4K4C | pdb_00004k4c

X-ray crystal structure of E. coli YbdB complexed with phenacyl-CoA

PDB DOI: https://doi.org/10.2210/pdb4K4C/pdb

Classification: HYDROLASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-04-12 Released: 2014-07-30
Deposition Author(s): Ru, W., Farelli, J.D., Dunaway-Mariano, D., Allen, K.N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.207 (Depositor), 0.210 (DCC)
R-Value Work:
0.166 (Depositor), 0.168 (DCC)
R-Value Observed:
0.168 (Depositor)

Starting Model: experimental
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Literature

Structure and Catalysis in the Escherichia coli Hotdog-fold Thioesterase Paralogs YdiI and YbdB.

Wu, R., Latham, J.A., Chen, D., Farelli, J., Zhao, H., Matthews, K., Allen, K.N., Dunaway-Mariano, D.

(2014) Biochemistry 53: 4788-4805

PubMed: 25010423 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/bi500334v
Primary Citation Related Structures:
4K49, 4K4A, 4K4B, 4K4C, 4K4D

PubMed Abstract:
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.

Organizational Affiliation

Department of Chemistry, Boston University , Boston, Massachusetts 02215, United States.

Macromolecule Content

Total Structure Weight: 63.5 kDa
Atom Count: 4,910
Modeled Residue Count: 548
Deposited Residue Count: 548
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proofreading thioesterase EntH	A, B, C, D	137	Escherichia coli K-12	Mutation(s): 0 Gene Names: b0597, entH, JW0589, ybdB EC: 3.1.2
UniProt
Find proteins for P0A8Y8 (Escherichia coli (strain K12)) Explore P0A8Y8 Go to UniProtKB: P0A8Y8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A8Y8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0FQ Query on 0FQ Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth C] mmCIF format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	phenacyl coenzyme A C₂₉ H₄₂ N₇ O₁₇ P₃ S WOEFYXMDPBOUAP-VXAHOBLNSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.207 (Depositor), 0.210 (DCC)
R-Value Work: 0.166 (Depositor), 0.168 (DCC)
R-Value Observed: 0.168 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.47	α = 90
b = 59.175	β = 90.2
c = 85.829	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-07-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-07-30
Type: Initial release
Version 1.1: 2014-08-20
Changes: Database references
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description