This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

2zm9

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Structure of 6-Aminohexanoate-dimer Hydrolase, A61V/S112A/A124V/R187S/F264C/G291R/G338A/D370Y mutant (Hyb-S4M94) with Substrate

Structural highlights

2zm9 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 1.5Å
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/2zm9"

@@ Line 1: / Line 1: @@
 ==Structure of 6-Aminohexanoate-dimer Hydrolase, A61V/S112A/A124V/R187S/F264C/G291R/G338A/D370Y mutant (Hyb-S4M94) with Substrate==
-<StructureSection load='2zm9' size='340' side='right' caption='[[2zm9]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
+<StructureSection load='2zm9' size='340' side='right'caption='[[2zm9]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2zm9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Flask Flask]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZM9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZM9 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2zm9]] 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=2ZM9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZM9 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACA:6-AMINOHEXANOIC+ACID'>ACA</scene>, <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]] 1.5&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1wyb|1wyb]], [[1wyc|1wyc]], [[2dcf|2dcf]], [[2e8i|2e8i]], [[2zm7|2zm7]], [[2zm8|2zm8]], [[2zma|2zma]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACA:6-AMINOHEXANOIC+ACID'>ACA</scene>, <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=261 FLASK])</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=2zm9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zm9 OCA], [https://pdbe.org/2zm9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zm9 RCSB], [https://www.ebi.ac.uk/pdbsum/2zm9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zm9 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=2zm9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zm9 OCA], [http://pdbe.org/2zm9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zm9 RCSB], [http://www.ebi.ac.uk/pdbsum/2zm9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2zm9 ProSAT]</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/zm/2zm9_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zm/2zm9_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 32: / Line 32: @@
 ==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: Flask]]
+[[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]]
-[[Category: Nylon degradation]]

2zm9

From Proteopedia

Current revision

Structure of 6-Aminohexanoate-dimer Hydrolase, A61V/S112A/A124V/R187S/F264C/G291R/G338A/D370Y mutant (Hyb-S4M94) with Substrate

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox