2pb2: Difference between revisions

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<StructureSection load='2pb2' size='340' side='right'caption='[[2pb2]], [[Resolution|resolution]] 1.91&Aring;' scene=''>
<StructureSection load='2pb2' size='340' side='right'caption='[[2pb2]], [[Resolution|resolution]] 1.91&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2pb2]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Salty Salty]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PB2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PB2 FirstGlance]. <br>
<table><tr><td colspan='2'>[[2pb2]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PB2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PB2 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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]] 1.91&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2pb0|2pb0]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">argD ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=99287 SALTY])</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=2pb2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pb2 OCA], [https://pdbe.org/2pb2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pb2 RCSB], [https://www.ebi.ac.uk/pdbsum/2pb2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pb2 ProSAT]</span></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=2pb2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pb2 OCA], [https://pdbe.org/2pb2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pb2 RCSB], [https://www.ebi.ac.uk/pdbsum/2pb2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pb2 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/ARGD_SALTY ARGD_SALTY]] Involved in both the arginine and lysine biosynthetic pathways (By similarity).[HAMAP-Rule:MF_01107]  
[https://www.uniprot.org/uniprot/ARGD_SALTY ARGD_SALTY] Involved in both the arginine and lysine biosynthetic pathways (By similarity).[HAMAP-Rule:MF_01107]
== 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=2pb2 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=2pb2 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Acetylornithine aminotransferase (AcOAT) is one of the key enzymes involved in arginine metabolism and catalyzes the conversion of N-acetylglutamate semialdehyde to N-acetylornithine (AcOrn) in the presence of L-glutamate. It belongs to the Type I subgroup II family of pyridoxal 5'-phosphate (PLP) dependent enzymes. E. coli biosynthetic AcOAT (eAcOAT) also catalyzes the conversion of N-succinyl-L-2-amino-6-oxopimelate to N-succinyl-L,L-diaminopimelate, one of the steps in lysine biosynthesis. In view of the critical role of AcOAT in lysine and arginine biosynthesis, structural studies were initiated on the enzyme from S. typhimurium (sAcOAT). The K(m) and k(cat)/K(m) values determined with the purified sAcOAT suggested that the enzyme had much higher affinity for AcOrn than for ornithine (Orn) and was more efficient than eAcOAT. sAcOAT was inhibited by gabaculine (Gcn) with an inhibition constant (K(i)) of 7 microM and a second-order rate constant (k(2)) of 0.16 mM(-1) s(-1). sAcOAT, crystallized in the unliganded form and in the presence of Gcn or L-glutamate, diffracted to a maximum resolution of 1.90 A and contained a dimer in the asymmetric unit. The structure of unliganded sAcOAT showed significant electron density for PLP in only one of the subunits (subunit A). The asymmetry in PLP binding could be attributed to the ordering of the loop L(alphak-) (betam) in only one subunit (subunit B; the loop from subunit B comes close to the phosphate group of PLP in subunit A). Structural and spectral studies of sAcOAT with Gcn suggested that the enzyme might have a low affinity for PLP-Gcn complex. Comparison of sAcOAT with T. thermophilus AcOAT and human ornithine aminotransferase suggested that the higher specificity of sAcOAT towards AcOrn may not be due to specific changes in the active site residues but could result from minor conformational changes in some of them. This is the first structural report of AcOAT from a mesophilic organism and could serve as a basis for drug design as the enzyme is important for bacterial cell wall biosynthesis.
Structure of biosynthetic N-acetylornithine aminotransferase from Salmonella typhimurium: studies on substrate specificity and inhibitor binding.,Rajaram V, Ratna Prasuna P, Savithri HS, Murthy MR Proteins. 2008 Feb 1;70(2):429-41. PMID:17680699<ref>PMID:17680699</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2pb2" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Salty]]
[[Category: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]]
[[Category: Murthy, M R.N]]
[[Category: Murthy MRN]]
[[Category: Prasuna, P Ratna]]
[[Category: Rajaram V]]
[[Category: Rajaram, V]]
[[Category: Ratna Prasuna P]]
[[Category: Savithri, H S]]
[[Category: Savithri HS]]
[[Category: Argd]]
[[Category: Arginine metabolism]]
[[Category: Gabaculine]]
[[Category: Lysine biosynthesis]]
[[Category: Pyridoxal 5'-phosphate]]
[[Category: Transferase]]

Latest revision as of 16:53, 13 March 2024

Structure of biosynthetic N-acetylornithine aminotransferase from Salmonella typhimurium: studies on substrate specificity and inhibitor bindingStructure of biosynthetic N-acetylornithine aminotransferase from Salmonella typhimurium: studies on substrate specificity and inhibitor binding

Structural highlights

2pb2 is a 2 chain structure with sequence from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.91Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ARGD_SALTY Involved in both the arginine and lysine biosynthetic pathways (By similarity).[HAMAP-Rule:MF_01107]

Evolutionary Conservation

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

2pb2, resolution 1.91Å

Drag the structure with the mouse to rotate

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