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[[Image:1erz.gif|left|200px]]<br /><applet load="1erz" size="350" color="white" frame="true" align="right" spinBox="true"
caption="1erz, resolution 1.70&Aring;" />
'''CRYSTAL STRUCTURE OF N-CARBAMYL-D-AMINO ACID AMIDOHYDROLASE WITH A NOVEL CATALYTIC FRAMEWORK COMMON TO AMIDOHYDROLASES'''<br />


==Overview==
==CRYSTAL STRUCTURE OF N-CARBAMYL-D-AMINO ACID AMIDOHYDROLASE WITH A NOVEL CATALYTIC FRAMEWORK COMMON TO AMIDOHYDROLASES==
BACKGROUND: N-carbamyl-D-amino acid amidohydrolase (DCase) catalyzes the hydrolysis of N-carbamyl-D-amino acids to the corresponding D-amino acids, which are useful intermediates in the preparation of beta-lactam antibiotics. To understand the catalytic mechanism of N-carbamyl-D-amino acid hydrolysis, the substrate specificity and thermostability of the enzyme, we have determined the structure of DCase from Agrobacterium sp. strain KNK712. RESULTS: The crystal structure of DCase has been determined to 1.7 A resolution. The enzyme forms a homotetramer and each monomer consists of a variant of the alpha + beta fold. The topology of the enzyme comprises a sandwich of parallel beta sheets surrounded by two layers of alpha helices, this topology has not been observed in other amidohydrolases such as the N-terminal nucleophile (Ntn) hydrolases. CONCLUSIONS: The catalytic center could be identified and consists of Glu46, Lys126 and Cys171. Cys171 was found to be the catalytic nucleophile, and its nucleophilic character appeared to be increased through general-base activation by Glu46. DCase shows only weak sequence similarity with a family of amidohydrolases, including beta-alanine synthase, aliphatic amidases and nitrilases, but might share highly conserved residues in a novel framework, which could provide a possible explanation for the catalytic mechanism for this family of enzymes.
<StructureSection load='1erz' size='340' side='right'caption='[[1erz]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[1erz]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Agrobacterium_sp._KNK712 Agrobacterium sp. KNK712]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ERZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ERZ FirstGlance]. <br>
1ERZ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Agrobacterium_sp. Agrobacterium sp.]. Active as [http://en.wikipedia.org/wiki/N-carbamoyl-D-amino_acid_hydrolase N-carbamoyl-D-amino acid hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.77 3.5.1.77] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ERZ 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]] 1.7&#8491;</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=1erz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1erz OCA], [https://pdbe.org/1erz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1erz RCSB], [https://www.ebi.ac.uk/pdbsum/1erz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1erz ProSAT]</span></td></tr>
==Reference==
</table>
Crystal structure of N-carbamyl-D-amino acid amidohydrolase with a novel catalytic framework common to amidohydrolases., Nakai T, Hasegawa T, Yamashita E, Yamamoto M, Kumasaka T, Ueki T, Nanba H, Ikenaka Y, Takahashi S, Sato M, Tsukihara T, Structure. 2000 Jul 15;8(7):729-37. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10903946 10903946]
== Function ==
[[Category: Agrobacterium sp.]]
[https://www.uniprot.org/uniprot/DCAS_AGRSK DCAS_AGRSK] The enzyme catalyzes the hydrolysis of N-carbamoyl-D-amino acids to the corresponding which are useful intermediates in the preparation of beta-lactam antibiotics. Industrial production of beta-lactam antibiotics is now being developed using this enzyme.
[[Category: N-carbamoyl-D-amino acid hydrolase]]
== Evolutionary Conservation ==
[[Category: Single protein]]
[[Image:Consurf_key_small.gif|200px|right]]
[[Category: Hasegawa, T.]]
Check<jmol>
[[Category: Ikenaka, Y.]]
  <jmolCheckbox>
[[Category: Kumasaka, T.]]
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/er/1erz_consurf.spt"</scriptWhenChecked>
[[Category: Nakai, T.]]
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
[[Category: Nanba, H.]]
    <text>to colour the structure by Evolutionary Conservation</text>
[[Category: Sato, M.]]
  </jmolCheckbox>
[[Category: Takahashi, S.]]
</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=1erz ConSurf].
[[Category: Tsukihara, T.]]
<div style="clear:both"></div>
[[Category: Ueki, T.]]
__TOC__
[[Category: Yamamoto, M.]]
</StructureSection>
[[Category: Yamashita, E.]]
[[Category: Agrobacterium sp. KNK712]]
[[Category: four-layer sandwich]]
[[Category: Large Structures]]
 
[[Category: Hasegawa T]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:30:52 2008''
[[Category: Ikenaka Y]]
[[Category: Kumasaka T]]
[[Category: Nakai T]]
[[Category: Nanba H]]
[[Category: Sato M]]
[[Category: Takahashi S]]
[[Category: Tsukihara T]]
[[Category: Ueki T]]
[[Category: Yamamoto M]]
[[Category: Yamashita E]]

Latest revision as of 07:06, 7 February 2024

CRYSTAL STRUCTURE OF N-CARBAMYL-D-AMINO ACID AMIDOHYDROLASE WITH A NOVEL CATALYTIC FRAMEWORK COMMON TO AMIDOHYDROLASES

1erz, resolution 1.70Å

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