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.

4k49

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

X-ray crystal structure of E. coli YdiI complexed with 2,4-dihydroxyphenacyl CoA

Structural highlights

4k49 is a 4 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.89Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

MENI_ECOLI Catalyzes the hydrolysis of 1,4-dihydroxy-2-naphthoyl-CoA (DHNA-CoA) to 1,4-dihydroxy-2-naphthoate (DHNA). Also shows significant activity toward a wide range of acyl-CoA thioesters, and minimal activity toward benzoyl-holoEntB.^[1] ^[2] ^[3]

Publication Abstract from PubMed

Herein, the structural determinants for substrate recognition and catalysis in two hotdog-fold thioesterase paralogs, YbdB and YdiI from Escherichia coli, are identified and analyzed to provide insight into the evolution of biological function in the hotdog-fold enzyme superfamily. The X-ray crystal structures of YbdB and YdiI, in complex with inert substrate analogs, determined in this study revealed the locations of the respective thioester substrate binding sites and the identity of the residues positioned for substrate binding and catalysis. The importance of each of these residues was assessed through amino acid replacements followed by steady-state kinetic analyses of the corresponding site-directed mutants. Transient kinetic and solvent (18)O-labeling studies were then carried out to provide insight into the role of Glu63 posited to function as the nucleophile or general base in catalysis. Finally, the structure-function-mechanism profiles of the two paralogs, along with that of a more distant homolog, were compared to identify conserved elements of substrate recognition and catalysis, which define the core traits of the hotdog-fold thioesterase family, as well as structural features that are unique to each thioesterase. Founded on the insight gained from this analysis, we conclude that the promiscuity revealed by in vitro substrate activity determinations, and posited to facilitate the evolution of new biological function, is the product of intrinsic plasticity in substrate binding as well as in the catalytic mechanism.

Structure and Catalysis in the Escherichia coli Hotdog-fold Thioesterase Paralogs YdiI and YbdB.,Wu R, Latham JA, Chen D, Farelli J, Zhao H, Matthews K, Allen KN, Dunaway-Mariano D Biochemistry. 2014 Jul 29;53(29):4788-805. doi: 10.1021/bi500334v. Epub 2014 Jul , 18. PMID:25010423^[4]

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

References

↑ Kuznetsova E, Proudfoot M, Sanders SA, Reinking J, Savchenko A, Arrowsmith CH, Edwards AM, Yakunin AF. Enzyme genomics: Application of general enzymatic screens to discover new enzymes. FEMS Microbiol Rev. 2005 Apr;29(2):263-79. PMID:15808744 doi:S0168-6445(05)00004-5
↑ Chen M, Ma X, Chen X, Jiang M, Song H, Guo Z. Identification of a hotdog fold thioesterase involved in the biosynthesis of menaquinone in Escherichia coli. J Bacteriol. 2013 Jun;195(12):2768-75. doi: 10.1128/JB.00141-13. Epub 2013 Apr 5. PMID:23564174 doi:http://dx.doi.org/10.1128/JB.00141-13
↑ Latham JA, Chen D, Allen KN, Dunaway-Mariano D. Divergence of substrate specificity and function in the Escherichia coli hotdog-fold thioesterase paralogs YdiI and YbdB. Biochemistry. 2014 Jul 29;53(29):4775-87. doi: 10.1021/bi500333m. Epub 2014 Jul , 18. PMID:24992697 doi:http://dx.doi.org/10.1021/bi500333m
↑ Wu R, Latham JA, Chen D, Farelli J, Zhao H, Matthews K, Allen KN, Dunaway-Mariano D. Structure and Catalysis in the Escherichia coli Hotdog-fold Thioesterase Paralogs YdiI and YbdB. Biochemistry. 2014 Jul 29;53(29):4788-805. doi: 10.1021/bi500334v. Epub 2014 Jul , 18. PMID:25010423 doi:http://dx.doi.org/10.1021/bi500334v

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4k49"

@@ Line 1: / Line 1: @@
 ==X-ray crystal structure of E. coli YdiI complexed with 2,4-dihydroxyphenacyl CoA==
-<StructureSection load='4k49' size='340' side='right' caption='[[4k49]], [[Resolution|resolution]] 1.89&Aring;' scene=''>
+<StructureSection load='4k49' size='340' side='right'caption='[[4k49]], [[Resolution|resolution]] 1.89&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4k49]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4K49 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4K49 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4k49]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4K49 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4K49 FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HFQ:2,4-DIHYDROXYPHENACYL+COENZYME+A'>HFQ</scene><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]] 1.89&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1sbk|1sbk]], [[4k4a|4k4a]], [[4k4b|4k4b]], [[4k4c|4k4c]], [[4k4d|4k4d]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HFQ:2,4-DIHYDROXYPHENACYL+COENZYME+A'>HFQ</scene></td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4k49 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k49 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4k49 RCSB], [http://www.ebi.ac.uk/pdbsum/4k49 PDBsum]</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=4k49 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4k49 OCA], [https://pdbe.org/4k49 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4k49 RCSB], [https://www.ebi.ac.uk/pdbsum/4k49 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4k49 ProSAT]</span></td></tr>
-<table>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/MENI_ECOLI MENI_ECOLI] Catalyzes the hydrolysis of 1,4-dihydroxy-2-naphthoyl-CoA (DHNA-CoA) to 1,4-dihydroxy-2-naphthoate (DHNA). Also shows significant activity toward a wide range of acyl-CoA thioesters, and minimal activity toward benzoyl-holoEntB.<ref>PMID:15808744</ref> <ref>PMID:23564174</ref> <ref>PMID:24992697</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 15: / Line 18: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 4k49" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Allen, K N.]]
+[[Category: Escherichia coli K-12]]
-[[Category: Dunaway-Mariano, D.]]
+[[Category: Large Structures]]
-[[Category: Farelli, J D.]]
+[[Category: Allen KN]]
-[[Category: Ru, W.]]
+[[Category: Dunaway-Mariano D]]
-[[Category: Hot-dog fold]]
+[[Category: Farelli JD]]
-[[Category: Hydrolase]]
+[[Category: Ru W]]
-[[Category: Thioesterase]]

4k49

From Proteopedia

Current revision

X-ray crystal structure of E. coli YdiI complexed with 2,4-dihydroxyphenacyl CoA

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox