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(-) Description

Title :  BASE PAIRING MECHANISM OF N2,3-ETHENOGUANINE WITH DCTP BY HUMAN POLYMERASE IOTA
 
Authors :  L. Zhao
Date :  26 Jun 12  (Deposition) - 29 Aug 12  (Release) - 31 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Human Dna Polymerase Iota, Dna Polymerase, Dna Replication, Lesion Bypass, 2'-Fluoro Arabinose, N2, 3-Ethenoguanine, Dttp, Template, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Zhao, M. G. Pence, P. P. Christov, Z. Wawrzak, J. Y. Choi, C. J. Rizzo, M. Egli, F. P. Guengerich
Basis Of Miscoding Of The Dna Adduct N2, 3-Ethenoguanine By Human Y-Family Dna Polymerases.
J. Biol. Chem. V. 287 35516 2012
PubMed-ID: 22910910  |  Reference-DOI: 10.1074/JBC.M112.403253

(-) Compounds

Molecule 1 - DNA (5'-D(*TP*CP*TP*(EFG) P*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*(DOC))-3')
    Chains: B, C
    Engineered: YES
    Organism Taxid: 32630
    Other Details: SITE-SPECIFICALLY MODIFIED OLIGONUCLEOTIDE
    Synthetic: YES
 
Molecule 2 - DNA POLYMERASE IOTA
    Chains: A
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 GOLD (DE3)
    Expression System Taxid: 562
    Gene: POLI, RAD30B
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ETA2, RAD30 HOMOLOG B

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 7)

Asymmetric/Biological Unit (5, 7)
No.NameCountTypeFull Name
1DCP1Ligand/Ion2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
2DOC1Mod. Nucleotide2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
3EFG1Mod. Nucleotide1-(2-DEOXY-2-FLUORO-5-O-PHOSPHONO-BETA-D-ARABINOFURANOSYL)-1H-IMIDAZO[2,1-B]PURIN-4(5H)-ONE
4MG3Ligand/IonMAGNESIUM ION
5NA1Ligand/IonSODIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:34 , LEU A:35 , ASP A:126 , DCP A:503 , MG A:505BINDING SITE FOR RESIDUE MG A 501
2AC2SOFTWARELYS A:237 , ILE A:239 , ILE A:242 , HOH A:677 , DC B:12 , HOH B:101BINDING SITE FOR RESIDUE NA A 502
3AC3SOFTWAREASP A:34 , LEU A:35 , ASP A:36 , CYS A:37 , PHE A:38 , TYR A:39 , VAL A:64 , THR A:65 , TYR A:68 , ARG A:71 , LYS A:77 , ASP A:126 , LYS A:214 , MG A:501 , MG A:505 , HOH A:653 , DOC B:13 , EFG C:840 , DG C:841BINDING SITE FOR RESIDUE DCP A 503
4AC4SOFTWARESER A:106 , ARG A:122 , GLY A:124 , PHE A:125 , GLU A:127 , ASN A:128 , HOH A:601BINDING SITE FOR RESIDUE MG A 504
5AC5SOFTWAREASP A:34 , ASP A:126 , GLU A:127 , MG A:501 , DCP A:503 , DOC B:13BINDING SITE FOR RESIDUE MG A 505

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4FS2)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Lys A:214 -Pro A:215
2Ser A:313 -Glu A:314
3Ser A:350 -Ser A:351

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4FS2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4FS2)

(-) Exons   (0, 0)

(no "Exon" information available for 4FS2)

(-) 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:383
                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.hhhhhhhhhhhhhhh...eeeee..eeeeehhhhhhh.....eehhhhhhhh...eeee...hhhhhhhhhhhhhhhhhhh..eeee...eeeeehhhhhhhhhhh.hhhhh.......ee.hhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhh......eee.hhhhhhhhhhhh.hhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............eeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeee.........eeeeee.hhhhh...hhhhhhhhhhhhhhhhh.......eeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fs2 A  26 SSRVIVHVDLDCFYAQVEMISNPELKDKPLGVQQKYLVVTCNYEARKLGVKKLMNVRDAKEKCPQLVLVNGEDLTRYREMSYKVTELLEEFSPVVERLGFDENFVDLTEMVEKRLQQLQSDELSAVTVSGHVYNNQSINLLDVLHIRLLVGSQIAAEMREAMYNQLGLTGCAGVASNKLLAKLVSGVFKPNQQTVLLPESCQHLIHSLNHIKEIPGIGYKTAKCLEALGINSVRDLQTFSPKILEKELGISVAQRIQKLSFGEDNSPVILSGPPQSFSEEDSFKKCSSEVEAKNKIEELLASLLNRVCQDGRKPHTVRLIIRRYSSEKHYGRESRQCPIPSHVIQKDVMTPMVDILMKLFRNMVNVKMPFHLTLLSVCFCNLK 414
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365     ||381       391       401       411   
                                                                                                                                                                                                                                                                                                                                                                                   371|                                    
                                                                                                                                                                                                                                                                                                                                                                                    378                                    


Chain B from PDB  Type:DNA  Length:7
                                       
                 4fs2 B   7 AGGACCc  13
                                  |
                                 13-DOC


Chain C from PDB  Type:DNA  Length:8
                                        
                 4fs2 C 840 gGGGTCCT 847
                            |       
                            |       
                          840-EFG
   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 4FS2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4FS2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4FS2)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Lys A:214 - Pro A:215   [ RasMol ]  
    Ser A:313 - Glu A:314   [ RasMol ]  
    Ser A:350 - Ser A:351   [ RasMol ]  
 

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  4fs2
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  POLI_HUMAN | Q9UNA4
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  2.7.7.7
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 Related Entries

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

UniProtKB/Swiss-Prot
        POLI_HUMAN | Q9UNA4: 1t3n 1zet 2alz 2dpi 2dpj 2fll 2fln 2flp 2khu 2khw 2ktf 2l0f 2l0g 2mbb 3epg 3epi 3g6v 3g6x 3g6y 3gv5 3gv7 3gv8 3h40 3h4b 3h4d 3ngd 3osn 3q8p 3q8q 3q8r 3q8s 4ebc 4ebd 4ebe 4eyh 4eyi 4fs1 5kt2 5kt3 5kt4 5kt5 5kt6 5kt7 5ulw 5ulx

(-) Related Entries Specified in the PDB File

3osn 3v6h 3v6j 3v6k 4fs1