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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PRE-CATALYTIC TERNARY COMPLEX OF DNA POLYMERASE LAMBDA WITH A TEMPLATING A AND AN INCOMING DTTP
 
Authors :  M. J. Burak, K. E. Guja, M. Garcia-Diaz
Date :  26 Jan 15  (Deposition) - 03 Feb 16  (Release) - 10 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,D,P,T
Keywords :  Dna Polymerase Lambda, Protein-Dna Complex, Helix-Hairpin-Helix, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. J. Burak, K. E. Guja, M. Garcia-Diaz
Nucleotide Binding Interactions Modulate Dntp Selectivity And Facilitate 8-Oxo-Dgtp Incorporation By Dna Polymerase Lambda.
Nucleic Acids Res. V. 43 8089 2015
PubMed-ID: 26220180  |  Reference-DOI: 10.1093/NAR/GKV760

(-) 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
    Fragment: UNP RESIDUES 251-575
    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*A)-3')
    Chains: P
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 4 - DNA (5'-D(*CP*GP*GP*CP*AP*GP*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
1DOC1Mod. Residue2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION
3TTP1Ligand/IonTHYMIDINE-5'-TRIPHOSPHATE

(-) 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 , THR A:507 , GLY A:508 , ALA A:510 , ASN A:513 , MG A:603 , HOH A:740 , HOH A:761 , HOH A:765 , HOH A:766 , DOC P:101 , HOH P:216 , DA T:5binding site for residue TTP A 601
2AC2SOFTWARESER A:339 , ILE A:341 , ALA A:344 , HOH A:753 , DA P:5 , HOH P:221binding site for residue MG A 602
3AC3SOFTWAREASP A:427 , ASP A:429 , TTP A:601 , HOH A:761binding site for residue MG A 603
4AC4SOFTWAREASP A:490 , TYR A:505 , TTP A:601 , HOH A:739 , DA P:5 , HOH P:209 , HOH P:215 , HOH P:216 , DA T:5 , DG T:6 , HOH T:113binding site for residue DOC P 101

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1His A:252 -Asn A:253
2Gly A:508 -Ser A:509

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4XUS)

(-) 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:323
                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhh....hhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhh....hhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhhhhhhhh.eehhhhhhhhhhhhhhhhhhh...eeeehhhhhh...ee..eeeeee........hhhhhhhhhhhhh..eeeeee.........eeeeee.........eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee....eee.............ee....hhhhhhhhh.....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xus A 252 HNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNHGCKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW 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       542       552       562       572   
                                                                                                                                                                                                                                                                                                                         539|                                  
                                                                                                                                                                                                                                                                                                                          541                                  


Chain D from PDB  Type:DNA  Length:4
                                    
                 4xus D   1 GCCG   4


Chain P from PDB  Type:DNA  Length:5
                                     
                 4xus P   1 CAGTA   5


Chain T from PDB  Type:DNA  Length:11
                                           
                 4xus T   1 CGGCAGTACTG  11
                                    10
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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 4XUS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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
        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 5ca7 5cb1 5chg 5cj7 5cp2 5cr0 5cwr 5ddm 5ddy 5dkw 5iii 5iij 5iik 5iil 5iim 5iin 5iio

(-) Related Entries Specified in the PDB File

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