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(-) Description

Title :  CONFORMATIONALLY RESTRAINED NORTH-METHANOCARBA-2'-DEOXYADENOSINE CORRECTS THE ERROR-PRONE NATURE OF HUMAN DNA POLYMERASE IOTA
 
Authors :  R. L. Eoff, A. Ketkar, S. Banerjee
Date :  23 Mar 12  (Deposition) - 13 Jun 12  (Release) - 11 Jul 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.57
Chains :  Asym./Biol. Unit :  A,P,T
Keywords :  Polymerase, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Ketkar, M. K. Zafar, S. Banerjee, V. E. Marquez, M. Egli, R. L. Eoff
A Nucleotide-Analogue-Induced Gain Of Function Corrects The Error-Prone Nature Of Human Dna Polymerase Iota.
J. Am. Chem. Soc. V. 134 10698 2012
PubMed-ID: 22632140  |  Reference-DOI: 10.1021/JA304176Q

(-) Compounds

Molecule 1 - DNA POLYMERASE IOTA
    Chains: A
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBG101
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    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 - 5'-D(P*AP*GP*GP*AP*CP*CP*(DOC))-3'
    Chains: P
    Engineered: YES
    Other Details: 7-MER PRIMER DNA
    Synthetic: YES
 
Molecule 3 - 5'-D(P*CP*TP*GP*GP*GP*TP*CP*CP*T)-3'
    Chains: T
    Engineered: YES
    Other Details: 9-MER TEMPLATE DNA
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : APT

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
10OJ1Ligand/IonSOUTH-METHANOCARBA-2'-DEOXYADENOSINE TRIPHOSPHATE
2CA3Ligand/IonCALCIUM ION
3DOC1Mod. Nucleotide2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
4GOL2Ligand/IonGLYCEROL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:35 , CYS A:37 , PHE A:38 , TYR A:39 , VAL A:64 , THR A:65 , TYR A:68 , ARG A:71 , LYS A:77 , LEU A:78 , ASP A:126 , LYS A:214 , CA A:503 , HOH A:616 , HOH A:650 , HOH A:651 , HOH A:652 , HOH A:662 , HOH A:722 , DOC P:7 , HOH P:101 , DT T:4 , DG T:5 , HOH T:110BINDING SITE FOR RESIDUE 0OJ A 501
2AC2SOFTWAREASP A:34 , GLU A:127 , HOH A:651 , HOH A:662 , HOH A:707BINDING SITE FOR RESIDUE CA A 502
3AC3SOFTWAREASP A:34 , LEU A:35 , ASP A:126 , 0OJ A:501BINDING SITE FOR RESIDUE CA A 503
4AC4SOFTWARELYS A:237 , ILE A:239 , ILE A:242 , HOH A:702 , HOH A:708 , DC P:6BINDING SITE FOR RESIDUE CA A 504
5AC5SOFTWAREASP A:98 , GLU A:304 , GLU A:305 , HOH A:611 , HOH A:629 , HOH A:701 , DG T:6 , HOH T:103BINDING SITE FOR RESIDUE GOL A 505
6AC6SOFTWAREGLU A:305 , ARG A:357 , HOH A:657 , HOH A:658 , DG T:5 , DG T:6 , DG T:7BINDING SITE FOR RESIDUE GOL A 506

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys A:214 -Pro A:215

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4EBD)

(-) 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:376
                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d4ebda1 A:26-299 DNA polymerase iota                                                                                                                                                                                                                                              d4ebda2 A:300-414 DNA polymerase iota                                                                  SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.hhhhhhhhhhh.......eeeee..eeeeehhhhhh......eehhhhhh.....eeee...hhhhhhhhhhhhhhhhhhh..eeee...eeeeehhhhhhhhhhhh..hhhhh.....ee.hhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhh.......eee.hhhhhhhhhhh..hhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh................eeeeee.....hhhhhhhhhhhhhhhhhhhh.....eeeeeeeee...eeeeeee.hhhhhh..hhhhhhhhhhhhhhhhh.........eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ebd A  26 SSRVIVHVDLDCFYAQVEMISNPELKDKPLGVQQKYLVVTCNYEARKLGVKKLMNVRDAKEKCPQLVLVNGEDLTRYREMSYKVTELLEEFSPVVERLGFDENFVDLTEMVEKRLQQLQSDELSAVTVSGHVYNNQSINLLDVLHIRLLVGSQIAAEMREAMYNQLGLTGCAGVASNKLLAKLVSGVFKPNQQTVLLPESCQHLIHSLNHIKEIPGIGYKTAKCLEALGINSVRDLQTFSPKILEKELGISVAQRIQKLSFGEDNSPVILSGPPQSFSEEDSFKKCSSEVEAKNKIEELLASLLNRVCQDRKPHTVRLIIRRYGRESRQCPIPSHVIQKDVMTPMVDILMKLFRNMVNVKMPFHLTLLSVCFCNLK 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|      346  ||   362       378       388       398       408      
                                                                                                                                                                                                                                                                                                                                               335|         349|            371|                                    
                                                                                                                                                                                                                                                                                                                                                337          356             378                                    


Chain P from PDB  Type:DNA  Length:7
                                       
                 4ebd P   1 AGGACCc   7
                                  |
                                  7-DOC


Chain T from PDB  Type:DNA  Length:9
                                         
                 4ebd T   3 CTGGGTCCT  11
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 ]  
 

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

(-) Related Entries Specified in the PDB File

1t3n 2alz 3gv5 3gv7 3gv8 3h40 4ebc 4ebe