1sjb

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:31, 14 February 2024) (edit) (undo)
 
(13 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1sjb.gif|left|200px]]<br /><applet load="1sjb" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1sjb, resolution 2.20&Aring;" />
 
-
'''X-ray structure of o-succinylbenzoate synthase complexed with o-succinylbenzoic acid'''<br />
 
-
==Overview==
+
==X-ray structure of o-succinylbenzoate synthase complexed with o-succinylbenzoic acid==
-
Divergent evolution of enzyme function is commonly explained by a gene duplication event followed by mutational changes that allow the protein encoded by the copy to acquire a new function. An alternate hypothesis is that this process is facilitated when the progenitor enzyme acquires a second function while maintaining the original activity. This phenomenon has been suggested to occur in the o-succinylbenzoate synthase (OSBS) from a species of Amycolatopsis that catalyzes not only the physiological syn-dehydration reaction of 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate but also an accidental racemization of N-acylamino acids [Palmer, D. R., Garrett, J. B., Sharma, V., Meganathan, R., Babbitt, P. C., and Gerlt, J. A. (1999) Biochemistry 38, 4252-4258]. To understand the molecular basis of this promiscuity, three-dimensional structures of liganded complexes of this enzyme have been determined, including the product of the OSBS reaction and three N-acylamino acid substrates for the N-acylamino acid racemase (NAAAR) reaction, N-acetylmethionine, N-succinylmethionine, and N-succinylphenylglycine, to 2.2, 2.3, 2.1, and 1.9 A resolution, respectively. These structures show how the active-site cavity can accommodate both the hydrophobic substrate for the OSBS reaction and the substrates for the accidental NAAAR reaction. As expected, the N-acylamino acid is sandwiched between lysines 163 and 263, which function as the catalytic bases for the abstraction of the alpha-proton in the (R)- and (S)-racemization reactions, respectively [Taylor Ringia, E. A., Garrett, J. B, Thoden, J. B., Holden, H. M., Rayment, I., and Gerlt, J. A. (2004) Biochemistry 42, 224-229]. Importantly, the protein forms specific favorable interactions with the hydrophobic amino acid side chain, alpha-carbon, carboxylate, and the polar components of the N-acyl linkage. Accommodation of the components of the N-acyl linkage appears to be the reason that this enzyme is capable of a racemization reaction on these substrates, whereas the orthologous OSBS from Escherichia coli lacks this functionality.
+
<StructureSection load='1sjb' size='340' side='right'caption='[[1sjb]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
-
 
+
== Structural highlights ==
-
==About this Structure==
+
<table><tr><td colspan='2'>[[1sjb]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Amycolatopsis_sp. Amycolatopsis sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SJB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SJB FirstGlance]. <br>
-
1SJB is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Amycolatopsis_sp. Amycolatopsis sp.] with <scene name='pdbligand=MG:'>MG</scene> and <scene name='pdbligand=OSB:'>OSB</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SJB 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]] 2.2&#8491;</td></tr>
-
 
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OSB:2-SUCCINYLBENZOATE'>OSB</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=1sjb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sjb OCA], [https://pdbe.org/1sjb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1sjb RCSB], [https://www.ebi.ac.uk/pdbsum/1sjb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1sjb ProSAT]</span></td></tr>
-
Evolution of enzymatic activity in the enolase superfamily: structural studies of the promiscuous o-succinylbenzoate synthase from Amycolatopsis., Thoden JB, Taylor Ringia EA, Garrett JB, Gerlt JA, Holden HM, Rayment I, Biochemistry. 2004 May 18;43(19):5716-27. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15134446 15134446]
+
</table>
-
[[Category: Amycolatopsis sp.]]
+
== Function ==
-
[[Category: Single protein]]
+
[https://www.uniprot.org/uniprot/NSAR_AMYSP NSAR_AMYSP] Acts as a N-succinylamino acid racemase (NSAR) that catalyzes the racemization of N-succinyl-phenylglycine and N-succinyl-methionine (PubMed:14705949, PubMed:24955846). Can catalyze the racemization of a broad range of N-acylamino acids, including N-acetyl-D/L-methionine, N-propionyl-D/L-methionine, N-butyryl-D/L-methionine and N-chloroacetyl-L-valine (PubMed:7766084, PubMed:10194342, PubMed:14705949, PubMed:23130969). Also converts 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate (SHCHC) to 2-succinylbenzoate (OSB) (PubMed:10194342, PubMed:14705949, PubMed:24955846). Catalyzes both N-succinylamino acid racemization and OSB synthesis at equivalent rates (PubMed:14705949, PubMed:24955846). NSAR is probably the biological function of this enzyme (Probable).<ref>PMID:10194342</ref> <ref>PMID:14705949</ref> <ref>PMID:23130969</ref> <ref>PMID:24955846</ref> <ref>PMID:7766084</ref> <ref>PMID:16740275</ref> <ref>PMID:24955846</ref>
-
[[Category: Garrett, J B.]]
+
== Evolutionary Conservation ==
-
[[Category: Gerlt, J A.]]
+
[[Image:Consurf_key_small.gif|200px|right]]
-
[[Category: Holden, H M.]]
+
Check<jmol>
-
[[Category: Rayment, I.]]
+
<jmolCheckbox>
-
[[Category: Taylor-Ringia, E A.]]
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sj/1sjb_consurf.spt"</scriptWhenChecked>
-
[[Category: Thoden, J B.]]
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
[[Category: MG]]
+
<text>to colour the structure by Evolutionary Conservation</text>
-
[[Category: OSB]]
+
</jmolCheckbox>
-
[[Category: racemase]]
+
</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=1sjb ConSurf].
-
 
+
<div style="clear:both"></div>
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:02:05 2008''
+
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Amycolatopsis sp]]
 +
[[Category: Large Structures]]
 +
[[Category: Garrett JB]]
 +
[[Category: Gerlt JA]]
 +
[[Category: Holden HM]]
 +
[[Category: Rayment I]]
 +
[[Category: Taylor-Ringia EA]]
 +
[[Category: Thoden JB]]

Current revision

X-ray structure of o-succinylbenzoate synthase complexed with o-succinylbenzoic acid

PDB ID 1sjb

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/1sjb"
Personal tools