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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN NEIL1(P2G) 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 :  2.48
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,E  (1x)
Biol. Unit 3:  C,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, C
    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
 
Molecule 2 - DNA (26-MER)
    Chains: D, E, F
    Engineered: YES
    Organism Scientific: UNIDENTIFIED
    Organism Taxid: 32644
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A  D  
Biological Unit 2 (1x):  B  E 
Biological Unit 3 (1x):   C  F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1CTG3Mod. Nucleotide(5R,6S)-5,6-DIHYDRO-5,6-DIHYDROXYTHYMIDINE-5'-MONOPHOSPHATE
2GOL1Ligand/IonGLYCEROL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CTG1Mod. Nucleotide(5R,6S)-5,6-DIHYDRO-5,6-DIHYDROXYTHYMIDINE-5'-MONOPHOSPHATE
2GOL-1Ligand/IonGLYCEROL
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1CTG1Mod. Nucleotide(5R,6S)-5,6-DIHYDRO-5,6-DIHYDROXYTHYMIDINE-5'-MONOPHOSPHATE
2GOL1Ligand/IonGLYCEROL
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1CTG1Mod. Nucleotide(5R,6S)-5,6-DIHYDRO-5,6-DIHYDROXYTHYMIDINE-5'-MONOPHOSPHATE
2GOL-1Ligand/IonGLYCEROL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:51 , LEU B:138 , GLN B:139 , GLU B:140 , TYR B:141binding site for residue GOL B 501
2AC2SOFTWAREGLY A:2 , GLU A:3 , GLU A:6 , MET A:81 , ARG A:118 , ASN A:176 , TYR A:177 , ARG A:242 , PHE A:256 , ARG A:257 , TYR A:263 , ARG A:277 , THR A:278 , HOH A:604 , DC D:295 , DG D:298 , DT D:312 , DG D:313 , HOH D:402 , HOH D:406 , HOH D:407 , HOH D:410 , HOH D:417binding site for Di-nucleotide DA D 296 and CTG D 297
3AC3SOFTWAREGLY A:2 , GLU A:3 , GLU A:6 , LYS A:54 , GLY A:80 , MET A:81 , PHE A:120 , GLY A:175 , ASN A:176 , TYR A:177 , ARG A:242 , PHE A:256 , ARG A:257 , TYR A:263 , ARG A:277 , HOH A:548 , HOH A:604 , DA D:296 , DT D:299 , DA D:309 , DC D:310 , HOH D:402 , HOH D:405 , HOH D:406binding site for Di-nucleotide CTG D 297 and DG D 298
4AC4SOFTWAREGLY B:2 , GLU B:3 , GLU B:6 , MET B:81 , ARG B:118 , ASN B:176 , TYR B:177 , ARG B:242 , PHE B:256 , TYR B:263 , ARG B:277 , THR B:278 , HOH B:658 , DC E:295 , DG E:298 , DT E:312 , DG E:313 , HOH E:405binding site for Di-nucleotide DA E 296 and CTG E 297
5AC5SOFTWAREGLY B:2 , GLU B:3 , GLU B:6 , LYS B:54 , MET B:81 , PHE B:120 , GLY B:175 , ASN B:176 , TYR B:177 , ARG B:242 , PHE B:256 , TYR B:263 , ARG B:277 , HOH B:658 , HOH B:669 , DA E:296 , DT E:299 , DA E:309 , DC E:310 , HOH E:405binding site for Di-nucleotide CTG E 297 and DG E 298
6AC6SOFTWAREGLY C:2 , GLU C:3 , GLU C:6 , MET C:81 , ARG C:118 , ASN C:176 , TYR C:177 , TYR C:263 , ARG C:277 , THR C:278 , DC F:295 , DG F:298 , DT F:312 , DG F:313binding site for Di-nucleotide DA F 296 and CTG F 297
7AC7SOFTWAREGLY C:2 , GLU C:3 , GLU C:6 , LYS C:54 , GLY C:80 , MET C:81 , PHE C:120 , GLY C:175 , ASN C:176 , TYR C:177 , TYR C:263 , ARG C:277 , DA F:296 , DT F:299 , DA F:309 , DC F:310binding site for Di-nucleotide CTG F 297 and DG F 298

