1m7j: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
New page: left|200px<br /><applet load="1m7j" size="450" color="white" frame="true" align="right" spinBox="true" caption="1m7j, resolution 1.5Å" /> '''Crystal structure of ...
 
No edit summary
 
(14 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1m7j.jpg|left|200px]]<br /><applet load="1m7j" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1m7j, resolution 1.5&Aring;" />
'''Crystal structure of D-aminoacylase defines a novel subset of amidohydrolases'''<br />


==Overview==
==Crystal structure of D-aminoacylase defines a novel subset of amidohydrolases==
D-Aminoacylase is an attractive candidate for commercial production of, D-amino acids through its catalysis in the hydrolysis of N-acyl-D-amino, acids. We report here the first D-aminoacylase crystal structure from A., faecalis at 1.5-A resolution. The protein comprises a small beta-barrel, and a catalytic (betaalpha)(8)-barrel with a 63-residue insertion. The, enzyme structure shares significant similarity to the alpha/beta-barrel, amidohydrolase superfamily, in which the beta-strands in both barrels, superimpose well. Unexpectedly, the enzyme binds two zinc ions with widely, different affinities, although only the tightly bound zinc ion is required, for activity. One zinc ion is coordinated by Cys(96), His(220), and, His(250), while the other is loosely chelated by His(67), His(69), and, Cys(96). This is the first example of the metal ion coordination by a, cysteine residue in the superfamily. Therefore, D-aminoacylase defines a, novel subset and is a mononuclear zinc metalloenzyme but containing a, binuclear active site. The preferred substrate was modeled into a, hydrophobic pocket, revealing the substrate specificity and enzyme, catalysis. The 63-residue insertion containing substrate-interacting, residues may act as a gate controlling access to the active site, revealing that the substrate binding would induce a closed conformation to, sequester the catalysis from solvent.
<StructureSection load='1m7j' size='340' side='right'caption='[[1m7j]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1m7j]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Alcaligenes_faecalis Alcaligenes faecalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M7J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M7J FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.5&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=1m7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m7j OCA], [https://pdbe.org/1m7j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m7j RCSB], [https://www.ebi.ac.uk/pdbsum/1m7j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m7j ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q9AGH8_ALCFA Q9AGH8_ALCFA]
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/m7/1m7j_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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=1m7j ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1M7J is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Alcaligenes_faecalis Alcaligenes faecalis] with ZN and ACT as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/N-acyl-D-amino-acid_deacylase N-acyl-D-amino-acid deacylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.81 3.5.1.81] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1M7J OCA].
*[[Aminoacylase 3D structures|Aminoacylase 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
Crystal structure of D-aminoacylase from Alcaligenes faecalis DA1. A novel subset of amidohydrolases and insights into the enzyme mechanism., Liaw SH, Chen SJ, Ko TP, Hsu CS, Chen CJ, Wang AH, Tsai YC, J Biol Chem. 2003 Feb 14;278(7):4957-62. Epub 2002 Nov 25. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12454005 12454005]
[[Category: Alcaligenes faecalis]]
[[Category: Alcaligenes faecalis]]
[[Category: N-acyl-D-amino-acid deacylase]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Chen S-J]]
[[Category: Chen, S.J.]]
[[Category: Hsu C-S]]
[[Category: Hsu, C.S.]]
[[Category: Ko T-P]]
[[Category: Ko, T.P.]]
[[Category: Liaw S-H]]
[[Category: Liaw, S.H.]]
[[Category: Tsai Y-C]]
[[Category: Tsai, Y.C.]]
[[Category: Wang AH-J]]
[[Category: Wang, A.H.J.]]
[[Category: ACT]]
[[Category: ZN]]
[[Category: metal-dependent amidohydrolase]]
[[Category: tin-barrel]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 03:54:55 2007''

Latest revision as of 16:26, 13 March 2024

Crystal structure of D-aminoacylase defines a novel subset of amidohydrolasesCrystal structure of D-aminoacylase defines a novel subset of amidohydrolases

Structural highlights

1m7j is a 1 chain structure with sequence from Alcaligenes faecalis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.5Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q9AGH8_ALCFA

Evolutionary Conservation

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

See Also

1m7j, resolution 1.50Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=1m7j&oldid=4087458"