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1xpy

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Structural Basis for Catalytic Racemization and Substrate Specificity of an N-Acylamino Acid Racemase Homologue from Deinococcus radiodurans

Structural highlights

1xpy is a 4 chain structure with sequence from Deinococcus radiodurans. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.3Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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).^[1] ^[2] ^[3] ^[4] ^[5]

Evolutionary Conservation

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

Publication Abstract from PubMed

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.

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:15313614^[6]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Wang WC, Chiu WC, Hsu SK, Wu CL, Chen CY, Liu JS, Hsu WH. Structural basis for catalytic racemization and substrate specificity of an N-acylamino acid racemase homologue from Deinococcus radiodurans. J Mol Biol. 2004 Sep 3;342(1):155-69. PMID:15313614 doi:http://dx.doi.org/10.1016/j.jmb.2004.07.023
↑ Chiu WC, You JY, Liu JS, Hsu SK, Hsu WH, Shih CH, Hwang JK, Wang WC. Structure-stability-activity relationship in covalently cross-linked N-carbamoyl D-amino acid amidohydrolase and N-acylamino acid racemase. J Mol Biol. 2006 Jun 9;359(3):741-53. Epub 2006 Apr 18. PMID:16650857 doi:http://dx.doi.org/10.1016/j.jmb.2006.03.063
↑ Odokonyero D, Sakai A, Patskovsky Y, Malashkevich VN, Fedorov AA, Bonanno JB, Fedorov EV, Toro R, Agarwal R, Wang C, Ozerova ND, Yew WS, Sauder JM, Swaminathan S, Burley SK, Almo SC, Glasner ME. Loss of quaternary structure is associated with rapid sequence divergence in the OSBS family. Proc Natl Acad Sci U S A. 2014 May 28. pii: 201318703. PMID:24872444 doi:http://dx.doi.org/10.1073/pnas.1318703111
↑ Soriano-Maldonado P, Andújar-Sánchez M, Clemente-Jiménez JM, Rodríguez-Vico F, Las Heras-Vázquez FJ, Martínez-Rodríguez S. Biochemical and Mutational Characterization of N-Succinyl-Amino Acid Racemase from Geobacillus stearothermophilus CECT49. Mol Biotechnol. 2015 May;57(5):454-65. PMID:25875730 doi:10.1007/s12033-015-9839-4
↑ Glasner ME, Fayazmanesh N, Chiang RA, Sakai A, Jacobson MP, Gerlt JA, Babbitt PC. Evolution of structure and function in the o-succinylbenzoate synthase/N-acylamino acid racemase family of the enolase superfamily. J Mol Biol. 2006 Jun 30;360(1):228-50. PMID:16740275 doi:10.1016/j.jmb.2006.04.055
↑ Wang WC, Chiu WC, Hsu SK, Wu CL, Chen CY, Liu JS, Hsu WH. Structural basis for catalytic racemization and substrate specificity of an N-acylamino acid racemase homologue from Deinococcus radiodurans. J Mol Biol. 2004 Sep 3;342(1):155-69. PMID:15313614 doi:http://dx.doi.org/10.1016/j.jmb.2004.07.023

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1xpy"

@@ Line 3: / Line 3: @@
 <StructureSection load='1xpy' size='340' side='right'caption='[[1xpy]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1xpy]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"micrococcus_radiodurans"_raj_et_al._1960 "micrococcus radiodurans" raj et al. 1960]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XPY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XPY FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1xpy]] 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=1XPY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XPY FirstGlance]. <br>
-</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=NLQ:N~2~-ACETYL-L-GLUTAMINE'>NLQ</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]] 2.3&#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;'>[[1r0m|1r0m]]</div></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=NLQ:N~2~-ACETYL-L-GLUTAMINE'>NLQ</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=1xpy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xpy OCA], [https://pdbe.org/1xpy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xpy RCSB], [https://www.ebi.ac.uk/pdbsum/1xpy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xpy ProSAT]</span></td></tr>
 </table>
+== Function ==
+[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>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 34: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Micrococcus radiodurans raj et al. 1960]]
+[[Category: Deinococcus radiodurans]]
 [[Category: Large Structures]]
-[[Category: Chen, C Y]]
+[[Category: Chen C-Y]]
-[[Category: Chiu, W C]]
+[[Category: Chiu W-C]]
-[[Category: Hsu, S K]]
+[[Category: Hsu S-K]]
-[[Category: Hsu, W H]]
+[[Category: Hsu W-H]]
-[[Category: Liu, J S]]
+[[Category: Liu J-S]]
-[[Category: Wang, W C]]
+[[Category: Wang W-C]]
-[[Category: Wu, C L]]
+[[Category: Wu C-L]]
-[[Category: Isomerase]]
-[[Category: Racemase]]

1xpy

From Proteopedia

Current revision

Structural Basis for Catalytic Racemization and Substrate Specificity of an N-Acylamino Acid Racemase Homologue from Deinococcus radiodurans

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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