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gln A:67 -Pro A:68
2Gln B:67 -Pro B:68
3Glu B:199 -Ala B:200

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5ITY)

(-) 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:265
                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh....eeeeeee...........eeeeeeeeeeee..eeeeeeee..........eeeeee....eeeeeee.......eeeeeee......eeeeeee.....eeee..............hhhhhhhhhhh...hhhhhhhhhhhh.........hhhhhhhhhhhh......hhhhhhh.....hhhhhhhhhhhhhhhhh.....hhhhhhhhhh........eeee.....eeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ity A   2 GEGPELHLASQFVNEACRALVFGGCVEKSSVSRNPEVPFESSAYRISASARGKELRLILSPLPGAQPQQEPLALVFRFGMSGSFQLVPREELPRHAHLRFYTAPPGPRLALCFVDIRRFGRWDLGGKWQPGRGPCVLQEYQQFRENVLRNLADKAFDRPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARSVLEALQNPDLLELCHSVPKEVVQLGGRGYEEDFAAFRAWLRCYGMPGMSSLQDRHGRTIWFQGDPGPLAP 290
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201||     230       240   ||  255       265       275       285     
                                                                                                                                                                                                                                  202|                   244|                                        
                                                                                                                                                                                                                                   222                    250                                        


Chain B from PDB  Type:PROTEIN  Length:262
                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh...eeeeeee...........eeeeeeeeeeee..eeeeeeee..........eeeeee....eeeeeee.......eeeeeee......eeeeeee.....eeee..............hhhhhhhhhhh...hhhhh.hhhhhh.........hhhhhhhhhhhh......hhhhhh.....hhhhhhhhhhhhhhhhh.....hhhhhhhh........eeee.....eeee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ity B   2 GEGPELHLASQFVNEACRALVFGGCVEKSSVSRNPEVPFESSAYRISASARGKELRLILSPLPGAQPQQEPLALVFRFGMSGSFQLVPREELPRHAHLRFYTAPPGPRLALCFVDIRRFGRWDLGGKWQPGRGPCVLQEYQQFRENVLRNLADKAFDRPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARSVLEALNPDLLELCHSVPKEVVQLGGRGYDFAAFRAWLRCYGMPGMSSLQDRHGRTIWFQGDPGPLAP 290
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201|      231       241  ||   258       268       278       288  
                                                                                                                                                                                                                                 201|                   244|                                      
                                                                                                                                                                                                                                  222                    252                                      


Chain C from PDB  Type:PROTEIN  Length:261
                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh...eeeeeee...............eeeeeee....eeeeeee..........eeeee........eee........eeeeeee.......eeeee........................hhhhhhhhhhh...hhhhhhhhhhhh.hhhhhh..hhhhhhhhhhh.......hhhhhhh...hhhhhhhhhhhhhhhhh.....hhhhhhhh........eeee.....eeee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ity C   2 GEGPELHLASQFVNEACRALVFGGCVEKSSVSRNPEVPFESSAYRISASARGKELRLILSPLPGAQPQQEPLALVFRFGMSGSFQLVPREELPRHAHLRFYTAPPGPRLALCFVDIRRFGRWDLGGKWQPGRGPCVLQEYQQFRENVLRNLADKAFDRPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARSVLEANPDLLELCHSVPKEVVQLGGRGYDFAAFRAWLRCYGMPGMSSLQDRHGRTIWFQGDPGPLAP 290
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       222       232       242 ||    259       269       279       289 
                                                                                                                                                                                                                                200|                   244|                                      
                                                                                                                                                                                                                                 222                    252                                      


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


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


Chain F from PDB  Type:DNA  Length:26
                                                          
                 5ity 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 5ITY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (26, 26)

Asymmetric Unit(hide GO term definitions)

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  5ity
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  NEIL1_HUMAN | Q96FI4
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  3.2.2.-
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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 5itx

(-) Related Entries Specified in the PDB File

5itq 5itr 5itt 5itu 5itx