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2zly

From Proteopedia

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Structure of 6-aminohexanoate-dimer hydrolase, D370Y mutant

Structural highlights

2zly is a 1 chain structure with sequence from Flavobacterium sp.. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.58Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NYLB2_FLASK Involved in nylon oligomer degradation.^[1] ^[2] NYLB_FLASK

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

Promiscuous 6-aminohexanoate-linear dimer (Ald)-hydrolytic activity originally obtained in a carboxylesterase with a beta-lactamase fold was enhanced about 80-fold by directed evolution using error-prone PCR and DNA shuffling. Kinetic studies of the mutant enzyme (Hyb-S4M94) demonstrated that the enzyme had acquired an increased affinity (K(m) = 15 mM) and turnover (k(cat) = 3.1 s(-1)) for Ald, and that a catalytic center suitable for nylon-6 byproduct hydrolysis had been generated. Construction of various mutant enzymes revealed that the enhanced activity in the newly evolved enzyme is due to the substitutions R187S/F264C/D370Y. Crystal structures of Hyb-S4M94 with bound substrate suggested that catalytic function for Ald was improved by hydrogen-bonding/hydrophobic interactions between the Ald--COOH and Tyr370, a hydrogen-bonding network from Ser187 to Ald--NH(3) (+), and interaction between Ald--NH(3) (+) and Gln27-O(epsilon) derived from another subunit in the homo-dimeric structure. In wild-type Ald-hydrolase (NylB), Ald-hydrolytic activity is thought to be optimized by the substitutions G181D/H266N, which improve an electrostatic interaction with Ald--NH(3) (+) (Kawashima et al., FEBS J 2009; 276:2547-2556). We propose here that there exist at least two alternative modes for optimizing the Ald-hydrolytic activity of a carboxylesterase with a beta-lactamase fold.

Two alternative modes for optimizing nylon-6 byproduct hydrolytic activity from a carboxylesterase with a beta-lactamase fold: X-ray crystallographic analysis of directly evolved 6-aminohexanoate-dimer hydrolase.,Ohki T, Shibata N, Higuchi Y, Kawashima Y, Takeo M, Kato D, Negoro S Protein Sci. 2009 Aug;18(8):1662-73. PMID:19521995^[3]

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

References

↑ Negoro S, Nakamura S, Kimura H, Fujiyama K, Zhang YZ, Kanzaki N, Okada H. Construction of hybrid genes of 6-aminohexanoic acid-oligomer hydrolase and its analogous enzyme. Estimation of the intramolecular regions important for the enzyme evolution. J Biol Chem. 1984 Nov 25;259(22):13648-51 PMID:6389532
↑ Okada H, Negoro S, Kimura H, Nakamura S. Evolutionary adaptation of plasmid-encoded enzymes for degrading nylon oligomers. Nature. 1983 Nov 10-16;306(5939):203-6. PMID:6646204 doi:10.1038/306203a0
↑ Ohki T, Shibata N, Higuchi Y, Kawashima Y, Takeo M, Kato D, Negoro S. Two alternative modes for optimizing nylon-6 byproduct hydrolytic activity from a carboxylesterase with a beta-lactamase fold: X-ray crystallographic analysis of directly evolved 6-aminohexanoate-dimer hydrolase. Protein Sci. 2009 Aug;18(8):1662-73. PMID:19521995 doi:10.1002/pro.185

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/2zly"

@@ Line 1: / Line 1: @@
 ==Structure of 6-aminohexanoate-dimer hydrolase, D370Y mutant==
-<StructureSection load='2zly' size='340' side='right' caption='[[2zly]], [[Resolution|resolution]] 1.58&Aring;' scene=''>
+<StructureSection load='2zly' size='340' side='right'caption='[[2zly]], [[Resolution|resolution]] 1.58&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2zly]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Flasp Flasp]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZLY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZLY FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2zly]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Flavobacterium_sp. Flavobacterium sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZLY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZLY FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.58&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1wyb|1wyb]], [[1wyc|1wyc]], [[2dcf|2dcf]], [[2zm0|2zm0]], [[2zm2|2zm2]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NYLB, NYLB' ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=239 FLASP])</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=2zly FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zly OCA], [https://pdbe.org/2zly PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zly RCSB], [https://www.ebi.ac.uk/pdbsum/2zly PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zly ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/6-aminohexanoate-dimer_hydrolase 6-aminohexanoate-dimer hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.46 3.5.1.46] </span></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=2zly FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zly OCA], [http://pdbe.org/2zly PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zly RCSB], [http://www.ebi.ac.uk/pdbsum/2zly PDBsum]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/NYLB2_FLASK NYLB2_FLASK] Involved in nylon oligomer degradation.<ref>PMID:6389532</ref> <ref>PMID:6646204</ref> [https://www.uniprot.org/uniprot/NYLB_FLASK NYLB_FLASK]
 == 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/zl/2zly_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zl/2zly_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 30: / Line 31: @@
 ==See Also==
-*[[6-aminohexanoate-dimer hydrolase|6-aminohexanoate-dimer hydrolase]]
+*[[6-aminohexanoate-dimer hydrolase 3D structures|6-aminohexanoate-dimer hydrolase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: 6-aminohexanoate-dimer hydrolase]]
+[[Category: Flavobacterium sp]]
-[[Category: Flasp]]
+[[Category: Large Structures]]
-[[Category: Higuchi, Y]]
+[[Category: Higuchi Y]]
-[[Category: Kato, D]]
+[[Category: Kato D]]
-[[Category: Kawashima, Y]]
+[[Category: Kawashima Y]]
-[[Category: Negoro, S]]
+[[Category: Negoro S]]
-[[Category: Ohki, T]]
+[[Category: Ohki T]]
-[[Category: Shibata, N]]
+[[Category: Shibata N]]
-[[Category: Takeo, M]]
+[[Category: Takeo M]]
-[[Category: Alpha-beta]]
-[[Category: Hydrolase]]

2zly

From Proteopedia

Current revision

Structure of 6-aminohexanoate-dimer hydrolase, D370Y mutant

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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