This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


2pb0

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /><applet load="2pb0" size="350" color="white" frame="true" align="right" spinBox="true" caption="2pb0, resolution 1.96&Aring;" /> '''Structure of biosynt...)
Current revision (06:30, 3 April 2024) (edit) (undo)
 
(15 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2pb0.jpg|left|200px]]<br /><applet load="2pb0" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="2pb0, resolution 1.96&Aring;" />
 
-
'''Structure of biosynthetic N-acetylornithine aminotransferase from Salmonella typhimurium: studies on substrate specificity and inhibitor binding'''<br />
 
-
==Overview==
+
==Structure of biosynthetic N-acetylornithine aminotransferase from Salmonella typhimurium: studies on substrate specificity and inhibitor binding==
-
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 muM 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. Proteins 2008. (c) 2007, Wiley-Liss, Inc.
+
<StructureSection load='2pb0' size='340' side='right'caption='[[2pb0]], [[Resolution|resolution]] 1.96&Aring;' scene=''>
-
 
+
== Structural highlights ==
-
==About this Structure==
+
<table><tr><td colspan='2'>[[2pb0]] 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=2PB0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PB0 FirstGlance]. <br>
-
2PB0 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Salmonella_typhimurium Salmonella typhimurium] with <scene name='pdbligand=PLP:'>PLP</scene> and <scene name='pdbligand=EDO:'>EDO</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PB0 OCA].
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.96&#8491;</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=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
-
==Reference==
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2pb0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pb0 OCA], [https://pdbe.org/2pb0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pb0 RCSB], [https://www.ebi.ac.uk/pdbsum/2pb0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pb0 ProSAT]</span></td></tr>
-
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. 2007 Aug 6;70(2):429-441. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17680699 17680699]
+
</table>
-
[[Category: Salmonella typhimurium]]
+
== Function ==
-
[[Category: Single protein]]
+
[https://www.uniprot.org/uniprot/ARGD_SALTY ARGD_SALTY] Involved in both the arginine and lysine biosynthetic pathways (By similarity).[HAMAP-Rule:MF_01107]
-
[[Category: Murthy, M.R.N.]]
+
== Evolutionary Conservation ==
-
[[Category: Prasuna, P.Ratna.]]
+
[[Image:Consurf_key_small.gif|200px|right]]
-
[[Category: Rajaram, V.]]
+
Check<jmol>
-
[[Category: Savithri, H.S.]]
+
<jmolCheckbox>
-
[[Category: EDO]]
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pb/2pb0_consurf.spt"</scriptWhenChecked>
-
[[Category: PLP]]
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
[[Category: argd]]
+
<text>to colour the structure by Evolutionary Conservation</text>
-
[[Category: arginine metabolism]]
+
</jmolCheckbox>
-
[[Category: gabaculine]]
+
</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=2pb0 ConSurf].
-
[[Category: lysine biosynthesis]]
+
<div style="clear:both"></div>
-
[[Category: pyridoxal-5'-phosphate]]
+
__TOC__
-
[[Category: transferase]]
+
</StructureSection>
-
 
+
[[Category: Large Structures]]
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 11:27:02 2008''
+
[[Category: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]]
 +
[[Category: Murthy MRN]]
 +
[[Category: Rajaram V]]
 +
[[Category: Ratna Prasuna P]]
 +
[[Category: Savithri HS]]

Current revision

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

PDB ID 2pb0

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2pb0"
Personal tools