1pt5: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(12 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1pt5.jpg|left|200px]]


{{Structure
==Crystal structure of gene yfdW of E. coli==
|PDB= 1pt5 |SIZE=350|CAPTION= <scene name='initialview01'>1pt5</scene>, resolution 2.00&Aring;
<StructureSection load='1pt5' size='340' side='right'caption='[[1pt5]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=ACO:ACETYL COENZYME *A'>ACO</scene>
<table><tr><td colspan='2'>[[1pt5]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Shigella_flexneri Shigella flexneri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PT5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PT5 FirstGlance]. <br>
|ACTIVITY=  
</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&#8491;</td></tr>
|GENE= YFDW OR B2374 OR SF2441 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id= Escherichia coli, and Shigella flexneri])
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACO:ACETYL+COENZYME+*A'>ACO</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=1pt5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pt5 OCA], [https://pdbe.org/1pt5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pt5 RCSB], [https://www.ebi.ac.uk/pdbsum/1pt5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pt5 ProSAT]</span></td></tr>
 
</table>
'''Crystal structure of gene yfdW of E. coli'''
== Function ==
 
[https://www.uniprot.org/uniprot/FCTA_ECOLI FCTA_ECOLI] Catalyzes the transfer of the CoA moiety from formyl-CoA to oxalate.
 
== Evolutionary Conservation ==
==Overview==
[[Image:Consurf_key_small.gif|200px|right]]
Because of its toxicity, oxalate accumulation from amino acid catabolism leads to acute disorders in mammals. Gut microflora are therefore pivotal in maintaining a safe intestinal oxalate balance through oxalate degradation. Oxalate catabolism was first identified in Oxalobacter formigenes, a specialized, strictly anaerobic bacterium. Oxalate degradation was found to be performed successively by two enzymes, a formyl-CoA transferase (frc) and an oxalate decarboxylase (oxc). These two genes are present in several bacterial genomes including that of Escherichia coli. The frc ortholog in E. coli is yfdW, with which it shares 61% sequence identity. We have expressed the YfdW open reading frame product and solved its crystal structure in the apo-form and in complex with acetyl-CoA and with a mixture of acetyl-CoA and oxalate. YfdW exhibits a novel and spectacular fold in which two monomers assemble as interlaced rings, defining the CoA binding site at their interface. From the structure of the complex with acetyl-CoA and oxalate, we propose a putative formyl/oxalate transfer mechanism involving the conserved catalytic residue Asp169. The similarity of yfdW with bacterial orthologs (approximately 60% identity) and paralogs (approximately 20-30% identity) suggests that this new fold and parts of the CoA transfer mechanism are likely to be the hallmarks of a wide family of CoA transferases.
Check<jmol>
 
  <jmolCheckbox>
==About this Structure==
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pt/1pt5_consurf.spt"</scriptWhenChecked>
1PT5 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli,_and_shigella_flexneri Escherichia coli, and shigella flexneri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PT5 OCA].  
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 
    <text>to colour the structure by Evolutionary Conservation</text>
==Reference==
  </jmolCheckbox>
The crystal structure of the Escherichia coli YfdW gene product reveals a new fold of two interlaced rings identifying a wide family of CoA transferases., Gruez A, Roig-Zamboni V, Valencia C, Campanacci V, Cambillau C, J Biol Chem. 2003 Sep 5;278(36):34582-6. Epub 2003 Jul 3. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12844490 12844490]
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1pt5 ConSurf].
[[Category: Escherichia coli, and shigella flexneri]]
<div style="clear:both"></div>
[[Category: Single protein]]
__TOC__
[[Category: Cambillau, C.]]
</StructureSection>
[[Category: Campanacci, V.]]
[[Category: Escherichia coli]]
[[Category: Gruez, A.]]
[[Category: Large Structures]]
[[Category: Roig-Zamboni, V.]]
[[Category: Shigella flexneri]]
[[Category: Valencia, C.]]
[[Category: Cambillau C]]
[[Category: ACO]]
[[Category: Campanacci V]]
[[Category: acetylcoa]]
[[Category: Gruez A]]
[[Category: coenzyme binding]]
[[Category: Roig-Zamboni V]]
[[Category: structural genomic]]
[[Category: Valencia C]]
[[Category: transferase]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 13:28:39 2008''

Latest revision as of 11:10, 14 February 2024

Crystal structure of gene yfdW of E. coliCrystal structure of gene yfdW of E. coli

Structural highlights

1pt5 is a 2 chain structure with sequence from Escherichia coli and Shigella flexneri. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

FCTA_ECOLI Catalyzes the transfer of the CoA moiety from formyl-CoA to oxalate.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

1pt5, resolution 2.00Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=1pt5&oldid=4053465"