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(-) Description

Title :  HUMAN DNA POLYMERASE KAPPA EXTENDING OPPOSITE A CIS-SYN THYMINE DIMER
 
Authors :  R. Vasquez-Del Carpio, T. D. Silverstein, S. Lone, R. E. Johnson, S. Pr L. Prakash, A. K. Aggarwal
Date :  14 Dec 10  (Deposition) - 28 Dec 11  (Release) - 28 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.34
Chains :  Asym. Unit :  A,B,P,Q,T,U
Biol. Unit 1:  A,P,T  (1x)
Biol. Unit 2:  B,Q,U  (1x)
Keywords :  Dna Nucleotidyltransferase, Dna Binding Nucleotide Binding Magnesium Binding, Nucleus, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Vasquez-Del Carpio, T. D. Silverstein, S. Lone, R. E. Johnson, L. Prakash, S. Prakash, A. K. Aggarwal
Role Of Human Dna Polymerase Kappa In Extension Opposite From A Cis-Syn Thymine Dimer.
J. Mol. Biol. V. 408 252 2011
PubMed-ID: 21354175  |  Reference-DOI: 10.1016/J.JMB.2011.02.042

(-) Compounds

Molecule 1 - DNA POLYMERASE KAPPA
    ChainsA, B
    EC Number2.7.7.7
    EngineeredYES
    Expression SystemSACCHAROMYCES CEREVISIAE
    Expression System PlasmidPBJ943
    Expression System StrainBJ5464
    Expression System Taxid4932
    Expression System Vector TypePLASMID
    FragmentRESIDUES 19-528
    GenePOLK, DINB1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDINB PROTEIN, DINP
 
Molecule 2 - 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*CP*A)-3'
    ChainsP, Q
    EngineeredYES
    Other DetailsOLIGONUCLEOTIDE
    SyntheticYES
 
Molecule 3 - 5'-D(*TP*TP*CP*CP*(TTD) P*GP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'
    ChainsT, U
    EngineeredYES
    Other DetailsOLIGONUCLEOTIDE
    SyntheticYES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABPQTU
Biological Unit 1 (1x)A P T 
Biological Unit 2 (1x) B Q U

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1DTP2Ligand/Ion2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
2MG4Ligand/IonMAGNESIUM ION
3TTD2Mod. NucleotideCIS-SYN CYCLOBUTANE THYMINE DIMER
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1DTP1Ligand/Ion2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3TTD1Mod. NucleotideCIS-SYN CYCLOBUTANE THYMINE DIMER
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1DTP1Ligand/Ion2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3TTD1Mod. NucleotideCIS-SYN CYCLOBUTANE THYMINE DIMER

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMG A:2 , ALA A:26 , ASP A:107 , MET A:108 , ASP A:109 , ALA A:110 , PHE A:111 , TYR A:112 , SER A:137 , THR A:138 , TYR A:141 , ARG A:144 , ASP A:198 , LYS A:328 , DA P:13 , TTD T:6BINDING SITE FOR RESIDUE DTP A 1
2AC2SOFTWAREDTP A:1 , ASP A:107 , MET A:108 , ASP A:198BINDING SITE FOR RESIDUE MG A 2
3AC3SOFTWAREARG A:352 , VAL A:354 , ILE A:357 , DC P:12BINDING SITE FOR RESIDUE MG A 3
4AC4SOFTWAREMG B:1 , ALA B:26 , ASP B:107 , MET B:108 , ALA B:110 , PHE B:111 , TYR B:112 , SER B:137 , THR B:138 , TYR B:141 , ARG B:144 , ALA B:151 , ASP B:198 , GLU B:199 , LYS B:328 , DA Q:13 , TTD U:6BINDING SITE FOR RESIDUE DTP B 2
5AC5SOFTWAREDTP B:2 , ASP B:107 , MET B:108 , ASP B:198BINDING SITE FOR RESIDUE MG B 1
6AC6SOFTWAREARG B:352 , VAL B:354 , ILE B:357 , DC Q:12BINDING SITE FOR RESIDUE MG B 4

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3PZP)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Lys A:328 -Pro A:329
2Phe A:500 -Pro A:501
3Gly B:30 -Leu B:31
4Lys B:328 -Pro B:329
5Arg B:409 -Asp B:410
6Phe B:500 -Pro B:501

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_048886S423RPOLK_HUMANPolymorphism35257416A/BS423R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_048886S423RPOLK_HUMANPolymorphism35257416AS423R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_048886S423RPOLK_HUMANPolymorphism35257416BS423R

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UMUCPS50173 UmuC domain profile.POLK_HUMAN103-358
 
