|
|
| (One intermediate revision not shown.) |
| Line 3: |
Line 3: |
| | <StructureSection load='2pyj' size='340' side='right'caption='[[2pyj]], [[Resolution|resolution]] 2.03Å' scene=''> | | <StructureSection load='2pyj' size='340' side='right'caption='[[2pyj]], [[Resolution|resolution]] 2.03Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2pyj]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpph2 Bpph2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PYJ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2PYJ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2pyj]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_virus_phi29 Bacillus virus phi29]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PYJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PYJ FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.03Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2py5|2py5]], [[2pyl|2pyl]], [[2pzs|2pzs]]</td></tr>
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2pyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pyj OCA], [https://pdbe.org/2pyj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pyj RCSB], [https://www.ebi.ac.uk/pdbsum/2pyj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pyj ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">2, gp2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10756 BPPH2])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></td></tr>
| + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2pyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pyj OCA], [http://pdbe.org/2pyj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pyj RCSB], [http://www.ebi.ac.uk/pdbsum/2pyj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2pyj ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DPOL_BPPH2 DPOL_BPPH2]] This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single-stranded DNA in the 3'- to 5'-direction. | + | [https://www.uniprot.org/uniprot/DPOL_BPPH2 DPOL_BPPH2] This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single-stranded DNA in the 3'- to 5'-direction. |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| Line 39: |
Line 36: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bpph2]] | + | [[Category: Bacillus virus phi29]] |
| - | [[Category: DNA-directed DNA polymerase]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Berman, A J]] | + | [[Category: Berman AJ]] |
| - | [[Category: Blanco, L]] | + | [[Category: Blanco L]] |
| - | [[Category: Goodman, J L]] | + | [[Category: Goodman JL]] |
| - | [[Category: Kamtekar, S]] | + | [[Category: Kamtekar S]] |
| - | [[Category: Lazaro, J M]] | + | [[Category: Lazaro JM]] |
| - | [[Category: Salas, M]] | + | [[Category: Salas M]] |
| - | [[Category: Steitz, T A]] | + | [[Category: Steitz TA]] |
| - | [[Category: Vega, M de]] | + | [[Category: De Vega M]] |
| - | [[Category: Protein-dna complex]]
| + | |
| - | [[Category: Replication]]
| + | |
| - | [[Category: Transferase-dna complex]]
| + | |
| Structural highlights
2pyj is a 8 chain structure with sequence from Bacillus virus phi29. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2.03Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
DPOL_BPPH2 This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single-stranded DNA in the 3'- to 5'-direction.
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
Replicative DNA polymerases (DNAPs) move along template DNA in a processive manner. The structural basis of the mechanism of translocation has been better studied in the A-family of polymerases than in the B-family of replicative polymerases. To address this issue, we have determined the X-ray crystal structures of phi29 DNAP, a member of the protein-primed subgroup of the B-family of polymerases, complexed with primer-template DNA in the presence or absence of the incoming nucleoside triphosphate, the pre- and post-translocated states, respectively. Comparison of these structures reveals a mechanism of translocation that appears to be facilitated by the coordinated movement of two conserved tyrosine residues into the insertion site. This differs from the mechanism employed by the A-family polymerases, in which a conserved tyrosine moves into the templating and insertion sites during the translocation step. Polymerases from the two families also interact with downstream single-stranded template DNA in very different ways.
Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases.,Berman AJ, Kamtekar S, Goodman JL, Lazaro JM, de Vega M, Blanco L, Salas M, Steitz TA EMBO J. 2007 Jul 25;26(14):3494-505. Epub 2007 Jul 5. PMID:17611604[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Berman AJ, Kamtekar S, Goodman JL, Lazaro JM, de Vega M, Blanco L, Salas M, Steitz TA. Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B-family polymerases. EMBO J. 2007 Jul 25;26(14):3494-505. Epub 2007 Jul 5. PMID:17611604
|
