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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PRE-CATALYTIC TERNARY COMPLEX OF DNA POLYMERASE LAMBDA WITH A TEMPLATING 8-OXO-DG AND AN INCOMING DCTP
 
Authors :  M. J. Burak, K. E. Guja, M. Garcia-Diaz
Date :  01 Mar 16  (Deposition) - 17 Aug 16  (Release) - 28 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.72
Chains :  Asym./Biol. Unit :  A,D,P,T
Keywords :  Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. J. Burak, K. E. Guja, E. Hambardjieva, B. Derkunt, M. Garcia-Diaz
A Fidelity Mechanism In Dna Polymerase Lambda Promotes Error-Free Bypass Of 8-Oxo-Dg.
Embo J. V. 35 2045 2016
PubMed-ID: 27481934  |  Reference-DOI: 10.15252/EMBJ.201694332

(-) Compounds

Molecule 1 - DNA POLYMERASE LAMBDA
    ChainsA
    EC Number2.7.7.7, 4.2.99.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    GenePOLL
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPOL LAMBDA,DNA POLYMERASE BETA-2,POL BETA2,DNA POLYMERASE KAPPA
 
Molecule 2 - DNA (5'-D(P*GP*CP*CP*G)-3')
    ChainsD
    EngineeredYES
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES
 
Molecule 3 - DNA (5'-D(*CP*AP*GP*TP*AP*(DOC))-3')
    ChainsP
    EngineeredYES
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES
 
Molecule 4 - DNA (5'-D(*CP*GP*GP*CP*(8OG)P*GP*TP*AP*CP*TP*G)-3')
    ChainsT
    EngineeredYES
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ADPT

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 6)

Asymmetric/Biological Unit (5, 6)
No.NameCountTypeFull Name
18OG1Mod. Nucleotide8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
2DCT1Ligand/Ion2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE
3DOC1Mod. Nucleotide2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
4MG1Ligand/IonMAGNESIUM ION
5NA2Ligand/IonSODIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:386 , GLY A:416 , SER A:417 , ARG A:420 , GLY A:426 , ASP A:427 , ASP A:429 , TYR A:505 , PHE A:506 , ALA A:510 , ASN A:513 , MG A:602 , HOH A:705 , HOH A:715 , HOH A:781 , HOH A:794 , HOH A:804 , HOH A:815 , HOH A:865 , DOC P:6 , HOH P:114 , 8OG T:5binding site for residue DCT A 601
2AC2SOFTWAREASP A:427 , ASP A:429 , DCT A:601 , HOH A:804binding site for residue MG A 602
3AC3SOFTWARESER A:339 , ILE A:341 , ALA A:344 , HOH A:928 , DA P:5 , HOH P:107binding site for residue NA A 603
4AC4SOFTWARESER A:463 , HOH A:800 , HOH A:922 , HOH A:998 , HOH T:104 , HOH T:121binding site for residue NA A 604

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asn A:253 -Leu A:254
2Gly A:508 -Ser A:509

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5IIJ)

(-) 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
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Chain A from PDB  Type:PROTEIN  Length:314
                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhh....hhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhhhhhhhh.eehhhhhhhhhhhhhhhhh.....eeeehhhhhh...ee..eeeeee.........hhhhhhhhhhhh..eeeeee.........eeeeee.........eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eee....eee..........hhhhhhhhh.....hhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5iij A 252 HNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVPGRVLPTPTEKDVFRLLGLPYREPAERDW 575
                                   261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531    || 551       561       571    
                                                                                                                                                                                                                                                                                                                      536|                            
                                                                                                                                                                                                                                                                                                                       547                            

Chain D from PDB  Type:DNA  Length:4
                                    
                 5iij D   1 GCCG   4

Chain P from PDB  Type:DNA  Length:6
                                      
                 5iij P   1 CAGTAc   6
                                 |
                                 6-DOC

Chain T from PDB  Type:DNA  Length:11
                                           
                 5iij T   1 CGGCxGTACTG  11
                                |   10 
                                |      
                                5-8OG  

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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 5IIJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asn A:253 - Leu A:254   [ RasMol ]  
    Gly A:508 - Ser A:509   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        DPOLL_HUMAN | Q9UGP51nzp 1rzt 1xsl 1xsn 1xsp 2bcq 2bcr 2bcs 2bcu 2bcv 2gws 2jw5 2pfn 2pfo 2pfp 2pfq 3c5f 3c5g 3hw8 3hwt 3hx0 3mda 3mdc 3mgh 3mgi 3pml 3pmn 3pnc 3upq 3uq0 3uq2 4fo6 4k4g 4k4h 4k4i 4x5v 4xa5 4xq8 4xrh 4xus 5ca7 5cb1 5chg 5cj7 5cp2 5cr0 5cwr 5ddm 5ddy 5dkw 5iii 5iik 5iil 5iim 5iin 5iio

(-) Related Entries Specified in the PDB File

5iii 5iik 5iil 5iim 5iin 5iio