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(-) Description

Title :  CRYSTAL STRUCTURE OF BACILLUS DNA POLYMERASE I FRAGMENT COMPLEXED TO 11 BASE PAIRS OF DUPLEX DNA AFTER ADDITION OF TWO DATP RESIDUES
 
Authors :  J. R. Kiefer, C. Mao, L. S. Beese
Date :  17 Nov 97  (Deposition) - 13 Jan 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,P,T
Keywords :  Bacillus Stearothermophilus Dna Polymerase, Bf Thermophilus Polymerase, Complex (Nucleotidyltransferase/Dna) (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. R. Kiefer, C. Mao, J. C. Braman, L. S. Beese
Visualizing Dna Replication In A Catalytically Active Bacillus Dna Polymerase Crystal.
Nature V. 391 304 1998
PubMed-ID: 9440698  |  Reference-DOI: 10.1038/34693
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'-D(*GP*CP*AP*TP*CP*AP*TP*GP*CP*AP*A)-3')
    ChainsP
    EngineeredYES
    SyntheticYES
 
Molecule 2 - DNA (5'- D(*TP*AP*TP*TP*GP*CP*AP*TP*GP*AP*TP*GP*C)-3')
    ChainsT
    EngineeredYES
    SyntheticYES
 
Molecule 3 - PROTEIN (DNA POLYMERASE I)
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentRESIDUES 297-876
    Organism ScientificGEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid1422
    SynonymBF

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit APT

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2SO43Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:682 , ARG A:702 , LYS A:706 , HOH A:2611BINDING SITE FOR RESIDUE SO4 A 910
2AC2SOFTWAREARG A:779 , ARG A:819 , MG A:952 , HOH A:2590BINDING SITE FOR RESIDUE SO4 A 911
3AC3SOFTWAREMET A:299 , ALA A:300 , ARG A:343 , ARG A:677BINDING SITE FOR RESIDUE SO4 A 912
4AC4SOFTWAREASP A:653 , TYR A:654 , ASP A:830BINDING SITE FOR RESIDUE MG A 950
5AC5SOFTWAREGLU A:817 , SO4 A:911 , HOH A:2516BINDING SITE FOR RESIDUE MG A 952

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:620 -Pro A:621

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (48, 48)

