1nfg

From Proteopedia

(Difference between revisions)

Current revision

Structure of D-hydantoinase

Structural highlights

1nfg is a 4 chain structure with sequence from Ralstonia pickettii. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.7Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

HYDA_RALPI Catalyzes the stereospecific hydrolysis of the cyclic amide bond of D-hydantoin derivatives.

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

D-Hydantoinase (D-HYD) is an industrial enzyme that is widely used in the production of D-amino acids which are precursors for semisynthesis of antibiotics, peptides, and pesticides. This report describes the crystal structure of D-hydantoinase from Burkholderia pickettii (HYD(Bp)) at a 2.7-A resolution. The structure of HYD(Bp) consists of a core (alpha/beta)(8) triose phosphate isomerase barrel fold and a beta-sheet domain, and the catalytic active site consists of two metal ions and six highly conserved amino acid residues. Although HYD(Bp) shares only moderate sequence similarity with D-HYDs from Thermus sp. (HYD(Tsp)) and Bacillus stearothermophilus (HYD(Bst)), whose structures have recently been solved, the overall structure and the structure of the catalytic active site are strikingly similar. Nevertheless, the amino acids that compose the substrate-binding site are less conserved and have different properties, which might dictate the substrate specificity. Structural comparison has revealed insights into the molecular basis of the differential thermostability of D-HYDs. The more thermostable HYD(Tsp) contains more aromatic residues in the interior of the structure than HYD(Bp) and HYD(Bst). Changes of large aromatic residues in HYD(Tsp) to smaller residues in HYD(Bp) or HYD(Bst) decrease the hydrophobicity and create cavities inside the structure. HYD(Tsp) has more salt bridges and hydrogen-bonding interactions and less oxidation susceptible Met and Cys residues on the protein surface than HYD(Bp) and HYD(Bst). Besides, HYD(Tsp) also contains more rigid Pro residues. These factors are likely to make major contributions to the varying thermostability of these enzymes. This information could be exploited in helping to engineer more thermostable mesophilic enzymes.

Crystal structure of D-Hydantoinase from Burkholderia pickettii at a resolution of 2.7 Angstroms: insights into the molecular basis of enzyme thermostability.,Xu Z, Liu Y, Yang Y, Jiang W, Arnold E, Ding J J Bacteriol. 2003 Jul;185(14):4038-49. PMID:12837777^[1]

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

References

↑ Xu Z, Liu Y, Yang Y, Jiang W, Arnold E, Ding J. Crystal structure of D-Hydantoinase from Burkholderia pickettii at a resolution of 2.7 Angstroms: insights into the molecular basis of enzyme thermostability. J Bacteriol. 2003 Jul;185(14):4038-49. PMID:12837777

