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(-) Description

Title :  RB69 DNA POLYMERASE TERNARY COMPLEX WITH DUPCPP OPPOSITE DA
 
Authors :  S. Xia, W. H. Konigsberg, J. Wang
Date :  04 Jul 11  (Deposition) - 12 Oct 11  (Release) - 02 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.82
Chains :  Asym./Biol. Unit :  A,P,T
Keywords :  Dupnpp, Mn2+, Wt, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Xia, M. Wang, G. Blaha, W. H. Konigsberg, J. Wang
Structural Insights Into Complete Metal Ion Coordination From Ternary Complexes Of B Family Rb69 Dna Polymerase.
Biochemistry V. 50 9114 2011
PubMed-ID: 21923197  |  Reference-DOI: 10.1021/BI201260H

(-) Compounds

Molecule 1 - DNA POLYMERASE
    ChainsA
    EC Number2.7.7.7
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Gene43
    MutationYES
    Organism ScientificENTEROBACTERIA PHAGE RB69
    Organism Taxid12353
    SynonymGP43
 
Molecule 2 - 5'-D(*TP*CP*GP*AP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G) -3'
    ChainsT
    EngineeredYES
    Other DetailsTEMPLATE
    SyntheticYES
 
Molecule 3 - 5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*(DOC))-3'
    ChainsP
    EngineeredYES
    Other DetailsPRIMER
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit APT

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1CA5Ligand/IonCALCIUM ION
2DOC1Mod. Nucleotide2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
3DUP1Ligand/Ion2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:411 , LEU A:412 , SER A:414 , LEU A:415 , TYR A:416 , ARG A:482 , LYS A:560 , ASN A:564 , THR A:622 , ASP A:623 , CA A:903 , CA A:905 , CA A:906 , HOH A:916 , HOH A:1064 , HOH A:1105 , HOH A:1125 , HOH A:1397 , HOH A:1412 , HOH A:1631 , DOC P:115 , DA T:4 , DG T:5BINDING SITE FOR RESIDUE DUP A 902
2AC2SOFTWAREASP A:411 , LEU A:412 , ASP A:623 , DUP A:902 , HOH A:1397BINDING SITE FOR RESIDUE CA A 903
3AC3SOFTWAREGLU A:660 , ASP A:684 , HOH A:1519BINDING SITE FOR RESIDUE CA A 904
4AC4SOFTWAREASP A:411 , ASP A:623 , DUP A:902 , HOH A:1275 , HOH A:1397 , HOH A:1465BINDING SITE FOR RESIDUE CA A 905
5AC5SOFTWAREASP A:411 , DUP A:902 , HOH A:1373 , HOH A:1387BINDING SITE FOR RESIDUE CA A 906
6AC6SOFTWAREASN A:505 , ASN A:507 , LYS A:531 , HOH A:1209 , HOH A:1655BINDING SITE FOR RESIDUE CA A 907

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3SQ1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3SQ1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3SQ1)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DNA_POLYMERASE_BPS00116 DNA polymerase family B signature.DPOL_BPR69619-627  1A:619-627

(-) Exons   (0, 0)

(no "Exon" information available for 3SQ1)

(-) 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:901
 aligned with DPOL_BPR69 | Q38087 from UniProtKB/Swiss-Prot  Length:903

