1k1d

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of D-hydantoinase

Structural highlights

1k1d is a 8 chain structure with sequence from Geobacillus stearothermophilus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.01Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

HYDA_GEOSE Catalyzes the stereospecific hydrolysis of the cyclic amide bond of D-hydantoin. Has no activity on dihydropyrimidines.

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

Industrial production of antibiotics, such as semisynthetic penicillins and cephalosporins, requires optically pure D-p-hydroxylphenylglycine and its derivatives as important side-chain precursors. To produce optically pure D-amino acids, microbial D-hydantoinase (E.C. 3.5.2.2) is used for stereospecific hydrolysis of chemically synthesized cyclic hydantoins. We report the apo-crystal structure of D-hydantoinase from B. stearothermophilus SD1 at 3.0 A resolution. The structure has a classic TIM barrel fold. Despite an undetectable similarity in sequence, D-hydantoinase shares a striking structural similarity with the recently solved structure of dihydroorotase. A structural comparison of hydantoinase with dihydroorotase revealed that the catalytic chemistry is conserved, while the substrate recognition is not. This structure provides insight into the stereochemistry of enantioselectivity in hydrolysis and illustrates how the enzyme recognizes stereospecific exocyclic substituents and hydrolyzes hydantoins. It should also provide a rationale for further directed evolution of this enzyme for hydrolysis of new hydantoins with novel exocyclic substituents.

Crystal structure of D-hydantoinase from Bacillus stearothermophilus: insight into the stereochemistry of enantioselectivity.,Cheon YH, Kim HS, Han KH, Abendroth J, Niefind K, Schomburg D, Wang J, Kim Y Biochemistry. 2002 Jul 30;41(30):9410-7. PMID:12135362^[1]

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

References

↑ Cheon YH, Kim HS, Han KH, Abendroth J, Niefind K, Schomburg D, Wang J, Kim Y. Crystal structure of D-hydantoinase from Bacillus stearothermophilus: insight into the stereochemistry of enantioselectivity. Biochemistry. 2002 Jul 30;41(30):9410-7. PMID:12135362

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/1k1d"

@@ Line 3: / Line 3: @@
 <StructureSection load='1k1d' size='340' side='right'caption='[[1k1d]], [[Resolution|resolution]] 3.01&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1k1d]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K1D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1K1D FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1k1d]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K1D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K1D FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 3.01&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1k1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k1d OCA], [http://pdbe.org/1k1d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1k1d RCSB], [http://www.ebi.ac.uk/pdbsum/1k1d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1k1d ProSAT]</span></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=1k1d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k1d OCA], [https://pdbe.org/1k1d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k1d RCSB], [https://www.ebi.ac.uk/pdbsum/1k1d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k1d ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/HYDA_GEOSE HYDA_GEOSE]] Catalyzes the stereospecific hydrolysis of the cyclic amide bond of D-hydantoin. Has no activity on dihydropyrimidines.
+[https://www.uniprot.org/uniprot/HYDA_GEOSE HYDA_GEOSE] Catalyzes the stereospecific hydrolysis of the cyclic amide bond of D-hydantoin. Has no activity on dihydropyrimidines.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 15: / Line 15: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k1/1k1d_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 33: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 12980]]
+[[Category: Geobacillus stearothermophilus]]
 [[Category: Large Structures]]
-[[Category: Abendroth, J]]
+[[Category: Abendroth J]]
-[[Category: Cheon, Y H]]
+[[Category: Cheon YH]]
-[[Category: Han, K H]]
+[[Category: Han KH]]
-[[Category: Kim, H S]]
+[[Category: Kim HS]]
-[[Category: Kim, Y]]
+[[Category: Kim Y]]
-[[Category: Niefind, K]]
+[[Category: Niefind K]]
-[[Category: Schomburg, D]]
+[[Category: Schomburg D]]
-[[Category: Wang, J]]
+[[Category: Wang J]]
-[[Category: D-hydantoinase]]
-[[Category: Hydrolase]]

1k1d

From Proteopedia

Current revision

Crystal structure of D-hydantoinase

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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