  2A:103-358
B:103-358
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UMUCPS50173 UmuC domain profile.POLK_HUMAN103-358
 
  1A:103-358
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UMUCPS50173 UmuC domain profile.POLK_HUMAN103-358
 
  1-
B:103-358

(-) Exons   (12, 24)

Asymmetric Unit (12, 24)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002414361aENSE00002022143chr5:74807581-74807739159POLK_HUMAN-00--
1.4aENST000002414364aENSE00002160720chr5:74842835-74842982148POLK_HUMAN1-45452A:25-45
B:19-45
21
27
1.5bENST000002414365bENSE00001649227chr5:74848297-74848416120POLK_HUMAN46-85402A:46-85
B:46-85
40
40
1.7bENST000002414367bENSE00001643362chr5:74865165-74865317153POLK_HUMAN86-136512A:86-136
B:86-136
51
51
1.8bENST000002414368bENSE00000827223chr5:74869563-74869694132POLK_HUMAN137-180442A:137-180
B:137-180
44
44
1.9bENST000002414369bENSE00000827224chr5:74872605-74872758154POLK_HUMAN181-232522A:181-224
B:181-224
44
44
1.10aENST0000024143610aENSE00000827225chr5:74877034-74877273240POLK_HUMAN232-312812A:281-312
B:282-312
32
31
1.11ENST0000024143611ENSE00000827226chr5:74879118-74879242125POLK_HUMAN312-353422A:312-353
B:312-353
42
42
1.12ENST0000024143612ENSE00000827227chr5:74880585-74880751167POLK_HUMAN354-409562A:354-409
B:354-409
56
56
1.13ENST0000024143613ENSE00001004825chr5:74882851-7488288333POLK_HUMAN409-420122A:409-420
B:409-420
12
12
1.14aENST0000024143614aENSE00000827228chr5:74886169-7488626597POLK_HUMAN420-452332A:420-452
B:420-452
33
33
1.15aENST0000024143615aENSE00000827229chr5:74889703-74889874172POLK_HUMAN453-510582A:453-510
B:453-510
58
58
1.16aENST0000024143616aENSE00001742078chr5:74892047-74893003957POLK_HUMAN510-8293202A:510-520
B:510-518
11
9
1.17bENST0000024143617bENSE00001614437chr5:74893572-7489361443POLK_HUMAN829-843150--
1.17lENST0000024143617lENSE00001905813chr5:74893759-748969693211POLK_HUMAN843-870280--

(-) Sequences/Alignments

Asymmetric 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:440
 aligned with POLK_HUMAN | Q9UBT6 from UniProtKB/Swiss-Prot  Length:870

    Alignment length:496
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514      
           POLK_HUMAN    25 KAGMEGLDKEKINKIIMEATKGSRFYGNELKKEKQVNQRIENMMQQKAQITSQQLRKAQLQVDRFAMELEQSRNLSNTIVHIDMDAFYAAVEMRDNPELKDKPIAVGSMSMLSTSNYHARRFGVRAAMPGFIAKRLCPQLIIVPPNFDKYRAVSKEVKEILADYDPNFMAMSLDEAYLNITKHLEERQNWPEDKRRYFIKMGSSVENDNPGKEVNKLSEHERSISPLLFEESPSDVQPPGDPFQVNFEEQNNPQILQNSVVFGTSAQEVVKEIRFRIEQKTTLTASAGIAPNTMLAKVCSDKNKPNGQYQILPNRQAVMDFIKDLPIRKVSGIGKVTEKMLKALGIITCTELYQQRALLSLLFSETSWHYFLHISLGLGSTHLTRDGERKSMSVERTFSEINKAEEQYSLCQELCSELAQDLQKERLKGRTVTIKLKNVNFEVKTRASTVSSVVSTAEEIFAIAKELLKTEIDADFPHPLRLRLMGVRISSFPNEE 520
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhh...eeeee..eeeeehhhhhh.......hhhhhhhhh...eee..hhhhhhhhhhhhhhhhhh...........eeeeehhhhhhhhh.......eee..--------------------------------------------------------..eee...hhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh.....eee...hhhhhhhhhhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............eeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhh.......eeeeeee....eeee.........hhhhhhhhhhhhhhhhhhhhh.....eeeeeeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------R------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------UMUC  PDB: A:103-358 UniProt: 103-358                                                                                                                                                                                                                           ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.4a            Exon 1.5b  PDB: A:46-85 UniProt: 46-85  Exon 1.7b  PDB: A:86-136 UniProt: 86-136           Exon 1.8b  PDB: A:137-180 UniProt: 137-180  ---------------------------------------------------Exon 1.10a  PDB: A:281-312 UniProt: 232-312 [INCOMPLETE]                         -----------------------------------------Exon 1.12  PDB: A:354-409 UniProt: 354-409              ----------Exon 1.14a  PDB: A:420-452       Exon 1.15a  PDB: A:453-510 UniProt: 453-510               ---------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9b  PDB: A:181-224 UniProt: 181-232          -------------------------------------------------------------------------------Exon 1.11  PDB: A:312-353 UniProt: 312-353-------------------------------------------------------Exon 1.13   -----------------------------------------------------------------------------------------Exon 1.16a  Transcript 1 (2)
                 3pzp A  25 KAGMEGLDKEKINKIIMEATKGSRFYGNELKKEKQVNQRIENMMQQKAQITSQQLRKAQLQVDRFAMELEQSRNLSNTIVHIDMDAFYAAVEMRDNPELKDKPIAVGSMSMLSTSNYHARRFGVRAAMPGFIAKRLCPQLIIVPPNFDKYRAVSKEVKEILADYDPNFMAMSLDEAYLNITKHLEERQNWPEDKRRYFIK--------------------------------------------------------QNSVVFGTSAQEVVKEIRFRIEQKTTLTASAGIAPNTMLAKVCSDKNKPNGQYQILPNRQAVMDFIKDLPIRKVSGIGKVTEKMLKALGIITCTELYQQRALLSLLFSETSWHYFLHISLGLGSTHLTRDGERKSMSVERTFSEINKAEEQYSLCQELCSELAQDLQKERLKGRTVTIKLKNVNFEVKTRASTVSSVVSTAEEIFAIAKELLKTEIDADFPHPLRLRLMGVRISSFPNEE 520
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224         -         -         -         -         -      |284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514      
                                                                                                                                                                                                                                 224                                                      281                                                                                                                                                                                                                                               