    Alignment length:901
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900 
           DPOL_BPR69     1 MKEFYLTVEQIGDSIFERYIDSNGRERTREVEYKPSLFAHCPESQATKYFDIYGKPCTRKLFANMRDASQWIKRMEDIGLEALGMDDFKLAYLSDTYNYEIKYDHTKIRVANFDIEVTSPDGFPEPSQAKHPIDAITHYDSIDDRFYVFDLLNSPYGNVEEWSIEIAAKLQEQGGDEVPSEIIDKIIYMPFDNEKELLMEYLNFWQQKTPVILTGWNVESFDIPYVYNRIKNIFGESTAKRLSPHRKTRVKVIENMYGSREIITLFGISVLDYIDLYKKFSFTNQPSYSLDYISEFELNVGKLKYDGPISKLRESNHQRYISYNIIDVYRVLQIDAKRQFINLSLDMGYYAKIQIQSVFSPIKTWDAIIFNSLKEQNKVIPQGRSHPVQPYPGAFVKEPIPNRYKYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAERPSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLYGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAFVLYGDTDSIYVSADKIIDKVGESKFRDTNHWVDFLDKFARERMEPAIDRGFREMCEYMNNKQHLMFMDREAIAGPPLGSKGIGGFWTGKKRYALNVWDMEGTRYAEPKLKIMGLETQKSSTPKAVQKALKECIRRMLQEGEESLQEYFKEFEKEFRQLNYISIASVSSANNIAKYDVGGFPGPKCPFHIRGILTYNRAIKGNIDAPQVVEGEKVYVLPLREGNPFGDKCIAWPSGTEITDLIKDDVLHWMDYTVLLEKTFIKPLEGFTSAAKLDYEKKASLFDMF 901
               SCOP domains d3sq1a1 A:1-375 Exonuclease domain of family B DNA polymerases                                                                                                                                                                                                                                                                                                                         d3sq1a2 A:376-901 Family B DNA polymerase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee..eeeeeee.....eeeeee....eeeee.........ee.....eeeee..hhhhhhhhhhhhhhhh.......hhhhhhhhhhh......hhhhh.eeeeeee..................eeeeee....eeeeeee.ee..ee....hhhhhhhhhhhh....hhhhhh.eeeeee.hhhhhhhhhhhhhhhh...eee......hhhhhhhhhhhhhhhhhhhhhhh....eeeeeee....eeeeeee...ee.hhhhhhhhhh.......hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..ee......................ee...eeeeee.hhhhhhhhhhh.hhh.eeee....hhhhhhh..........ee....eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...................hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee..eeeeehhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeeee..........eeeee..eeeeeeeee..eeeeeeeeeee.hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeee...hhh.ee..ee....hhhhhhhhhhhhhh.............eeeeee..........eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_POLYM---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sq1 A   1 MKEFYLTVEQIGDSIFERYIDSNGRERTREVEYKPSLFAHCPESQATKYFDIYGKPCTRKLFANMRDASQWIKRMEDIGLEALGMDDFKLAYLSDTYNYEIKYDHTKIRVANFDIEVTSPDGFPEPSQAKHPIDAITHYDSIDDRFYVFDLLNSPYGNVEEWSIEIAAKLQEQGGDEVPSEIIDKIIYMPFDNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIFGESTAKRLSPHRKTRVKVIENMYGSREIITLFGISVLDYIDLYKKFSFTNQPSYSLDYISEFELNVGKLKYDGPISKLRESNHQRYISYNIIAVYRVLQIDAKRQFINLSLDMGYYAKIQIQSVFSPIKTWDAIIFNSLKEQNKVIPQGRSHPVQPYPGAFVKEPIPNRYKYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAERPSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLYGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAFVLYGDTDSIYVSADKIIDKVGESKFRDTNHWVDFLDKFARERMEPAIDRGFREMCEYMNNKQHLMFMDREAIAGPPLGSKGIGGFWTGKKRYALNVWDMEGTRYAEPKLKIMGLETQKSSTPKAVQKALKECIRRMLQEGEESLQEYFKEFEKEFRQLNYISIASVSSANNIAKYDVGGFPGPKCPFHIRGILTYNRAIKGNIDAPQVVEGEKVYVLPLREGNPFGDKCIAWPSGTEITDLIKDDVLHWMDYTVLLEKTFIKPLEGFTSAAKLDYEKKASLFDMF 901
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900 

Chain P from PDB  Type:DNA  Length:13
                                             
                 3sq1 P 103 GCGGACTGCTTAc 115
                                   112  |
                                      115-DOC

Chain T from PDB  Type:DNA  Length:18
                                                  
                 3sq1 T   1 TCGAGTAAGCAGTCCGCG  18
                                    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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3SQ1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3SQ1)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DPOL_BPR69 | Q38087)
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: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:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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: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:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0039693    viral DNA genome replication    The replication of a viral DNA genome.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DPOL_BPR69 | Q380871b1f 1b8h 1clq 1ig9 1ih7 1q9x 1q9y 1qe4 1waf 1wag 1wah 1wai 1waj 2atq 2dtu 2dy4 2oyq 2ozm 2ozs 2p5g 2p5o 3cfo 3cfp 3cfr 3cq8 3kd1 3kd5 3l8b 3lds 3lzi 3lzj 3nae 3nci 3ndk 3ne6 3ngi 3nhg 3qei 3qep 3qer 3qes 3qet 3qev 3qew 3qex 3qnn 3qno 3rma 3rmb 3rmc 3rmd 3rwu 3s9h 3scx 3si6 3sjj 3snn 3spy 3spz 3sq0 3sq2 3sq4 3sun 3suo 3sup 3suq 3tab 3tae 3taf 3tag 3uiq 4dtj 4dtm 4dtn 4dto 4dtp 4dtr 4dts 4dtu 4dtx 4du1 4du3 4du4 4e3s 4fj5 4fj7 4fj8 4fj9 4fjg 4fjh 4fji 4fjj 4fjk 4fjl 4fjm 4fjn 4fjx 4fk0 4fk2 4fk4 4i9l 4i9q 4j2a 4j2b 4j2d 4j2e 4khn 4khq 4khs 4khu 4khw 4khy 4ki4 4ki6 4m3r 4m3t 4m3u 4m3w 4m3x 4m3y 4m3z 4m41 4m42 4m45

(-) Related Entries Specified in the PDB File

3spy RB69 DNA POLYMERASE(L415A/L561A/S565G/Y567A) TERNARY COMPLEX WITH DUPCPP OPPOSITE DA
3spz RB69 DNA POLYMERASE(L415A/L561A/S565G/Y567A) TERNARY COMPLEX WITH DUPCPP OPPOSITE DA (CA2+)
3sq0 RB69 DNA POLYMERASE(L561A/S565G/Y567A) TERNARY COMPLEX WITH DUPNPP OPPOSITE DA (MN2+)
3sq2 RB69 DNA POLYMERASE TERNARY COMPLEX WITH DTTP OPPOSITE 2AP (AT RICH SEQUENCE)
3sq4 RB69 DNA POLYMERASE TERNARY COMPLEX WITH DTTP OPPOSITE 2AP (GC RICH SEQUENCE)