  Dna Glycosylase Neil1 Fpg Nei Base Excision Repair, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Zhu, L. Lu, J. Zhang, Z. Yue, J. Song, S. Zong, M. Liu, O. Stovicek, Y. Q. Gao, C. Yi
Tautomerization-Dependent Recognition And Excision Of Oxidation Damage In Base-Excision Dna Repair
Proc. Natl. Acad. Sci. Usa V. 113 7792 2016
PubMed-ID: 27354518  |  Reference-DOI: 10.1073/PNAS.1604591113

(-) Compounds

Molecule 1 - ENDONUCLEASE 8-LIKE 1
    Chains: A, B
    EC Number: 3.2.2.-, 4.2.99.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: NEIL1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DNA GLYCOSYLASE/AP LYASE NEIL1,DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE NEIL1,ENDONUCLEASE VIII-LIKE 1,FPG1,NEI HOMOLOG 1,NEH1, NEI-LIKE PROTEIN 1
 
Molecule 2 - DNA (26-MER)
    Chains: D, C, F
    Engineered: YES
    Organism Scientific: UNIDENTIFIED
    Organism Taxid: 32644
    Synthetic: YES
 
Molecule 3 - ENDONUCLEASE 8-LIKE 1
    Chains: E
    EC Number: 3.2.2.-, 4.2.99.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: NEIL1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DNA GLYCOSYLASE/AP LYASE NEIL1,DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE NEIL1,ENDONUCLEASE VIII-LIKE 1,FPG1,NEI HOMOLOG 1,NEH1, NEI-LIKE PROTEIN 1

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A  D  
Biological Unit 2 (1x):  BC   
Biological Unit 3 (1x):     EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1CTG3Mod. Nucleotide(5R,6S)-5,6-DIHYDRO-5,6-DIHYDROXYTHYMIDINE-5'-MONOPHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CTG1Mod. Nucleotide(5R,6S)-5,6-DIHYDRO-5,6-DIHYDROXYTHYMIDINE-5'-MONOPHOSPHATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CTG1Mod. Nucleotide(5R,6S)-5,6-DIHYDRO-5,6-DIHYDROXYTHYMIDINE-5'-MONOPHOSPHATE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1CTG1Mod. Nucleotide(5R,6S)-5,6-DIHYDRO-5,6-DIHYDROXYTHYMIDINE-5'-MONOPHOSPHATE

(-) Sites  (0, 0)

(no "Site" information available for 5ITX)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5ITX)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gln B:67 -Pro B:68
2Leu B:125 -Gly B:126

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5ITX)

(-) Sequences/Alignments

Asymmetric 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:264
                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh....eeeeeee........eeeeeeeeeeeeeee..eeeeeeee..........eeeeee....eeeeeee.......eeeeeee......eeeeeee.....eeee..............hhhhhhhhhhhh..hhhhhhhhhhhh.........hhhhhhhhhhhhh.....hhhhhhh......hhhhhhhhhhhhhhhhh.....hhhhhhhh........eeee.....eeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5itx A   2 PEGPELHLASQFVNEACRALVFGGCVEKSSVSRNPEVPFESSAYRISASARGKELRLILSPLPGAQPQQEPLALVFRFGMSGSFQLVPREELPRHAHLRFYTAPPGPRLALCFVDIRRFGRWDLGGKWQPGRGPCVLQEYQQFRENVLRNLADKAFDRPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARSVLEALQQNPDLLELCHSVPKEVVQLGGKGYDFAAFRAWLRCYGMPGMSSLQDRHGRTIWFQGDPGPLAP 290
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201 ||    229       239    || 256       266       276       286    
                                                                                                                                                                                                                                   203|                   244|                                      
                                                                                                                                                                                                                                    222                    252                                      


Chain B from PDB  Type:PROTEIN  Length:263
                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh...eeee.ee...........eeeeeeeeeeee..eeeeeeee..........eeeeee....eeeeeee.......eeeeee.......eeeeeee.....eeee..............hhhhhhhhhhh...hhhhhhhhhhhh.........hhhhhhhhhh........hhhhhhh....hhhhhhhhhhhhhhhh......hhhhhhhhh........eeee.....eeee......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5itx B   2 PEGPELHLASQFVNEACRALVFGGCVEKSSVSRNPEVPFESSAYRISASARGKELRLILSPLPGAQPQQEPLALVFRFGMSGSFQLVPREELPRHAHLRFYTAPPGPRLALCFVDIRRFGRWDLGGKWQPGRGPCVLQEYQQFRENVLRNLADKAFDRPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARSVLEALNPDLLELCHSVPKEVVQLGGKGYEDFAAFRAWLRCYGMPGMSSLQDRHGRTIWFQGDPGPLAP 290
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201|      231       241  ||   257       267       277       287   
                                                                                                                                                                                                                                 201|                   244|                                       
                                                                                                                                                                                                                                  222                    251                                       


Chain C from PDB  Type:DNA  Length:26
                                                          
                 5itx C 291 CGTCCAxGTCTACTAGACCTGGACGG 318
                                  |300  ||   312      
                                297-CTG03|            
                                       306            


Chain D from PDB  Type:DNA  Length:26
                                                          
                 5itx D 291 CGTCCAxGTCTACTAGACCTGGACGG 318
                                  |300  ||   312      
                                297-CTG03|            
                                       306            


Chain E from PDB  Type:PROTEIN  Length:260
                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh...eeeeeee..................ee.....eeeee..............eeeee......eeeee.......eeeeeee......eeeeee.......eee..............hhhhhhhhhhhh...hhhhhhhhhhh.........hhhhhhhhhhh.......hhhhhhh...hhhhhhhhhhhhhhh......hhhhhhhh........eeee.....eeee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5itx E   2 GEGPELHLASQFVNEACRALVFGGCVEKSSVSRNPEVPFESSAYRISASARGKELRLILSPLPGAQPQQEPLALVFRFGMSGSFQLVPREELPRHAHLRFYTAPPGPRLALCFVDIRRFGRWDLGGKWQPGRGPCVLQEYQQFRENVLRNLADKAFDRPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARSVLEANPDLLELCHSVPKEVVQLGRGYDFAAFRAWLRCYGMPGMSSLQDRHGRTIWFQGDPGPLAP 290
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       222       232      |243||     260       270       280       290
                                                                                                                                                                                                                                200|              239|  ||                                      
                                                                                                                                                                                                                                 222               241  ||                                      
                                                                                                                                                                                                                                                      244|                                      
                                                                                                                                                                                                                                                       252                                      


Chain F from PDB  Type:DNA  Length:26
                                                          
                 5itx F 291 CGTCCAxGTCTACTAGACCTGGACGG 318
                                  |300  ||   312      
                                297-CTG03|            
                                       306
   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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (26, 26)

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    Gln B:67 - Pro B:68   [ RasMol ]  
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  5itx
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 Related Entries

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

UniProtKB/Swiss-Prot
        NEIL1_HUMAN | Q96FI4: 1tdh 4nrv 5itq 5itr 5itt 5itu 5ity

(-) Related Entries Specified in the PDB File

5itq 5itr 5itt 5itu 5ity