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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN DNA POLYMERASE LAMBDA IN COMPLEX WITH NICKED DNA AND PYROPHOSPHATE
 
Authors :  M. Garcia-Diaz, K. Bebenek, J. M. Krahn, T. A. Kunkel, L. C. Pedersen
Date :  19 Oct 04  (Deposition) - 18 Jan 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
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. Garcia-Diaz, K. Bebenek, J. M. Krahn, T. A. Kunkel, L. C. Pedersen
A Closed Conformation For The Pol Lambda Catalytic Cycle.
Nat. Struct. Mol. Biol. V. 12 97 2005
PubMed-ID: 15608652  |  Reference-DOI: 10.1038/NSMB876
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*CP*GP*GP*CP*CP*GP*TP*AP*CP*TP*G)-3'
    ChainsT
    EngineeredYES
    Other DetailsTEMPLATE DNA
    SyntheticYES
 
Molecule 2 - 5'-D(*CP*AP*GP*TP*AP*CP*G)-3'
    ChainsP
    EngineeredYES
    Other DetailsPRIMER DNA
    SyntheticYES
 
Molecule 3 - 5'-D(P*GP*CP*CP*G)-3'
    ChainsD
    EngineeredYES
    Other DetailsDOWNSTREAM PRIMER DNA
    SyntheticYES
 
Molecule 4 - DNA POLYMERASE LAMBDA
    ChainsA
    EC Number2.7.7.7
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET22-B
    Expression System StrainBL21(DE3)RIL
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Fragment39 KDA CATALYTIC C-TERMINAL DOMAIN
    GenePOLL
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPOL LAMBDA, DNA POLYMERASE BETA-2, POL BETA2

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ADPT

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1NA4Ligand/IonSODIUM ION
2PPV1Ligand/IonPYROPHOSPHATE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:427 , ASP A:429 , PPV A:579 , HOH A:608 , HOH A:686 , DG P:7BINDING SITE FOR RESIDUE NA A 576
2AC2SOFTWARESER A:339 , ILE A:341 , ALA A:344 , DA P:5 , HOH P:40 , HOH P:172BINDING SITE FOR RESIDUE NA A 577
3AC3SOFTWARESER A:463 , HOH A:613 , HOH A:691 , HOH A:738 , HOH T:21 , HOH T:44BINDING SITE FOR RESIDUE NA A 578
4AC4SOFTWARELYS A:324 , DG D:1BINDING SITE FOR RESIDUE NA D 503
5AC5SOFTWAREARG A:386 , GLY A:416 , SER A:417 , ARG A:420 , GLY A:426 , ASP A:429 , NA A:576 , HOH A:584 , HOH A:631 , HOH A:686 , DG P:7BINDING SITE FOR RESIDUE PPV A 579

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1XSP)

(-) Cis Peptide Bonds  (1, 1)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_020269R438WDPOLL_HUMANPolymorphism3730477AR438W

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DNA_POLYMERASE_XPS00522 DNA polymerase family X signature.DPOLL_HUMAN416-435  1A:416-435

(-) Exons   (5, 5)

Asymmetric/Biological Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1kENST000003701691kENSE00001451987chr10:103347178-103347003176DPOLL_HUMAN1-39390--
1.3ENST000003701693ENSE00001731892chr10:103345913-103345619295DPOLL_HUMAN39-137990--
1.4bENST000003701694bENSE00001100422chr10:103345235-103345073163DPOLL_HUMAN137-191550--
1.5eENST000003701695eENSE00001617344chr10:103344676-103344359318DPOLL_HUMAN192-2971061A:249-29749
1.6bENST000003701696bENSE00002151653chr10:103343438-103343265174DPOLL_HUMAN298-355581A:298-35558
1.7bENST000003701697bENSE00001593760chr10:103342648-103342520129DPOLL_HUMAN356-398431A:356-39843
1.8cENST000003701698cENSE00001691940chr10:103340173-103340005169DPOLL_HUMAN399-455571A:399-45557
1.9gENST000003701699gENSE00001451993chr10:103339574-103338639936DPOLL_HUMAN455-5751211A:455-575121