Asymmetric/Biological Unit (48, 48)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_DPO1_GEOSE_001 *G298KDPO1_GEOSE  ---  ---AA298K
02UniProtVAR_DPO1_GEOSE_002 *D300ADPO1_GEOSE  ---  ---AA300A
03UniProtVAR_DPO1_GEOSE_003 *S306RDPO1_GEOSE  ---  ---AR306R
04UniProtVAR_DPO1_GEOSE_004 *D309EDPO1_GEOSE  ---  ---AE309E
05UniProtVAR_DPO1_GEOSE_005 *V320LDPO1_GEOSE  ---  ---AV320L
06UniProtVAR_DPO1_GEOSE_006 *H329DDPO1_GEOSE  ---  ---AD329D
07UniProtVAR_DPO1_GEOSE_007 *R341HDPO1_GEOSE  ---  ---AH341H
08UniProtVAR_DPO1_GEOSE_008 *K356QDPO1_GEOSE  ---  ---AQ356Q
09UniProtVAR_DPO1_GEOSE_009 *L358VDPO1_GEOSE  ---  ---AV358V
10UniProtVAR_DPO1_GEOSE_010 *T369SDPO1_GEOSE  ---  ---AS369S
11UniProtVAR_DPO1_GEOSE_011 *R388CDPO1_GEOSE  ---  ---AC388C
12UniProtVAR_DPO1_GEOSE_012 *V391SDPO1_GEOSE  ---  ---AS391S
13UniProtVAR_DPO1_GEOSE_013 *A411RDPO1_GEOSE  ---  ---AR411R
14UniProtVAR_DPO1_GEOSE_014 *V413ADPO1_GEOSE  ---  ---AA413A
15UniProtVAR_DPO1_GEOSE_015 *H417KDPO1_GEOSE  ---  ---AK417K
16UniProtVAR_DPO1_GEOSE_016 *S424PDPO1_GEOSE  ---  ---AP424P
17UniProtVAR_DPO1_GEOSE_017 *T436ADPO1_GEOSE  ---  ---AA436A
18UniProtVAR_DPO1_GEOSE_018 *T442VDPO1_GEOSE  ---  ---AV442V
19UniProtVAR_DPO1_GEOSE_019 *A456EDPO1_GEOSE  ---  ---AE456E
20UniProtVAR_DPO1_GEOSE_020 *E459RDPO1_GEOSE  ---  ---AR459R
21UniProtVAR_DPO1_GEOSE_021 *T475VDPO1_GEOSE  ---  ---AV475V
22UniProtVAR_DPO1_GEOSE_022 *N487EDPO1_GEOSE  ---  ---AE487E
23UniProtVAR_DPO1_GEOSE_023 *T491ADPO1_GEOSE  ---  ---AA491A
24UniProtVAR_DPO1_GEOSE_024 *A505KDPO1_GEOSE  ---  ---AK505K
25UniProtVAR_DPO1_GEOSE_025 *T508RDPO1_GEOSE  ---  ---AA508R
26UniProtVAR_DPO1_GEOSE_026 *Q510KDPO1_GEOSE  ---  ---AQ510K
27UniProtVAR_DPO1_GEOSE_027 *R516QDPO1_GEOSE  ---  ---AQ516Q
28UniProtVAR_DPO1_GEOSE_028 *D540EDPO1_GEOSE  ---  ---AE540E
29UniProtVAR_DPO1_GEOSE_029 *H567YDPO1_GEOSE  ---  ---AY567Y
30UniProtVAR_DPO1_GEOSE_030 *H573NDPO1_GEOSE  ---  ---AN573N
31UniProtVAR_DPO1_GEOSE_031 *H596RDPO1_GEOSE  ---  ---AR596R
32UniProtVAR_DPO1_GEOSE_032 *V598DDPO1_GEOSE  ---  ---AD598D
33UniProtVAR_DPO1_GEOSE_033 *G600KDPO1_GEOSE  ---  ---AK600K
34UniProtVAR_DPO1_GEOSE_034 *M605IDPO1_GEOSE  ---  ---AI605I
35UniProtVAR_DPO1_GEOSE_035 *V619TDPO1_GEOSE  ---  ---AT619T
36UniProtVAR_DPO1_GEOSE_036 *P645SDPO1_GEOSE  ---  ---AS645S
37UniProtVAR_DPO1_GEOSE_037 *I672MDPO1_GEOSE  ---  ---AM672M
38UniProtVAR_DPO1_GEOSE_038 *G678DDPO1_GEOSE  ---  ---AD678D
39UniProtVAR_DPO1_GEOSE_039 *H691QDPO1_GEOSE  ---  ---AQ691Q
40UniProtVAR_DPO1_GEOSE_040 *A699PDPO1_GEOSE  ---  ---AP699P
41UniProtVAR_DPO1_GEOSE_041 *T728SDPO1_GEOSE  ---  ---AS728S
42UniProtVAR_DPO1_GEOSE_042 *A741EDPO1_GEOSE  ---  ---AE741E
43UniProtVAR_DPO1_GEOSE_043 *Q748RDPO1_GEOSE  ---  ---AR748R
44UniProtVAR_DPO1_GEOSE_044 *D751EDPO1_GEOSE  ---  ---AE751E
45UniProtVAR_DPO1_GEOSE_045 *T790MDPO1_GEOSE  ---  ---AM790M
46UniProtVAR_DPO1_GEOSE_046 *R816KDPO1_GEOSE  ---  ---AK816K
47UniProtVAR_DPO1_GEOSE_047 *I841MDPO1_GEOSE  ---  ---AM841M
48UniProtVAR_DPO1_GEOSE_048 *P870SDPO1_GEOSE  ---  ---AS870S
   * ID not provided by source

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DNA_POLYMERASE_APS00447 DNA polymerase family A signature.DPO1_GEOSE702-721  1A:702-721

(-) Exons   (0, 0)

(no "Exon" information available for 4BDP)

(-) 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:580
 aligned with DPO1_GEOSE | P52026 from UniProtKB/Swiss-Prot  Length:876