Chain B from PDB  Type:PROTEIN  Length:443
 aligned with POLK_HUMAN | Q9UBT6 from UniProtKB/Swiss-Prot  Length:870

    Alignment length:500
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       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
           POLK_HUMAN    19 MGLNDNKAGMEGLDKEKINKIIMEATKGSRFYGNELKKEKQVNQRIENMMQQKAQITSQQLRKAQLQVDRFAMELEQSRNLSNTIVHIDMDAFYAAVEMRDNPELKDKPIAVGSMSMLSTSNYHARRFGVRAAMPGFIAKRLCPQLIIVPPNFDKYRAVSKEVKEILADYDPNFMAMSLDEAYLNITKHLEERQNWPEDKRRYFIKMGSSVENDNPGKEVNKLSEHERSISPLLFEESPSDVQPPGDPFQVNFEEQNNPQILQNSVVFGTSAQEVVKEIRFRIEQKTTLTASAGIAPNTMLAKVCSDKNKPNGQYQILPNRQAVMDFIKDLPIRKVSGIGKVTEKMLKALGIITCTELYQQRALLSLLFSETSWHYFLHISLGLGSTHLTRDGERKSMSVERTFSEINKAEEQYSLCQELCSELAQDLQKERLKGRTVTIKLKNVNFEVKTRASTVSSVVSTAEEIFAIAKELLKTEIDADFPHPLRLRLMGVRISSFPN 518
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.......eeeeee.hhhhhhhhhhhhhhh...eeeee..ee...hhhhhh.......hhhhhhhhh...eee..hhhhhhhhhhhhhhhhhh.....eeee..eeee.hhhhhhhhh.......ee...---------------------------------------------------------..ee...hhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhh.............hhhhhhhhhhh.hhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............eeeeeeeeeee...hhhhhhhhhhhhhhhhhhhh....eeeeeeeeee....ee..eeeeeeee.hhhhhhhhhhhhhhhhhhh.......eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------R----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------UMUC  PDB: B:103-358 UniProt: 103-358                                                                                                                                                                                                                           ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.4a  PDB: B:19-45    Exon 1.5b  PDB: B:46-85 UniProt: 46-85  Exon 1.7b  PDB: B:86-136 UniProt: 86-136           Exon 1.8b  PDB: B:137-180 UniProt: 137-180  ---------------------------------------------------Exon 1.10a  PDB: B:282-312 UniProt: 232-312 [INCOMPLETE]                         -----------------------------------------Exon 1.12  PDB: B:354-409 UniProt: 354-409              ----------Exon 1.14a  PDB: B:420-452       Exon 1.15a  PDB: B:453-510 UniProt: 453-510               -------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9b  PDB: B:181-224 UniProt: 181-232          -------------------------------------------------------------------------------Exon 1.11  PDB: B:312-353 UniProt: 312-353-------------------------------------------------------Exon 1.13   -----------------------------------------------------------------------------------------1.16a     Transcript 1 (2)
                 3pzp B  19 MGLNDNKAGMEGLDKEKINKIIMEATKGSRFYGNELKKEKQVNQRIENMMQQKAQITSQQLRKAQLQVDRFAMELEQSRNLSNTIVHIDMDAFYAAVEMRDNPELKDKPIAVGSMSMLSTSNYHARRFGVRAAMPGFIAKRLCPQLIIVPPNFDKYRAVSKEVKEILADYDPNFMAMSLDEAYLNITKHLEERQNWPEDKRRYFIK---------------------------------------------------------NSVVFGTSAQEVVKEIRFRIEQKTTLTASAGIAPNTMLAKVCSDKNKPNGQYQILPNRQAVMDFIKDLPIRKVSGIGKVTEKMLKALGIITCTELYQQRALLSLLFSETSWHYFLHISLGLGSTHLTRDGERKSMSVERTFSEINKAEEQYSLCQELCSELAQDLQKERLKGRTVTIKLKNVNFEVKTRASTVSSVVSTAEEIFAIAKELLKTEIDADFPHPLRLRLMGVRISSFPN 518
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218     |   -         -         -         -         -         -   |   288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518
                                                                                                                                                                                                                                       224                                                       282                                                                                                                                                                                                                                            

