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(-) Description

Authors :  W. A. Beard, D. D. Shock, V. K. Batra, L. C. Pedersen, S. H. Wilson
Date :  25 Aug 09  (Deposition) - 15 Sep 09  (Release) - 24 Nov 09  (Revision)
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,D,P,T
Keywords :  Nucleotidyl Transferase, Dna Polymerase Beta, Binary Complex, Gapped Dna, Dna Damage, Dna Repair, Dna Replication, Dna Synthesis, Dna-Binding, Dna-Directed Dna Polymerase, Lyase, Magnesium, Metal-Binding, Methylation, Nucleotidyltransferase, Nucleus, Polymorphism, Sodium, Transferase, Transferase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  W. A. Beard, D. D. Shock, V. K. Batra, L. C. Pedersen, S. H. Wilson
Dna Polymerase Beta Substrate Specificity: Side Chain Modulation Of The "A-Rule".
J. Biol. Chem. V. 284 31680 2009
PubMed-ID: 19759017  |  Reference-DOI: 10.1074/JBC.M109.029843
(for further references see the PDB file header)

(-) Compounds

    EC Number2.7.7.7, 4.2.99.-
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPWL11
    Expression System StrainTAP56
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
Molecule 2 - 5'- D(*CP*CP*GP*AP*CP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'
Molecule 3 - 5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3'
Molecule 4 - 5'-D(P*GP*TP*CP*GP*G)-3'

 Structural Features

(-) Chains, Units

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

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
1AC1SOFTWARETHR A:101 , VAL A:103 , ILE A:106 , NA A:403 , DG P:9 , HOH P:11 , HOH P:12BINDING SITE FOR RESIDUE NA A 401
3AC3SOFTWARETHR A:101 , HOH A:341 , NA A:401 , HOH A:566 , HOH A:687 , HOH P:11 , HOH P:12BINDING SITE FOR RESIDUE NA A 403
5AC5SOFTWAREDT P:6 , DG P:7 , DC P:8 , HOH P:35 , HOH P:64 , HOH P:450 , DC T:8 , DG T:9 , HOH T:390BINDING SITE FOR RESIDUE SO4 P 405

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
1Gly A:274 -Ser A:275

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

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

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
1DNA_POLYMERASE_XPS00522 DNA polymerase family X signature.DPOLB_HUMAN179-198  1A:179-198

(-) Exons   (14, 14)

Asymmetric/Biological Unit (14, 14)
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.13bENST0000026542113bENSE00000692502chr8:42218813-4221888371DPOLB_HUMAN184-207241A:184-207 (gaps)24

(-) 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 DPOLB_HUMAN | P06746 from UniProtKB/Swiss-Prot  Length:335

    Alignment length:329
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --3isbA01 A:9-91  [code=, no name defined]                               3isbA02 A:92-148                                         3isbA03 A:149-271 Beta Polymerase, domain 2                                                                                3isbA04 A:272-334 Beta Polymerase, domain 3                    - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------R--------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_POLYMERASE_X    ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1b      ------------------Exon 1.4a  PDB: A:40-62Exon 1.5a  PDB: A:63-87  Exon 1.6            ---------------------------------Exon 1.10b         Exon 1.11a  PDB: A:160-18-----------------------Exon 1.14  PDB: A:208-236    Exon 1.15d            ----------------------------------------------Exon 1.18c  PDB: A:305-335      Transcript 1 (1)
           Transcript 1 (2) --------------Exon 1.2a           ------------------------------------------------------------------Exon 1.7          -----------------------------------------------------------Exon 1.13b              --------------------------------------------------Exon 1.16b  PDB: A:258-305 UniProt: 258-305     ------------------------------ Transcript 1 (2)
           Transcript 1 (3) ---------------------------------------------------------------------------------------------------------------------Exon 1.9b         -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (3)
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       | -|      216       226       236       246       256       266       276       286       296       306       316       326         
                                                                                                                                                                                                                               204  |                                                                                                                                

Chain D from PDB  Type:DNA  Length:5
                 3isb D   1 GTCGG   5

Chain P from PDB  Type:DNA  Length:10
                 3isb P   1 GCTGATGCGC  10

Chain T from PDB  Type:DNA  Length:16
                 3isb T   1 CCGACGGCGCATCAGC  16

   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 3ISB)

(-) CATH Domains  (4, 4)