    Alignment length:580
                                   306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856       866       876
           DPO1_GEOSE   297 AGMDFAIADSVTDEMLADKAALVVEVVGDNYHHAPIVGIALANERGRFFLRPETALADPKFLAWLGDETKKKTMFDSKRAAVALKWKGIELRGVVFDLLLAAYLLDPAQAAGDVAAVAKMHQYEAVRSDEAVYGKGAKRTVPDEPTLAEHLVRKAAAIWALEEPLMDELRRNEQDRLLTELEQPLAGILANMEFTGVKVDTKRLEQMGAELTEQLQAVERRIYELAGQEFNINSPKQLGTVLFDKLQLPVLKKTKTGYSTSADVLEKLAPHHEIVEHILHYRQLGKLQSTYIEGLLKVVHPVTGKVHTMFNQALTQTGRLSSVEPNLQNIPIRLEEGRKIRQAFVPSEPDWLIFAADYSQIELRVLAHIAEDDNLIEAFRRGLDIHTKTAMDIFHVSEEDVTANMRRQAKAVNFGIVYGISDYGLAQNLNITRKEAAEFIERYFASFPGVKQYMDNIVQEAKQKGYVTTLLHRRRYLPDITSRNFNVRSFAERTAMNTPIQGSAADIIKKAMIDLSVRLREERLQARLLLQVHDELILEAPKEEIERLCRLVPEVMEQAVTLRVPLKVDYHYGPTWYDAK 876
               SCOP domains d4bdpa1 A:297-468 Exonuclease domain of prokaryotic DNA polymerase                                                                                                          d4bdpa2 A:469-876 DNA polymerase I (Klenow fragment)                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 4bdpA01 A:297-490  [code=3.30.420.10, no name defined]                                                                                                                                            4bdpA02 A:491-605 Taq DNA Polymerase; Chain T, domain 4                                                            4bdpA03 A:606-656,A:801-875                        4bdpA04 A:657-800 5' to 3' exonuclease, C-terminal subdomain                                                                                    4bdpA03 A:606-656,A:801-875  [code=3.30.70.370, no name defined]           - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee....hhhh..eeeeeee............eeeeee..eeeee.hhhh...hhhhhhhh....eeee..hhhhhhhhhhh......eeeehhhhhhhh.hhh....hhhhhhhh.......hhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh.hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhh..................hhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.hhhhhh..........eee.........eee...........hhhhhhhhh.......eeeeeeee..hhhhhhhhhh..hhhhhhhh....hhhhhhhhh....hhh..hhhhhhhhhhhhhhhh...hhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.eee.....eee.hhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee...eeeeeeehhhhhhhhhhhhhhhhh.........eeeeee..hhh.. Sec.struct. author
                 SAPs(SNPs) -K-A-----R--E----------L--------D-----------H--------------Q-V----------S------------------C--S-------------------R-A---K------P-----------A-----V-------------E--R---------------V-----------E---A-------------K--R-K-----Q-----------------------E--------------------------Y-----N----------------------R-D-K----I-------------T-------------------------S--------------------------M-----D------------Q-------P----------------------------S------------E------R--E--------------------------------------M-------------------------K------------------------M----------------------------S------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_POLYMERASE_A    ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bdp A 297 AAMAFTLADRVTEEMLADKAALVVEVVEENYHDAPIVGIAVVNEHGRFFLRPETALADPQFVAWLGDETKKKSMFDSKRAAVALKWKGIELCGVSFDLLLAAYLLDPAQGVDDVRAAAKMKQYEAVRPDEAVYGKGAKRAVPDEPVLAEHLVRKAAAIWELERPFLDELRRNEQDRLLVELEQPLSSILAEMEFAGVKVDTKRLEQMGKELAEQLGTVEQRIYELAGQEFNINSPKQLGVILFEKLQLPVLKKTKTGYSTSADVLEKLAPYHEIVENILHYRQLGKLQSTYIEGLLKVVRPDTKKVHTIFNQALTQTGRLSSTEPNLQNIPIRLEEGRKIRQAFVPSESDWLIFAADYSQIELRVLAHIAEDDNLMEAFRRDLDIHTKTAMDIFQVSEDEVTPNMRRQAKAVNFGIVYGISDYGLAQNLNISRKEAAEFIERYFESFPGVKRYMENIVQEAKQKGYVTTLLHRRRYLPDITSRNFNVRSFAERMAMNTPIQGSAADIIKKAMIDLNARLKEERLQAHLLLQVHDELILEAPKEEMERLCRLVPEVMEQAVTLRVPLKVDYHYGSTWYDAK 876
                                   306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856       866       876

Chain P from PDB  Type:DNA  Length:11
                                           
                 4bdp P  19 GCATCATGCAA  29
                                    28 

Chain T from PDB  Type:DNA  Length:13
                                             
                 4bdp T   2 TATTGCATGATGC  14
                                    11   

   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (4, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DPO1_GEOSE | P52026)
molecular function
    GO:0008408    3'-5' exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end.
    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:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004527    exonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    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: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: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:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0006139    nucleobase-containing compound metabolic process    Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DPO1_GEOSE | P520261l3s 1l3t 1l3u 1l3v 1l5u 1lv5 1njx 1njy 1njz 1nk0 1nk4 1nk5 1nk6 1nk7 1nk8 1nk9 1nkb 1nkc 1nke 1u45 1u47 1u48 1u49 1u4b 1ua1 1xc9 1xwl 2bdp 3bdp 3eyz 3ez5

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4BDP)