Chain P from PDB  Type:DNA  Length:13
                                             
                 3pzp P   1 GGGGGAAGGACCA  13
                                    10   

Chain Q from PDB  Type:DNA  Length:12
                                            
                 3pzp Q   2 GGGGAAGGACCA  13
                                    11  

Chain T from PDB  Type:DNA  Length:15
                                               
                 3pzp T   4 CCtGGTCCTTCCCCC  18
                              |     13     
                              6-TTD        

Chain U from PDB  Type:DNA  Length:14
                                              
                 3pzp U   4 CCtGGTCCTTCCCC  17
                              |     13    
                              6-TTD       

   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 3PZP)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3PZP)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3PZP)

(-) Gene Ontology  (19, 19)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (POLK_HUMAN | Q9UBT6)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:0003684    damaged DNA binding    Interacting selectively and non-covalently with damaged DNA.
    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: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:0042276    error-prone translesion synthesis    The conversion of DNA-damage induced single-stranded gaps into large molecular weight DNA after replication by using a specialized DNA polymerase or replication complex to insert a defined nucleotide across the lesion. This process does not remove the replication-blocking lesions and causes an increase in the endogenous mutation level. For example, in E. coli, a low fidelity DNA polymerase, pol V, copies lesions that block replication fork progress. This produces mutations specifically targeted to DNA template damage sites, but it can also produce mutations at undamaged sites.
    GO:0006297    nucleotide-excision repair, DNA gap filling    Repair of the gap in the DNA helix by DNA polymerase and DNA ligase after the portion of the strand containing the lesion has been removed by pyrimidine-dimer repair enzymes.
    GO:0033683    nucleotide-excision repair, DNA incision    A process that results in the endonucleolytic cleavage of the damaged strand of DNA. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound.
    GO:0006296    nucleotide-excision repair, DNA incision, 5'-to lesion    The endonucleolytic cleavage of the damaged strand of DNA 5' to the site of damage. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound. The incision follows the incision formed 3' to the site of damage.
    GO:0006283    transcription-coupled nucleotide-excision repair    The nucleotide-excision repair process that carries out preferential repair of DNA lesions on the actively transcribed strand of the DNA duplex. In addition, the transcription-coupled nucleotide-excision repair pathway is required for the recognition and repair of a small subset of lesions that are not recognized by the global genome nucleotide excision repair pathway.
    GO:0019985    translesion synthesis    The replication of damaged DNA by synthesis across a lesion in the template strand; a specialized DNA polymerase or replication complex inserts a defined nucleotide across from the lesion which allows DNA synthesis to continue beyond the lesion. This process can be mutagenic depending on the damaged nucleotide and the inserted nucleotide.
cellular component
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    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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Asymmetric Unit
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 Related Entries

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

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        POLK_HUMAN | Q9UBT61t94 2lsi 2oh2 2w7o 2w7p 3in5 4ba9 4gk5 4u6p 4u7c 5t14

(-) Related Entries Specified in the PDB File

1t94 CRYSTAL STRUCTURE OF THE CATALYTIC CORE OF HUMAN DNA POLYMERASE KAPPA
2oh2 TERNARY COMPLEX OF HUMAN DNA POLYMERASE KAPPA
3in5 STRUCTURE OF HUMAN DNA POLYMERASE KAPPA INSERTING DATP OPPOSITE AN 8-OXOG DNA LESION