4pth: Difference between revisions
No edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
==Ensemble model for Escherichia coli dihydrofolate reductase at 100K== | ==Ensemble model for Escherichia coli dihydrofolate reductase at 100K== | ||
<StructureSection load='4pth' size='340' side='right' caption='[[4pth]], [[Resolution|resolution]] 0.85Å' scene=''> | <StructureSection load='4pth' size='340' side='right'caption='[[4pth]], [[Resolution|resolution]] 0.85Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4pth]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PTH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PTH FirstGlance]. <br> | <table><tr><td colspan='2'>[[4pth]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecodh Ecodh]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PTH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PTH FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FOL:FOLIC+ACID'>FOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FOL:FOLIC+ACID'>FOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene></td></tr> | ||
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene></td></tr> | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSD:3-SULFINOALANINE'>CSD</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4pss|4pss]], [[4psy|4psy]], [[4ptj|4ptj]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4pss|4pss]], [[4psy|4psy]], [[4ptj|4ptj]]</td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">folA, ECDH10B_0049 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=316385 ECODH])</td></tr> | |||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dihydrofolate_reductase Dihydrofolate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.1.3 1.5.1.3] </span></td></tr> | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dihydrofolate_reductase Dihydrofolate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.1.3 1.5.1.3] </span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4pth FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pth OCA], [http://pdbe.org/4pth PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4pth RCSB], [http://www.ebi.ac.uk/pdbsum/4pth PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4pth ProSAT]</span></td></tr> | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4pth FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4pth OCA], [http://pdbe.org/4pth PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4pth RCSB], [http://www.ebi.ac.uk/pdbsum/4pth PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4pth ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[[http://www.uniprot.org/uniprot/B1XC49_ECODH B1XC49_ECODH]] Key enzyme in folate metabolism. Catalyzes an essential reaction for de novo glycine and purine synthesis, and for DNA precursor synthesis (By similarity).[PIRNR:PIRNR000194] | [[http://www.uniprot.org/uniprot/B1XC49_ECODH B1XC49_ECODH]] Key enzyme in folate metabolism. Catalyzes an essential reaction for de novo glycine and purine synthesis, and for DNA precursor synthesis (By similarity).[PIRNR:PIRNR000194] | ||
| Line 30: | Line 30: | ||
</StructureSection> | </StructureSection> | ||
[[Category: Dihydrofolate reductase]] | [[Category: Dihydrofolate reductase]] | ||
[[Category: Ecodh]] | |||
[[Category: Large Structures]] | |||
[[Category: Bedem, H van den]] | [[Category: Bedem, H van den]] | ||
[[Category: Fraser, J S]] | [[Category: Fraser, J S]] | ||
Revision as of 11:00, 17 April 2019
Ensemble model for Escherichia coli dihydrofolate reductase at 100KEnsemble model for Escherichia coli dihydrofolate reductase at 100K
Structural highlights
Function[B1XC49_ECODH] Key enzyme in folate metabolism. Catalyzes an essential reaction for de novo glycine and purine synthesis, and for DNA precursor synthesis (By similarity).[PIRNR:PIRNR000194] Publication Abstract from PubMedMost macromolecular X-ray structures are determined from cryocooled crystals, but it is unclear whether cryocooling distorts functionally relevant flexibility. Here we compare independently acquired pairs of high-resolution data sets of a model Michaelis complex of dihydrofolate reductase (DHFR), collected by separate groups at both room and cryogenic temperatures. These data sets allow us to isolate the differences between experimental procedures and between temperatures. Our analyses of multiconformer models and time-averaged ensembles suggest that cryocooling suppresses and otherwise modifies side-chain and main-chain conformational heterogeneity, quenching dynamic contact networks. Despite some idiosyncratic differences, most changes from room temperature to cryogenic temperature are conserved and likely reflect temperature-dependent solvent remodeling. Both cryogenic data sets point to additional conformations not evident in the corresponding room temperature data sets, suggesting that cryocooling does not merely trap preexisting conformational heterogeneity. Our results demonstrate that crystal cryocooling consistently distorts the energy landscape of DHFR, a paragon for understanding functional protein dynamics. Crystal Cryocooling Distorts Conformational Heterogeneity in a Model Michaelis Complex of DHFR.,Keedy DA, van den Bedem H, Sivak DA, Petsko GA, Ringe D, Wilson MA, Fraser JS Structure. 2014 Jun 10;22(6):899-910. doi: 10.1016/j.str.2014.04.016. Epub 2014, May 29. PMID:24882744[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
|
| ||||||||||||||||||||||||