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==Crystal Structure of a new transcarbamylase from the anaerobic bacterium Bacteroides fragilis at 2.0 A resolution==
==Crystal Structure of a new transcarbamylase from the anaerobic bacterium Bacteroides fragilis at 2.0 A resolution==
<StructureSection load='1js1' size='340' side='right' caption='[[1js1]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
<StructureSection load='1js1' size='340' side='right'caption='[[1js1]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1js1]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacteroides_inaequalis"_eggerth_and_gagnon_1933 "bacteroides inaequalis" eggerth and gagnon 1933]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JS1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JS1 FirstGlance]. <br>
<table><tr><td colspan='2'>[[1js1]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_fragilis Bacteroides fragilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JS1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JS1 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
</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>
<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=1js1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1js1 OCA], [http://pdbe.org/1js1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1js1 RCSB], [http://www.ebi.ac.uk/pdbsum/1js1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1js1 ProSAT]</span></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=1js1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1js1 OCA], [https://pdbe.org/1js1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1js1 RCSB], [https://www.ebi.ac.uk/pdbsum/1js1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1js1 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/AOTC_BACTN AOTC_BACTN]] Catalyzes the conversion of N-acetylornithine to N-acetylcitrulline in an alternative arginine biosynthesis pathway. The enzyme has no activity with ornithine.  
[https://www.uniprot.org/uniprot/SOTC_BACTN SOTC_BACTN] Catalyzes the transfer of the carbamoyl group from carbamoyl phosphate to the delta-amino group of N(2)-succinyl-L-ornithine to produce N(2)-succinyl-L-citrulline. Is essential for arginine biosynthesis. Has no activity with either L-ornithine or L-aspartate as substrate. Has also no detectable AOTCase activity, being unable to convert N(2)-acetyl-L-ornithine to N(2)-acetyl-L-citrulline.[UniProtKB:E1WKT5]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=1js1 ConSurf].
</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=1js1 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
A transcarbamylase-like protein essential for arginine biosynthesis in the anaerobic bacterium Bacteroides fragilis has been purified and crystallized in space group P4(3)2(1)2 (a=b=153.4 A, c=94.8 A). The structure was solved using a single isomorphous replacement with anomalous scattering (SIRAS) and was refined at 2.0 A resolution to an R-factor of 20.6% (R-free=25.2%). The molecular model is trimeric and comprises 960 amino acid residues, two phosphate groups and 422 water molecules. The monomer has the consensus transcarbamylase fold with two structural domains linked by two long interdomain helices: the putative carbamoyl phosphate-binding domain and a binding domain for the second substrate. Each domain has a central parallel beta-sheet surrounded by alpha-helices and loops with alpha/beta topology. The putative carbamoyl phosphate-binding site is similar to those in ornithine transcarbamylases (OTCases) and aspartate transcarbamylases (ATCases); however, the second substrate-binding site is strikingly different. This site has several insertions and deletions, and residues critical to substrate binding and catalysis in other known transcarbamylases are not conserved. The three-dimensional structure and the fact that this protein is essential for arginine biosynthesis suggest strongly that it is a new member of the transcarbamylase family. A similar protein has been found in Xylella fastidiosa, a bacterium that infects grapes, citrus and other plants.
Crystal structure of a transcarbamylase-like protein from the anaerobic bacterium Bacteroides fragilis at 2.0 A resolution.,Shi D, Gallegos R, DePonte J 3rd, Morizono H, Yu X, Allewell NM, Malamy M, Tuchman M J Mol Biol. 2002 Jul 19;320(4):899-908. PMID:12095263<ref>PMID:12095263</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1js1" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bacteroides inaequalis eggerth and gagnon 1933]]
[[Category: Bacteroides fragilis]]
[[Category: Allewell, N M]]
[[Category: Large Structures]]
[[Category: Gallegos, R]]
[[Category: Allewell NM]]
[[Category: III, J DePonte]]
[[Category: DePonte III J]]
[[Category: Malamy, M]]
[[Category: Gallegos R]]
[[Category: Morizono, H]]
[[Category: Malamy M]]
[[Category: Shi, D]]
[[Category: Morizono H]]
[[Category: Tuchman, M]]
[[Category: Shi D]]
[[Category: Yu, X]]
[[Category: Tuchman M]]
[[Category: Alpha/beta topology]]
[[Category: Yu X]]
[[Category: Transferase]]
[[Category: Two domain]]

Latest revision as of 10:41, 7 February 2024

Crystal Structure of a new transcarbamylase from the anaerobic bacterium Bacteroides fragilis at 2.0 A resolutionCrystal Structure of a new transcarbamylase from the anaerobic bacterium Bacteroides fragilis at 2.0 A resolution

Structural highlights

1js1 is a 3 chain structure with sequence from Bacteroides fragilis. 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

SOTC_BACTN Catalyzes the transfer of the carbamoyl group from carbamoyl phosphate to the delta-amino group of N(2)-succinyl-L-ornithine to produce N(2)-succinyl-L-citrulline. Is essential for arginine biosynthesis. Has no activity with either L-ornithine or L-aspartate as substrate. Has also no detectable AOTCase activity, being unable to convert N(2)-acetyl-L-ornithine to N(2)-acetyl-L-citrulline.[UniProtKB:E1WKT5]

Evolutionary Conservation

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

1js1, resolution 2.00Å

Drag the structure with the mouse to rotate

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