(-) 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:327
 aligned with DPOLL_HUMAN | Q9UGP5 from UniProtKB/Swiss-Prot  Length:575

    Alignment length:327
                                   258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       
          DPOLL_HUMAN   249 ATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGCKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW 575
               SCOP domains ---d1xspa1 A:252-327 DNA polymerase lambda                                     -d1xspa2 A:329-385 DNA polymerase lambda                  d1xspa3 A:386-575 DNA polymerase lambda                                                                                                                                                        SCOP domains
               CATH domains 1xspA01 A:249-331  [code=1.10.150.110, no name defined]                            1xspA02 A:332-385                                     1xspA03 A:386-508 Beta Polymerase, domain 2                                                                                1xspA04 A:509-575 Beta Polymerase, domain 3                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------DNA_pol_lambd_f-1xspA01 A:335-385                  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhh....hhhhhhhhhhhhhh..hhhhhhh..hhhhhhhhhh....hhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhh.hhhhh.eehhhhhhhhhhhhhhhhh.....eeeehhhhhh...ee..eeeeee.........hhhhhhhhhhhh..eeeeee.........eeeeee.........eeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee....eee..ee.....eee..ee....hhhhhhhhh.....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------W----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_POLYMERASE_X    -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5e  PDB: A:249-297 UniProt: 192-297       Exon 1.6b  PDB: A:298-355 UniProt: 298-355                Exon 1.7b  PDB: A:356-398 UniProt: 356-398 Exon 1.8c  PDB: A:399-455 UniProt: 399-455               ------------------------------------------------------------------------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9g  PDB: A:455-575 UniProt: 455-575                                                                                Transcript 1 (2)
                 1xsp A 249 ATNHNLHITEKLEVLAKAYSVQGDKWRALGYAKAINALKSFHKPVTSYQEACSIPGIGKRMAEKIIEILESGHLRKLDHISESVPVLELFSNIWGAGTKTAQMWYQQGFRSLEDIRSQASLTTQQAIGLKHYSDFLERMPREEATEIEQTVQKAAQAFNSGLLCVACGSYRRGKATCGDVDVLITHPDGRSHRGIFSRLLDSLRQEGFLTDDLVSQEENGQQQKYLGVCRLPGPGRRHRRLDIIVVPYSEFACALLYFTGSAHFNRSMRALAKTKGMSLSEHALSTAVVRNTHGAKVGPGRVLPTPTEKDVFRLLGLPYREPAERDW 575
                                   258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       

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

Chain P from PDB  Type:DNA  Length:7
                                       
                 1xsp P   1 CAGTACG   7

Chain T from PDB  Type:DNA  Length:11
                                           
                 1xsp T   1 CGGCCGTACTG  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

(-) CATH Domains  (4, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DPOLL_HUMAN | Q9UGP5)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0034061    DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a nucleic acid template and a 3'hydroxyl group.
    GO:0003887    DNA-directed DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and a 3'hydroxyl group.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0071897    DNA biosynthetic process    The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0006303    double-strand break repair via nonhomologous end joining    The repair of a double-strand break in DNA in which the two broken ends are rejoined with little or no sequence complementarity. Information at the DNA ends may be lost due to the modification of broken DNA ends. This term covers instances of separate pathways, called classical (or canonical) and alternative nonhomologous end joining (C-NHEJ and A-NHEJ). These in turn may further branch into sub-pathways, but evidence is still unclear.
    GO:0006289    nucleotide-excision repair    A DNA repair process in which a small region of the strand surrounding the damage is removed from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. Nucleotide excision repair recognizes a wide range of substrates, including damage caused by UV irradiation (pyrimidine dimers and 6-4 photoproducts) and chemicals (intrastrand cross-links and bulky adducts).
    GO:0016446    somatic hypermutation of immunoglobulin genes    Mutations occurring somatically that result in amino acid changes in the rearranged V regions of immunoglobulins.
cellular component
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DPOLL_HUMAN | Q9UGP51nzp 1rzt 1xsl 1xsn 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 5iil 5iim 5iin 5iio

(-) Related Entries Specified in the PDB File

1xsl 1xsn