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(-) Description

Title :  HUMAN DNA POLYMERASE IOTA INCORPORATING DATP OPPOSITE N-(DEOXYGUANOSIN-8-YL)-1-AMINOPYRENE LESION
 
Authors :  K. Kirouac, H. Ling
Date :  01 May 12  (Deposition) - 09 Jan 13  (Release) - 20 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  B,P,T
Keywords :  Dna Polymerase, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. N. Kirouac, A. K. Basu, H. Ling
Replication Of A Carcinogenic Nitropyrene Dna Lesion By Human Y-Family Dna Polymerase.
Nucleic Acids Res. V. 41 2060 2013
PubMed-ID: 23268450  |  Reference-DOI: 10.1093/NAR/GKS1296

(-) Compounds

Molecule 1 - DNA POLYMERASE IOTA
    Chains: B
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 26-445
    Gene: POLI, RAD30B
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ETA2, RAD30 HOMOLOG B
 
Molecule 2 - DNA TEMPLATE
    Chains: T
    Engineered: YES
    Other Details: SYNTHESIZED
    Synthetic: YES
 
Molecule 3 - DNA PRIMER
    Chains: P
    Engineered: YES
    Other Details: SYNTHESIZED
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : BPT

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1DG81Mod. Nucleotide2'-DEOXY-8-(PYREN-1-YLAMINO)GUANOSINE 5'-(DIHYDROGENPHOSPHATE)
2DTP1Ligand/Ion2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
3MG3Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS B:37 , PHE B:38 , TYR B:39 , VAL B:64 , THR B:65 , TYR B:68 , ARG B:71 , LYS B:77 , ASP B:126 , LYS B:214 , MG B:502 , MG B:503 , DC P:873 , DG8 T:840BINDING SITE FOR RESIDUE DTP B 501
2AC2SOFTWAREASP B:34 , ASP B:126 , GLU B:127 , DTP B:501 , MG B:503 , DC P:873BINDING SITE FOR RESIDUE MG B 502
3AC3SOFTWAREASP B:34 , LEU B:35 , ASP B:126 , DTP B:501 , MG B:502BINDING SITE FOR RESIDUE MG B 503
4AC4SOFTWARELYS B:237 , ILE B:239 , ILE B:242 , HOH B:602 , DC P:872BINDING SITE FOR RESIDUE MG B 504

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ser B:149 -Ala B:150
2Lys B:214 -Pro B:215
3Lys B:414 -Ala B:415

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4EYI)

(-) 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 B from PDB  Type:PROTEIN  Length:378
                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee.hhhhhhhhhhhhhhh...eeeee..eeeee.hhhh.......eehhhhhhhh...eeee...hhhhhhhhhhhhhhhhh....eeee...eeeeehhhhhhhhhhh.hhhhh.......ee.hhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhh.......eee.hhhhhhhhhhh..hhhhh...hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............eeeeeee.........hhhhhhhhhhhhhhhhhhhh.eeeeeeeee....eeeeee.........hhhhhhhhhhhhhhhhh.........eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4eyi B  26 SSRVIVHVDLDCFYAQVEMISNPELKDKPLGVQQKYLVVTCNYEARKLGVKKLMNVRDAKEKCPQLVLVNGEDLTRYREMSYKVTELLEEFSPVVERLGFDENFVDLTEMVEKRLQQLQSDELSAVTVSGHVYNNQSINLLDVLHIRLLVGSQIAAEMREAMYNQLGLTGCAGVASNKLLAKLVSGVFKPNQQTVLLPESCQHLIHSLNHIKEIPGIGYKTAKCLEALGINSVRDLQTFSPKILEKELGISVAQRIQKLSFGEDNSPVILSGPPQSFSEEDSFKKCSSEVEAKNKIEELLASLLNRVCQDGRKPHTVRLIIRRYRESRQCPIPSHVIQKDVMTPMVDILMKLFRNMVNVKMPFHLTLLSVCFCNLKAL 416
                                    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   ||  362       378       388       398       408        
                                                                                                                                                                                                                                                                                                                                                             349|           371|                                      
                                                                                                                                                                                                                                                                                                                                                              357            378                                      


Chain P from PDB  Type:DNA  Length:7
                                       
                 4eyi P 867 AGGACCC 873


Chain T from PDB  Type:DNA  Length:8
                                        
                 4eyi T 840 gGGGTCCT 847
                            |       
                          840-DG8
   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 4EYI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)

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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 4fs1 4fs2 5kt2 5kt3 5kt4 5kt5 5kt6 5kt7 5ulw 5ulx

(-) Related Entries Specified in the PDB File

4eyh