3l04: Difference between revisions
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==Crystal structure of N-acetyl-L-ornithine transcarbamylase E92P mutant complexed with carbamyl phosphate and N-succinyl-L-norvaline== | ==Crystal structure of N-acetyl-L-ornithine transcarbamylase E92P mutant complexed with carbamyl phosphate and N-succinyl-L-norvaline== | ||
<StructureSection load='3l04' size='340' side='right' caption='[[3l04]], [[Resolution|resolution]] 2.50Å' scene=''> | <StructureSection load='3l04' size='340' side='right'caption='[[3l04]], [[Resolution|resolution]] 2.50Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3l04]] is a 1 chain structure with sequence from [ | <table><tr><td colspan='2'>[[3l04]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Xanthomonas_campestris_pv._campestris_str._ATCC_33913 Xanthomonas campestris pv. campestris str. ATCC 33913]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2g68 2g68]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3L04 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3L04 FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CP:PHOSPHORIC+ACID+MONO(FORMAMIDE)ESTER'>CP</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=SN0:N-(3-CARBOXYPROPANOYL)-L-NORVALINE'>SN0</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=3l04 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3l04 OCA], [https://pdbe.org/3l04 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3l04 RCSB], [https://www.ebi.ac.uk/pdbsum/3l04 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3l04 ProSAT]</span></td></tr> | |||
< | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [https://www.uniprot.org/uniprot/AOTC_XANCP AOTC_XANCP] Catalyzes the conversion of N-acetylornithine to N-acetylcitrulline in an alternative arginine biosynthesis pathway. The enzyme has no activity with ornithine. | ||
== 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: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Xanthomonas campestris pv. campestris str. ATCC 33913]] | ||
[[Category: Allewell | [[Category: Allewell NM]] | ||
[[Category: Shi | [[Category: Shi D]] | ||
[[Category: Tuchman | [[Category: Tuchman M]] | ||
[[Category: Yu | [[Category: Yu X]] | ||
Latest revision as of 11:28, 6 September 2023
Crystal structure of N-acetyl-L-ornithine transcarbamylase E92P mutant complexed with carbamyl phosphate and N-succinyl-L-norvalineCrystal structure of N-acetyl-L-ornithine transcarbamylase E92P mutant complexed with carbamyl phosphate and N-succinyl-L-norvaline
Structural highlights
FunctionAOTC_XANCP Catalyzes the conversion of N-acetylornithine to N-acetylcitrulline in an alternative arginine biosynthesis pathway. The enzyme has no activity with ornithine. 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 PubMedTranscarbamylases catalyze the transfer of the carbamyl group from carbamyl phosphate (CP) to an amino group of a second substrate such as aspartate, ornithine, or putrescine. Previously, structural determination of a transcarbamylase from Xanthomonas campestris led to the discovery of a novel N-acetylornithine transcarbamylase (AOTCase) that catalyzes the carbamylation of N-acetylornithine. Recently, a novel N-succinylornithine transcarbamylase (SOTCase) from Bacteroides fragilis was identified. Structural comparisons of AOTCase from X. campestris and SOTCase from B. fragilis revealed that residue Glu92 (X. campestris numbering) plays a critical role in distinguishing AOTCase from SOTCase. Enzymatic assays of E92P, E92S, E92V, and E92A mutants of AOTCase demonstrate that each of these mutations converts the AOTCase to an SOTCase. Similarly, the P90E mutation in B. fragilis SOTCase (equivalent to E92 in X. campestris AOTCase) converts the SOTCase to AOTCase. Hence, a single amino acid substitution is sufficient to swap the substrate specificities of AOTCase and SOTCase. X-ray crystal structures of these mutants in complexes with CP and N-acetyl-L-norvaline (an analog of N-acetyl-L-ornithine) or N-succinyl-L-norvaline (an analog of N-succinyl-L-ornithine) substantiate this conversion. In addition to Glu92 (X. campestris numbering), other residues such as Asn185 and Lys30 in AOTCase, which are involved in binding substrates through bridging water molecules, help to define the substrate specificity of AOTCase. These results provide the correct annotation (AOTCase or SOTCase) for a set of the transcarbamylase-like proteins that have been erroneously annotated as ornithine transcarbamylase (OTCase, EC 2.1.3.3). A single mutation in the active site swaps the substrate specificity of N-acetyl-L-ornithine transcarbamylase and N-succinyl-L-ornithine transcarbamylase.,Shi D, Yu X, Cabrera-Luque J, Chen TY, Roth L, Morizono H, Allewell NM, Tuchman M Protein Sci. 2007 Aug;16(8):1689-99. Epub 2007 Jun 28. PMID:17600144[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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