5ahf: Difference between revisions
No edit summary |
No edit summary |
||
| (3 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
==Crystal structure of Salmonella enterica HisA D7N with ProFAR== | ==Crystal structure of Salmonella enterica HisA D7N with ProFAR== | ||
<StructureSection load='5ahf' size='340' side='right' caption='[[5ahf]], [[Resolution|resolution]] 2.20Å' scene=''> | <StructureSection load='5ahf' size='340' side='right'caption='[[5ahf]], [[Resolution|resolution]] 2.20Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5ahf]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AHF OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[5ahf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica Salmonella enterica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AHF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5AHF FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=GUO:[(2R,3S,4R,5R)-5-[4-AMINOCARBONYL-5-[(E)-[[(2R,3R,4S,5R)-3,4-BIS(OXIDANYL)-5-(PHOSPHONOOXYMETHYL)OXOLAN-2-YL]AMINO]METHYLIDENEAMINO]IMIDAZOL-1-YL]-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHYL+DIHYDROGEN+PHOSPHATE'>GUO</scene | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.201Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=GUO:[(2R,3S,4R,5R)-5-[4-AMINOCARBONYL-5-[(E)-[[(2R,3R,4S,5R)-3,4-BIS(OXIDANYL)-5-(PHOSPHONOOXYMETHYL)OXOLAN-2-YL]AMINO]METHYLIDENEAMINO]IMIDAZOL-1-YL]-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHYL+DIHYDROGEN+PHOSPHATE'>GUO</scene></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=5ahf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ahf OCA], [https://pdbe.org/5ahf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ahf RCSB], [https://www.ebi.ac.uk/pdbsum/5ahf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ahf ProSAT]</span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/HIS4_SALTY HIS4_SALTY] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
HisA is a (betaalpha)8 barrel enzyme that catalyzes the Amadori rearrangement of ProFAR to PRFAR in the histidine biosynthesis pathway and it is a paradigm for the study of enzyme evolution. Still, its exact catalytic mechanism has remained unclear. Here, we present crystal structures of wild type Salmonella enterica HisA (SeHisA) in its apo state and of mutants D7N and D7N/D176A in complex with two different conformations of the labile substrate ProFAR, which was structurally visualized for the first time. Site-directed mutagenesis and kinetics demonstrated that Asp7 acts as the catalytic base and Asp176 as the catalytic acid. The SeHisA structures with ProFAR display two different states of the long loops on the catalytic face of the structure, and demonstrate that initial binding of ProFAR to the active site is independent of loop interactions. When the long loops enclose the substrate, ProFAR adopts an extended conformation where its non-reacting half is in a product-like conformation. This change is associated with shifts in a hydrogen-bond network including His47, Asp129, Thr171 and Ser202, all shown to be functionally important. The closed-conformation structure is highly similar to the bi-functional HisA homologue PriA in complex with PRFAR, thus proving that structure and mechanism are conserved between HisA and PriA. This study clarifies the mechanistic cycle of HisA and provides a striking example of how an enzyme and its substrate can undergo coordinated conformational changes before catalysis. | |||
Two-step Ligand Binding in a (betaalpha)8 Barrel Enzyme - Substrate-bound Structures Shed New Light on the Catalytic Cycle of HisA.,Soderholm A, Guo X, Newton MS, Evans GB, Nasvall J, Patrick WM, Selmer M J Biol Chem. 2015 Aug 20. pii: jbc.M115.678086. PMID:26294764<ref>PMID:26294764</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 5ahf" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Salmonella enterica]] | ||
[[Category: | [[Category: Evans GB]] | ||
[[Category: | [[Category: Guo X]] | ||
[[Category: | [[Category: Nasvall J]] | ||
[[Category: | [[Category: Newton MS]] | ||
[[Category: | [[Category: Patrick WM]] | ||
[[Category: | [[Category: Selmer M]] | ||
[[Category: | [[Category: Soderholm A]] | ||
Latest revision as of 14:40, 9 May 2024
Crystal structure of Salmonella enterica HisA D7N with ProFARCrystal structure of Salmonella enterica HisA D7N with ProFAR
Structural highlights
FunctionPublication Abstract from PubMedHisA is a (betaalpha)8 barrel enzyme that catalyzes the Amadori rearrangement of ProFAR to PRFAR in the histidine biosynthesis pathway and it is a paradigm for the study of enzyme evolution. Still, its exact catalytic mechanism has remained unclear. Here, we present crystal structures of wild type Salmonella enterica HisA (SeHisA) in its apo state and of mutants D7N and D7N/D176A in complex with two different conformations of the labile substrate ProFAR, which was structurally visualized for the first time. Site-directed mutagenesis and kinetics demonstrated that Asp7 acts as the catalytic base and Asp176 as the catalytic acid. The SeHisA structures with ProFAR display two different states of the long loops on the catalytic face of the structure, and demonstrate that initial binding of ProFAR to the active site is independent of loop interactions. When the long loops enclose the substrate, ProFAR adopts an extended conformation where its non-reacting half is in a product-like conformation. This change is associated with shifts in a hydrogen-bond network including His47, Asp129, Thr171 and Ser202, all shown to be functionally important. The closed-conformation structure is highly similar to the bi-functional HisA homologue PriA in complex with PRFAR, thus proving that structure and mechanism are conserved between HisA and PriA. This study clarifies the mechanistic cycle of HisA and provides a striking example of how an enzyme and its substrate can undergo coordinated conformational changes before catalysis. Two-step Ligand Binding in a (betaalpha)8 Barrel Enzyme - Substrate-bound Structures Shed New Light on the Catalytic Cycle of HisA.,Soderholm A, Guo X, Newton MS, Evans GB, Nasvall J, Patrick WM, Selmer M J Biol Chem. 2015 Aug 20. pii: jbc.M115.678086. PMID:26294764[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
|
| ||||||||||||||||||