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

@@ Line 1: / Line 1: @@
-[[Image:1nfg.gif|left|200px]]<br /><applet load="1nfg" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1nfg, resolution 2.7&Aring;" />
-'''Structure of D-hydantoinase'''<br />
-==Overview==
+==Structure of D-hydantoinase==
-D-Hydantoinase (D-HYD) is an industrial enzyme that is widely used in the, production of D-amino acids which are precursors for semisynthesis of, antibiotics, peptides, and pesticides. This report describes the crystal, structure of D-hydantoinase from Burkholderia pickettii (HYD(Bp)) at a, 2.7-A resolution. The structure of HYD(Bp) consists of a core, (alpha/beta)(8) triose phosphate isomerase barrel fold and a beta-sheet, domain, and the catalytic active site consists of two metal ions and six, highly conserved amino acid residues. Although HYD(Bp) shares only, moderate sequence similarity with D-HYDs from Thermus sp. (HYD(Tsp)) and, Bacillus stearothermophilus (HYD(Bst)), whose structures have recently, been solved, the overall structure and the structure of the catalytic, active site are strikingly similar. Nevertheless, the amino acids that, compose the substrate-binding site are less conserved and have different, properties, which might dictate the substrate specificity. Structural, comparison has revealed insights into the molecular basis of the, differential thermostability of D-HYDs. The more thermostable HYD(Tsp), contains more aromatic residues in the interior of the structure than, HYD(Bp) and HYD(Bst). Changes of large aromatic residues in HYD(Tsp) to, smaller residues in HYD(Bp) or HYD(Bst) decrease the hydrophobicity and, create cavities inside the structure. HYD(Tsp) has more salt bridges and, hydrogen-bonding interactions and less oxidation susceptible Met and Cys, residues on the protein surface than HYD(Bp) and HYD(Bst). Besides, HYD(Tsp) also contains more rigid Pro residues. These factors are likely, to make major contributions to the varying thermostability of these, enzymes. This information could be exploited in helping to engineer more, thermostable mesophilic enzymes.
+<StructureSection load='1nfg' size='340' side='right'caption='[[1nfg]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1nfg]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Ralstonia_pickettii Ralstonia pickettii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NFG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NFG 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]] 2.7&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</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=1nfg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nfg OCA], [https://pdbe.org/1nfg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nfg RCSB], [https://www.ebi.ac.uk/pdbsum/1nfg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nfg ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/HYDA_RALPI HYDA_RALPI] Catalyzes the stereospecific hydrolysis of the cyclic amide bond of D-hydantoin derivatives.
+== 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/nf/1nfg_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=1nfg ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+D-Hydantoinase (D-HYD) is an industrial enzyme that is widely used in the production of D-amino acids which are precursors for semisynthesis of antibiotics, peptides, and pesticides. This report describes the crystal structure of D-hydantoinase from Burkholderia pickettii (HYD(Bp)) at a 2.7-A resolution. The structure of HYD(Bp) consists of a core (alpha/beta)(8) triose phosphate isomerase barrel fold and a beta-sheet domain, and the catalytic active site consists of two metal ions and six highly conserved amino acid residues. Although HYD(Bp) shares only moderate sequence similarity with D-HYDs from Thermus sp. (HYD(Tsp)) and Bacillus stearothermophilus (HYD(Bst)), whose structures have recently been solved, the overall structure and the structure of the catalytic active site are strikingly similar. Nevertheless, the amino acids that compose the substrate-binding site are less conserved and have different properties, which might dictate the substrate specificity. Structural comparison has revealed insights into the molecular basis of the differential thermostability of D-HYDs. The more thermostable HYD(Tsp) contains more aromatic residues in the interior of the structure than HYD(Bp) and HYD(Bst). Changes of large aromatic residues in HYD(Tsp) to smaller residues in HYD(Bp) or HYD(Bst) decrease the hydrophobicity and create cavities inside the structure. HYD(Tsp) has more salt bridges and hydrogen-bonding interactions and less oxidation susceptible Met and Cys residues on the protein surface than HYD(Bp) and HYD(Bst). Besides, HYD(Tsp) also contains more rigid Pro residues. These factors are likely to make major contributions to the varying thermostability of these enzymes. This information could be exploited in helping to engineer more thermostable mesophilic enzymes.
-==About this Structure==
+Crystal structure of D-Hydantoinase from Burkholderia pickettii at a resolution of 2.7 Angstroms: insights into the molecular basis of enzyme thermostability.,Xu Z, Liu Y, Yang Y, Jiang W, Arnold E, Ding J J Bacteriol. 2003 Jul;185(14):4038-49. PMID:12837777<ref>PMID:12837777</ref>
-NFG is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Ralstonia_pickettii Ralstonia pickettii] with ZN as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Dihydropyrimidinase Dihydropyrimidinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.2 3.5.2.2] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1NFG OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Crystal structure of D-Hydantoinase from Burkholderia pickettii at a resolution of 2.7 Angstroms: insights into the molecular basis of enzyme thermostability., Xu Z, Liu Y, Yang Y, Jiang W, Arnold E, Ding J, J Bacteriol. 2003 Jul;185(14):4038-49. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12837777 12837777]
+</div>
-[[Category: Dihydropyrimidinase]]
+<div class="pdbe-citations 1nfg" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Ralstonia pickettii]]
-[[Category: Single protein]]
+[[Category: Arnold E]]
-[[Category: Arnold, E.]]
+[[Category: Ding J]]
-[[Category: Ding, J.]]
+[[Category: Jiang W]]
-[[Category: Jiang, W.]]
+[[Category: Xu Z]]
-[[Category: Xu, Z.]]
+[[Category: Yang Y]]
-[[Category: Yang, Y.]]
-[[Category: ZN]]
-[[Category: tim barrel]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 22:12:44 2007''

1nfg

From Proteopedia

Current revision

Structure of D-hydantoinase

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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