2fmq: Difference between revisions
No edit summary |
No edit summary |
||
| Line 4: | Line 4: | ||
|PDB= 2fmq |SIZE=350|CAPTION= <scene name='initialview01'>2fmq</scene>, resolution 2.20Å | |PDB= 2fmq |SIZE=350|CAPTION= <scene name='initialview01'>2fmq</scene>, resolution 2.20Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand= | |LIGAND= <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=DUP:2'-DEOXYURIDINE+5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE'>DUP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene> | ||
|ACTIVITY= [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] | |ACTIVITY= <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> | ||
|GENE= POLB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]) | |GENE= POLB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]) | ||
|DOMAIN= | |||
|RELATEDENTRY=[[2fmp|2FMP]], [[2fms|2FMS]] | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2fmq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fmq OCA], [http://www.ebi.ac.uk/pdbsum/2fmq PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2fmq RCSB]</span> | |||
}} | }} | ||
| Line 29: | Line 32: | ||
[[Category: Shock, D D.]] | [[Category: Shock, D D.]] | ||
[[Category: Wilson, S H.]] | [[Category: Wilson, S H.]] | ||
[[Category: nucleotidyl transferase]] | [[Category: nucleotidyl transferase]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 03:04:57 2008'' | ||
Revision as of 00:04, 31 March 2008
| |||||||||||||
| 2fmq, resolution 2.20Å | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Ligands: | DA, DC, DG, DT, DUP, MG, NA | ||||||||||||
| Gene: | POLB (Homo sapiens) | ||||||||||||
| Activity: | DNA-directed DNA polymerase, with EC number 2.7.7.7 | ||||||||||||
| Related: | 2FMP, 2FMS
| ||||||||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||||||
Sodium in active site of DNA Polymerase Beta
Overview
The molecular details of the nucleotidyl transferase reaction have remained speculative, as strategies to trap catalytic intermediates for structure determination utilize substrates lacking the primer terminus 3'-OH and catalytic Mg2+, resulting in an incomplete and distorted active site geometry. Since the geometric arrangement of these essential atoms will impact chemistry, structural insight into fidelity strategies has been hampered. Here, we present a crystal structure of a precatalytic complex of a DNA polymerase with bound substrates that include the primer 3'-OH and catalytic Mg2+. This catalytic intermediate was trapped with a nonhydrolyzable deoxynucleotide analog. Comparison with two new structures of DNA polymerase beta lacking the 3'-OH or catalytic Mg2+ is described. These structures provide direct evidence that both atoms are required to achieve a proper geometry necessary for an in-line nucleophilic attack of O3' on the alphaP of the incoming nucleotide.
About this Structure
2FMQ is a Single protein structure of sequence from Homo sapiens. Full crystallographic information is available from OCA.
Reference
Magnesium-induced assembly of a complete DNA polymerase catalytic complex., Batra VK, Beard WA, Shock DD, Krahn JM, Pedersen LC, Wilson SH, Structure. 2006 Apr;14(4):757-66. PMID:16615916
Page seeded by OCA on Mon Mar 31 03:04:57 2008
