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1r0m

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[[Image:1r0m.gif|left|200px]]<br /><applet load="1r0m" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1r0m, resolution 1.3&Aring;" />
 
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'''Structure of Deinococcus radiodurans N-acylamino acid racemase at 1.3 : insights into a flexible binding pocket and evolution of enzymatic activity'''<br />
 
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==Overview==
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==Structure of Deinococcus radiodurans N-acylamino acid racemase at 1.3 : insights into a flexible binding pocket and evolution of enzymatic activity==
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N-acylamino acid racemase (NAAAR) catalyzes the racemization of N-acylamino acids and can be used in concert with an aminoacylase to produce enantiopure alpha-amino acids, a process that has potential industrial applications. Here we have cloned and characterized an NAAAR homologue from a radiation-resistant ancient bacterium, Deinococcus radiodurans. The expressed NAAAR racemized various substrates at an optimal temperature of 60 degrees C and had Km values of 24.8 mM and 12.3 mM for N-acetyl-D-methionine and N-acetyl-L-methionine, respectively. The crystal structure of NAAAR was solved to 1.3 A resolution using multiwavelength anomalous dispersion (MAD) methods. The structure consists of a homooctamer in which each subunit has an architecture characteristic of enolases with a capping domain and a (beta/alpha)7 beta barrel domain. The NAAAR.Mg2+ and NAAAR.N-acetyl-L-glutamine.Mg2+ structures were also determined, allowing us to define the Lys170-Asp195-Glu220-Asp245-Lys269 framework for catalyzing 1,1-proton exchange of N-acylamino acids. Four subsites enclosing the substrate are identified: catalytic site, metal-binding site, side-chain-binding region, and a flexible lid region. The high conservation of catalytic and metal-binding sites in different enolases reflects the essentiality of a common catalytic platform, allowing these enzymes to robustly abstract alpha-protons of various carboxylate substrates efficiently. The other subsites involved in substrate recognition are less conserved, suggesting that divergent evolution has led to functionally distinct enzymes.
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<StructureSection load='1r0m' size='340' side='right'caption='[[1r0m]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1r0m]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1R0M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1R0M FirstGlance]. <br>
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1R0M is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1R0M OCA].
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.3&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1r0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1r0m OCA], [https://pdbe.org/1r0m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1r0m RCSB], [https://www.ebi.ac.uk/pdbsum/1r0m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1r0m ProSAT]</span></td></tr>
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==Reference==
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</table>
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Structural basis for catalytic racemization and substrate specificity of an N-acylamino acid racemase homologue from Deinococcus radiodurans., Wang WC, Chiu WC, Hsu SK, Wu CL, Chen CY, Liu JS, Hsu WH, J Mol Biol. 2004 Sep 3;342(1):155-69. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15313614 15313614]
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== Function ==
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[https://www.uniprot.org/uniprot/NSAR_DEIRA NSAR_DEIRA] Acts as a N-succinylamino acid racemase (NSAR) that catalyzes the racemization of N-succinyl-L-phenylglycine and N-succinyl-D/L-phenylalanine (PubMed:24872444, PubMed:25875730). Can catalyze the racemization of a broad range of N-acylamino acids, including N-acetyl-D/L-methionine, N-acetyl-D/L-phenylalanine, N-acetyl-L-glutamine, N-acetyl-L-tryptophan, N-acetyl-L-leucine, N-formyl-D-methionine, N-formyl-D-norleucine, N-carbamoyl-D-methionine and N-carbamoyl-D-norleucine (PubMed:15313614, PubMed:16650857, PubMed:25875730). Also converts 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate (SHCHC) to 2-succinylbenzoate (OSB) (PubMed:24872444). Catalyzes both N-succinylamino acid racemization and OSB synthesis at equivalent rates (PubMed:24872444). However, NSAR activity is probably the protein's biological function, because menaquinone biosynthesis genes are missing in this species (Probable).<ref>PMID:15313614</ref> <ref>PMID:16650857</ref> <ref>PMID:24872444</ref> <ref>PMID:25875730</ref> <ref>PMID:16740275</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r0/1r0m_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=1r0m ConSurf].
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<div style="clear:both"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Deinococcus radiodurans]]
[[Category: Deinococcus radiodurans]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Chen, C Y.]]
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[[Category: Chen C-Y]]
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[[Category: Chiu, W C.]]
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[[Category: Chiu W-C]]
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[[Category: Hsu, S K.]]
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[[Category: Hsu S-K]]
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[[Category: Hsu, W H.]]
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[[Category: Hsu W-H]]
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[[Category: Liu, J S.]]
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[[Category: Liu J-S]]
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[[Category: Wang, W C.]]
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[[Category: Wang W-C]]
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[[Category: Wu, C L.]]
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[[Category: Wu C-L]]
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[[Category: racemase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:45:43 2008''
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Current revision

Structure of Deinococcus radiodurans N-acylamino acid racemase at 1.3 : insights into a flexible binding pocket and evolution of enzymatic activity

PDB ID 1r0m

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