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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PRE-CATALYTIC TERNARY COMPLEX OF POLYMERASE LAMBDA WITH A DATP ANALOG OPPOSITE A TEMPLATING T AND AN RCMP AT THE PRIMER TERMINUS.
 
Authors :  R. A. Gosavi, A. F. Moon, T. A. Kunkel, L. C. Pedersen, K. Bebenek
Date :  20 Jun 12  (Deposition) - 11 Jul 12  (Release) - 11 Jul 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.01
Chains :  Asym./Biol. Unit :  A,D,H,I,P,T
Keywords :  Dna Polymerase, Transferase, Lyase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. A. Gosavi, A. F. Moon, T. A. Kunkel, L. C. Pedersen, K. Bebenek
The Catalytic Cycle For Ribonucleotide Incorporation By Human Dna Pol Lambda
Nucleic Acids Res. V. 40 1 2012
PubMed-ID: 22584622  |  Reference-DOI: 10.1093/NAR/GKS413

(-) 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 Taxid: 562
    Fragment: LOOP MUTANT OF DNA POLYMERASE LAMBDA
    Gene: POLL
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: POL LAMBDA, DNA POLYMERASE BETA-2, POL BETA2, DNA POLYMERASE KAPPA
 
Molecule 2 - 5'-D(*CP*GP*GP*CP*TP*GP*TP*AP*CP*TP*G)-3'
    Chains: T
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - 5'-D(*CP*AP*GP*TP*AP)-R(P*C)-3'
    Chains: P
    Engineered: YES
    Synthetic: YES
 
Molecule 4 - 5'-D(P*GP*CP*CP*G)-3'
    Chains: D
    Engineered: YES
    Synthetic: YES
 
Molecule 5 - 5'-D(P*TP*AP*CP*TP*G)-3'
    Chains: H
    Engineered: YES
    Synthetic: YES
 
Molecule 6 - 5'-D(P*CP*AP*GP*TP*A)-3'
    Chains: I
    Engineered: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ADHIPT

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (5, 6)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2F2A1Ligand/Ion2'-DEOXY-5'-O-[(S)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]METHYL}PHOSPHORYL]ADENOSINE
3MG1Ligand/IonMAGNESIUM ION
4MN1Ligand/IonMANGANESE (II) ION
5NA2Ligand/IonSODIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:427 , ASP A:429 , MN A:604 , F2A A:606 , HOH A:701BINDING SITE FOR RESIDUE MG A 601
2AC2SOFTWARECYS A:300 , ILE A:302 , ILE A:305 , DC D:3BINDING SITE FOR RESIDUE NA A 602
3AC3SOFTWAREARG A:517 , GLU A:529 , DG T:6BINDING SITE FOR RESIDUE CL A 603
4AC4SOFTWAREASP A:427 , ASP A:429 , ASP A:490 , MG A:601 , F2A A:606 , HOH A:823 , C P:6BINDING SITE FOR RESIDUE MN A 604
5AC5SOFTWARESER A:339 , ILE A:341 , ALA A:344 , HOH A:704 , HOH A:728 , DA P:5BINDING SITE FOR RESIDUE NA A 605
6AC6SOFTWAREARG A:386 , GLY A:416 , SER A:417 , ARG A:420 , CYS A:425 , 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:601 , MN A:604 , HOH A:701 , HOH A:703 , HOH A:735 , HOH A:737 , HOH A:782 , HOH A:823 , C P:6 , DT T:5 , DG T:6BINDING SITE FOR RESIDUE F2A A 606

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4FO6)

(-) 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 4FO6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4FO6)

(-) Exons   (0, 0)

(no "Exon" information available for 4FO6)

(-) 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:315
                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains d4fo6a1 A:252-328 DNA polymerase lambda                                      d4fo6a2 A:329-385 DNA polymerase lambda                  d4fo6a3 A:386-575 DNA polymerase lambda                                                                                                                                               SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh......hhhhhh.....hhhhhhhhhhhhhhh.hhhhhh...hhhhhhhhhh....hhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhh.hhhhh.eehhhhhhhhhhhhhhhhh.....eeeehhhhhh...ee..eeeeeee....hhhhhhhhhhhh..eeeeeee...eeeeee.........eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhh..ee....eee..ee.....eee..ee....hhhhhhhhh.....hhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fo6 A 252 HNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGGIFSRLLDSLRQEGFLTDDLVKGETKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGAKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW 575
                                   261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431     ||445       455       470       480       490       500       510       520       530       540       550       560       570     
                                                                                                                                                                                                                   437|                   464|                                                                                                         
                                                                                                                                                                                                                    442                    470                                                                                                         


Chain D from PDB  Type:DNA  Length:4
                                    
                 4fo6 D   1 GCCG   4


Chain H from PDB  Type:DNA  Length:5
                                     
                 4fo6 H   7 TACTG  11


Chain I from PDB  Type:DNA  Length:5
                                     
                 4fo6 I   1 CAGTA   5


Chain P from PDB  Type:DNA/RNA  Length:6
                                      
                 4fo6 P   1 CAGTAC   6


Chain T from PDB  Type:DNA  Length:11
                                           
                 4fo6 T   1 CGGCTGTACTG  11
                                    10
   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  (3, 3)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4FO6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4FO6)

(-) 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 4k4g 4k4h 4k4i 4x5v 4xa5 4xq8 4xrh 4xus 5ca7 5cb1 5chg 5cj7 5cp2 5cr0 5cwr 5ddm 5ddy 5dkw 5iii 5iij 5iik 5iil 5iim 5iin 5iio

(-) Related Entries Specified in the PDB File

3upq CRYSTAL STRUCTURE OF THE PRE-CATALYTIC TERNARY COMPLEX OF POLYMERASE LAMBDA WITH AN RATP ANALOG OPPOSITE A TEMPLATING T.
3uq0 CRYSTAL STRUCTURE OF THE POST-CATALYTIC PRODUCT COMPLEX OF POLYMERASE LAMBDA WITH AN RAMP AT THE PRIMER TERMINUS.
3uq2 CRYSTAL STRUCTURE OF THE POST-CATALYTIC PRODUCT COMPLEX OF POLYMERASE LAMBDA WITH AN RAMP INSERTED OPPOSITE A TEMPLATING G AND DAMP INSERTED OPPOSITE A TEMPLATING T AT THE PRIMER TERMINUS.