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Theoretical Model  (Jmol Viewer)

(-) Description

Title :  MODEL OF RB69 DNA POLYMERASE WITH T7 DNA POLYMERASE PRIMER/ TEMPLATE
 
Authors :  D. M. Coen
Date :  20 Nov 98  (Deposition) - 20 Jan 99  (Release) - 01 Apr 03  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  P,R,T,_#
( #:   chains that contain no standard or modified protein/DNA/RNA residue)
 
Keywords :  Dna Polymerase, Hsv Dna Polymerase, Acyclovir Triphosphate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Huang, K. K. Ishii, H. Zuccola, A. M. Gehring, C. B. Hwang, J. Hogle, D. M. Coen
The Enzymological Basis For Resistance Of Herpesvirus Dna Polymerase Mutants To Acyclovir: Relationship To The Structure Of Alpha-Like Dna Polymerases.
Proc. Natl. Acad. Sci. Usa V. 96 447 1999
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (DNA POLYMERASE)
    Chains: R
    Organism Scientific: BACTERIOPHAGE RB69
 
Molecule 2 - DNA (5'- D(P*CP*CP*TP*TP*GP*GP*CP*AP*CP*TP*GP*GP*C)-3')
    Chains: T
    EC Number: 2.7.7.7
    Engineered: YES
    Fragment: POLYMERASE DOMAIN
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(P*GP*CP*CP*AP*GP*TP*GP*CP*CP*A)-3')
    Chains: P
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  
Theoretical Model : 
( #:   chains that contain no standard or modified protein/DNA/RNA residue)
 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Theoretical Model (1, 1)
No.NameCountTypeFull Name
1AVP1Ligand/IonACYCLOVIR TRIPHOSPHATE

(-) Sites  (0, 0)

(no "Site" information available for 1B1F)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1B1F)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1B1F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1B1F)

(-) PROSITE Motifs  (1, 1)

Theoretical Model (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DNA_POLYMERASE_BPS00116 DNA polymerase family B signature.DPOL_BPR69619-627  1R:619-627

(-) Exons   (0, 0)

(no "Exon" information available for 1B1F)

(-) Sequences/Alignments

Theoretical Model
   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 P from PDB  Type:DNA  Length:10
                                          
                 1b1f P  12 GCCAGTGCCA  21
                                    21


Chain R from PDB  Type:PROTEIN  Length:405
 aligned with DPOL_BPR69 | Q38087 from UniProtKB/Swiss-Prot  Length:903

    Alignment length:506
                                   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       886      
           DPOL_BPR69   387 PVQPYPGAFVKEPIPNRYKYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAERPSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLYGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAFVLYGDTDSIYVSADKIIDKVGESKFRDTNHWVDFLDKFARERMEPAIDRGFREMCEYMNNKQHLMFMDREAIAGPPLGSKGIGGFWTGKKRYALNVWDMEGTRYAEPKLKIMGLETQKSSTPKAVQKALKECIRRMLQEGEESLQEYFKEFEKEFRQLNYISIASVSSANNIAKYDVGGFPGPKCPFHIRGILTYNRAIKGNIDAPQVVEGEKVYVLPLREGNPFGDKCIAWPSGTEITDLIKDDVLHWMDYTVLLEKTFIKPLEGFTSAAKLDYE 892
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................eeeeee..hhhhhhhhh...............hhhh.............................-----------------------------------------------------------------------------------------------------.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeee..eeeee.hhhhhhh.hhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.........eeeeeee..........eeeee..eeeeeeeee........eeeee..........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..hhhh.........hhhh..........hhhhhhhhhhhhhh.......................................hhhhhhhhhh..hhhhhhhh.hhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_POLYM------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1b1f R 387 PVQPYPGAFVKEPIPNRYKYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAERPSDVYSCSPNGMMYYKDRDGVV-----------------------------------------------------------------------------------------------------VWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAFVLYGDTDSIYVSADKIIDKVGESKFRDTNHWVDFLDKFARERMEPAIDRGFREMCEYMNNKQHLMFMDREAIAGPPLGSKGIGGFWTGKKRYALNVWDMEGTRYAEPKLKIMGLETQKSSTPKAVQKALKECIRRMLQEGEESLQEYFKEFEKEFRQLNYISIASVSSANNIAKYDVGGFPGPKCPFHIRGILTYNRAIKGNIDAPQVVEGEKVYVLPLREGNPFGDKCIAWPSGTEITDLIKDDVLHWMDYTVLLEKTFIKPLEGFTSAAKLDYE 892
                                   396       406       416       426       436       446       456       466    |    -         -         -         -         -         -         -         -         -         -      |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       886      
                                                                                                              471                                                                                                   573                                                                                                                                                                                                                                                                                                                               


Chain T from PDB  Type:DNA  Length:13
                                             
                 1b1f T   3 CCTTGGCACTGGC  15
                                    12
   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 1B1F)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1B1F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1B1F)

(-) Gene Ontology  (14, 14)

Theoretical Model(hide GO term definitions)
Chain R   (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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  DPOL_BPR69 | Q38087
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 Related Entries

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

UniProtKB/Swiss-Prot
        DPOL_BPR69 | Q38087: 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 3sq1 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

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