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(-) Description

Title :  CRYSTAL STRUCTURE OF THE POST-CATALYTIC NICK COMPLEX OF DNA POLYMERASE LAMBDA WITH A TEMPLATING 8-OXO-DG AND INCORPORATED DA
 
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 :  1.96
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
    Chains: A
    EC Number: 2.7.7.7, 4.2.99.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Gene: POLL
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: POL LAMBDA,DNA POLYMERASE BETA-2,POL BETA2,DNA POLYMERASE KAPPA
 
Molecule 2 - DNA (5'-D(P*GP*CP*CP*G)-3')
    Chains: D
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*CP*AP*GP*TP*AP*AP*T)-3')
    Chains: P
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 4 - DNA (5'-D(*CP*GP*GP*CP*AP*(8OG)P*TP*AP*CP*TP*G)-3')
    Chains: T
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ADPT

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
18OG1Mod. Nucleotide8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
2CIT1Ligand/IonCITRIC ACID
3NA2Ligand/IonSODIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:386 , GLY A:416 , SER A:417 , ARG A:420 , GLY A:426 , ASP A:427 , ASP A:429 , ARG A:488 , NA A:603 , HOH A:741 , HOH A:781 , HOH A:802 , HOH A:867 , DT P:7binding site for residue CIT A 601
2AC2SOFTWARESER A:339 , ILE A:341 , ALA A:344 , HOH A:917 , DA P:5 , HOH P:113binding site for residue NA A 602
3AC3SOFTWAREASP A:427 , ASP A:429 , CIT A:601 , HOH A:851 , DT P:7binding site for residue NA A 603

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:508 -Ser A:509

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5IIL)

(-) 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:326
                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.....hhhhhhhh...hhhhhhhhhhhhhhh.hhhhhh...hhhhhhhhhh....hhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhh.hhhhh.eehhhhhhhhhhhhhhhhhhh...eeeehhhhhh...ee.eeeeeee........hhhhhhhhhhhhh..eeeeee.........eeeeee.........eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee....eee..ee.....eee..eee...hhhhhhhhh.....hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5iil A 250 TNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGCKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW 575
                                   259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569      


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


Chain P from PDB  Type:DNA  Length:7
                                       
                 5iil P   1 CAGTAAT   7


Chain T from PDB  Type:DNA  Length:11
                                           
                 5iil T   1 CGGCAxTACTG  11
                                 |  10 
                                 6-8OG
   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 5IIL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    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 | Q9UGP5: 1nzp 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 5iij 5iik 5iim 5iin 5iio

(-) Related Entries Specified in the PDB File

5iii 5iij 5iik 5iim 5iin 5iio