Asymmetric/Biological Unit
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (44, 44)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DPOLB_HUMAN | P06746)
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:0003906    DNA-(apurinic or apyrimidinic site) lyase activity    Catalysis of the cleavage of the C-O-P bond 3' to the apurinic or apyrimidinic site in DNA by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate.
    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:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    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:0008017    microtubule binding    Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers.
    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:0006261    DNA-dependent DNA replication    A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands.
    GO:0007568    aging    A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0006284    base-excision repair    In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase.
    GO:0006288    base-excision repair, DNA ligation    The ligation by DNA ligase of DNA strands. Ligation occurs after polymerase action to fill the gap left by the action of endonucleases during base-excision repair.
    GO:0006286    base-excision repair, base-free sugar-phosphate removal    Excision of the sugar phosphate residue at an AP site, i.e. a deoxyribose sugar with a missing base, by a phosphodiesterase enzyme.
    GO:0006287    base-excision repair, gap-filling    Repair of the damaged strand by the combined action of an apurinic endouclease that degrades a few bases on the damaged strand and a polymerase that synthesizes a 'patch' in the 5' to 3' direction, using the undamaged strand as a template.
    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:0048872    homeostasis of number of cells    Any biological process involved in the maintenance of the steady-state number of cells within a population of cells.
    GO:0071707    immunoglobulin heavy chain V-D-J recombination    The process in which immunoglobulin heavy chain V, D, and J gene segments are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS).
    GO:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0008630    intrinsic apoptotic signaling pathway in response to DNA damage    A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced by the detection of DNA damage, and ends when the execution phase of apoptosis is triggered.
    GO:0048535    lymph node development    The process whose specific outcome is the progression of lymph nodes over time, from their formation to the mature structure. A lymph node is a round, oval, or bean shaped structure localized in clusters along the lymphatic vessels, with a distinct internal structure including specialized vasculature and B- and T-zones for the activation of lymphocytes.
    GO:0051402    neuron apoptotic process    Any apoptotic process in a neuron, the basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
    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:0006290    pyrimidine dimer repair    The repair of UV-induced T-T, C-T and C-C dimers.
    GO:0045471    response to ethanol    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ethanol stimulus.
    GO:0010332    response to gamma radiation    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a gamma radiation stimulus. Gamma radiation is a form of electromagnetic radiation (EMR) or light emission of a specific frequency produced from sub-atomic particle interaction, such as electron-positron annihilation and radioactive decay. Gamma rays are generally characterized as EMR having the highest frequency and energy, and also the shortest wavelength, within the electromagnetic radiation spectrum.
    GO:0055093    response to hyperoxia    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating increased oxygen tension.
    GO:0007435    salivary gland morphogenesis    The process in which the anatomical structures of the salivary gland are generated and organized.
    GO:0016445    somatic diversification of immunoglobulins    The somatic process that results in the generation of sequence diversity of immunoglobulins.
    GO:0016446    somatic hypermutation of immunoglobulin genes    Mutations occurring somatically that result in amino acid changes in the rearranged V regions of immunoglobulins.
    GO:0048536    spleen development    The process whose specific outcome is the progression of the spleen over time, from its formation to the mature structure. The spleen is a large vascular lymphatic organ composed of white and red pulp, involved both in hemopoietic and immune system functions.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005874    microtubule    Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.
    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.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
    GO:0005876    spindle microtubule    Any microtubule that is part of a mitotic or meiotic spindle; anchored at one spindle pole.


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 Related Entries

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

        DPOLB_HUMAN | P067461bpx 1bpy 1bpz 1mq2 1mq3 1tv9 1tva 1zjm 1zjn 1zqa 1zqb 1zqc 1zqd 1zqe 1zqf 1zqg 1zqh 1zqi 1zqj 1zqk 1zql 1zqm 1zqn 1zqo 1zqp 1zqq 1zqr 1zqs 1zqt 2fmp 2fmq 2fms 2i9g 2iso 2isp 2p66 2pxi 3c2k 3c2l 3c2m 3gdx 3isc 3isd 3jpn 3jpo 3jpp 3jpq 3jpr 3jps 3jpt 3lk9 3mby 3ogu 3rh4 3rh5 3rh6 3rje 3rjf 3rjg 3rjh 3rji 3rjj 3rjk 3tfr 3tfs 4do9 4doa 4dob 4doc 4f5n 4f5o 4f5p 4f5q 4f5r 4gxi 4gxj 4gxk 4jwm 4jwn 4kld 4kle 4klf 4klg 4klh 4kli 4klj 4kll 4klm 4klo 4klq 4kls 4klt 4klu 4lvs 4m2y 4m47 4m9g 4m9h 4m9j 4m9l 4m9n 4mf2 4mf8 4mfa 4mfc 4mff 4nlk 4nln 4nlz 4nm1 4nm2 4nxz 4ny8 4o5c 4o5e 4o5k 4o9m 4p2h 4pgq 4pgx 4pgy 4ph5 4pha 4phd 4phe 4php 4ppx 4r63 4r64 4r65 4r66 4rpx 4rpy 4rpz 4rq0 4rq1 4rq2 4rq3 4rq4 4rq5 4rq6 4rq7 4rq8 4rt2 4rt3 4tup 4tuq 4tur 4tus 4uaw 4uay 4uaz 4ub1 4ub2 4ub3 4ub4 4ub5 4ubb 4ubc 4ymm 4ymn 4ymo 4yn4 4z6c 4z6d 4z6e 4z6f 5bol 5bom 5bpc 5db6 5db7 5db8 5db9 5dba 5dbb 5dbc 5eoz 5hhh 5hhi 5j0o 5j0p 5j0q 5j0r 5j0s 5j0t 5j0u 5j0w 5j0x 5j0y 5j29 5j2a 5j2b 5j2c 5j2d 5j2e 5j2f 5j2g 5j2h 5j2i 5j2j 5j2k 5tb8 5tb9 5tba 5tbb 5tbc 5tzv 5u2r 5u2s 5u2t 5u8g 5u8h 5u8i 5u9h 5v1f 5v1g 5v1h 5v1i 5v1j 5v1n 5v1o 5v1p 5v1r 5vez 7ice 7icf 7icg 7ich 7ici 7icj 7ick 7icl 7icm 7icn 7ico 7icp 7icq 7icr 7ics 7ict 7icu 7icv 8ica 8icb 8icc 8ice 8icf 8icg 8ich 8ici 8icj 8ick 8icl 8icm 8icn 8ico 8icp 8icq 8icr 8ics 8ict 8icu 8icv 8icw 8icx 8icy 8icz 9ica 9icb 9icc 9ice 9icf 9icg 9ich 9ici 9icj 9ick 9icl 9icm 9icn 9ico 9icp 9icq 9icr 9ics 9ict 9icu 9icv 9icw 9icx 9icy

(-) Related Entries Specified in the PDB File