3F5O | pdb_00003f5o

Crystal Structure of hTHEM2(undecan-2-one-CoA) complex

PDB DOI: https://doi.org/10.2210/pdb3F5O/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-11-04 Released: 2009-08-18
Deposition Author(s): Xu, H., Gong, W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.237 (Depositor), 0.236 (DCC)
R-Value Work:
0.199 (Depositor), 0.197 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

The mechanisms of human hotdog-fold thioesterase 2 (hTHEM2) substrate recognition and catalysis illuminated by a structure and function based analysis

Cao, J., Xu, H., Zhao, H., Gong, W., Dunaway-Mariano, D.

(2009) Biochemistry 48: 1293-1304

PubMed: 19170545 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/bi801879z
Primary Citation Related Structures:
3F5O

PubMed Abstract:
The focus of this paper is the hotdog-fold thioesterase THEM2 from human (hTHEM2; Swiss-Prot entry Q9NPJ3 ). In an earlier communication (Cheng, Z., Song, F., Shan, X., Wei, Z., Wang, Y., Dunaway-Mariano, D., and Gong, W. (2006) Crystal structure of human thioesterase superfamily member 2, Biochem. Biophys. Res. Commun. 349, 172-177) we reported the apo crystal structure of hTHEM2. Herein, we report the results of an extensive hTHEM2 substrate screen, the structure determination of hTHEM2 complexed with the inert substrate analogue undecan-2-one-CoA (in which OC-CH(2)-S substitutes for OC-S) and the kinetic analysis of active site mutants. The work described in this paper represents the first reported structure-function based analysis of a human hotdog-fold thioesterase. The catalytic mechanism proposed involves the Asp65/Ser83 assisted attack of a water molecule at the Gly57/Asn50 polarized thioester CO and the Asn50 assisted departure of the thiolate leaving group. Thioesterase activity was observed with acyl-CoAs but not with the human acyl-ACP or with an acyl-Cys peptide. The medium-to-long-chain fatty acyl-CoAs displayed the smallest K(m) values. The substrate specificity profile was analyzed within the context of the liganded enzyme to define the structural determinants of substrate recognition. Based on the results of this structure-function analysis we hypothesize that the physiological role of hTHEM2 involves catalysis of the hydrolysis of cytosolic medium-to-long-chain acyl-CoA thioesters.

Organizational Affiliation

Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, USA.

Macromolecule Content

Total Structure Weight: 137.3 kDa
Atom Count: 9,600
Modeled Residue Count: 1,098
Deposited Residue Count: 1,184
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioesterase superfamily member 2	A, B, C, D, E A, B, C, D, E, F, G, H	148	Homo sapiens	Mutation(s): 0 EC: 3.1.2.2 (UniProt), 3.1.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NPJ3 (Homo sapiens) Explore Q9NPJ3 Go to UniProtKB: Q9NPJ3
PHAROS: Q9NPJ3 GTEx: ENSG00000112304
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NPJ3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COA Query on COA Download:Ideal Coordinates CCD File SDF format, chain X [auth E] SDF format, chain U [auth D] SDF format, chain Q [auth C] SDF format, chain M [auth B] SDF format, chain K [auth A] SDF format, chain IA [auth H] SDF format, chain EA [auth G] SDF format, chain BA [auth F] MOL2 format, chain X [auth E] MOL2 format, chain U [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain M [auth B] MOL2 format, chain K [auth A] MOL2 format, chain IA [auth H] MOL2 format, chain EA [auth G] MOL2 format, chain BA [auth F] mmCIF format, chain X [auth E] mmCIF format, chain U [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain M [auth B] mmCIF format, chain K [auth A] mmCIF format, chain IA [auth H] mmCIF format, chain EA [auth G] mmCIF format, chain BA [auth F]	BA [auth F] EA [auth G] IA [auth H] K [auth A] M [auth B] BA [auth F], EA [auth G], IA [auth H], K [auth A], M [auth B], Q [auth C], U [auth D], X [auth E]	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Interactions Focus chain BA [auth F] Focus chain EA [auth G] Focus chain IA [auth H] Focus chain K [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain U [auth D] Focus chain X [auth E] Interactions & Density Focus chain BA [auth F] Focus chain EA [auth G] Focus chain IA [auth H] Focus chain K [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain U [auth D] Focus chain X [auth E]
P6G Query on P6G Download:Ideal Coordinates CCD File SDF format, chain Y [auth E] SDF format, chain R [auth C] SDF format, chain N [auth B] SDF format, chain FA [auth G] MOL2 format, chain Y [auth E] MOL2 format, chain R [auth C] MOL2 format, chain N [auth B] MOL2 format, chain FA [auth G] mmCIF format, chain Y [auth E] mmCIF format, chain R [auth C] mmCIF format, chain N [auth B] mmCIF format, chain FA [auth G]	FA [auth G], N [auth B], R [auth C], Y [auth E]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain FA [auth G] Focus chain N [auth B] Focus chain R [auth C] Focus chain Y [auth E] Interactions & Density Focus chain FA [auth G] Focus chain N [auth B] Focus chain R [auth C] Focus chain Y [auth E]
UOC Query on UOC Download:Ideal Coordinates CCD File SDF format, chain W [auth E] SDF format, chain T [auth D] SDF format, chain P [auth C] SDF format, chain L [auth B] SDF format, chain J [auth A] SDF format, chain HA [auth H] SDF format, chain DA [auth G] SDF format, chain AA [auth F] MOL2 format, chain W [auth E] MOL2 format, chain T [auth D] MOL2 format, chain P [auth C] MOL2 format, chain L [auth B] MOL2 format, chain J [auth A] MOL2 format, chain HA [auth H] MOL2 format, chain DA [auth G] MOL2 format, chain AA [auth F] mmCIF format, chain W [auth E] mmCIF format, chain T [auth D] mmCIF format, chain P [auth C] mmCIF format, chain L [auth B] mmCIF format, chain J [auth A] mmCIF format, chain HA [auth H] mmCIF format, chain DA [auth G] mmCIF format, chain AA [auth F]	AA [auth F] DA [auth G] HA [auth H] J [auth A] L [auth B] AA [auth F], DA [auth G], HA [auth H], J [auth A], L [auth B], P [auth C], T [auth D], W [auth E]	undecan-2-one C₁₁ H₂₂ O KYWIYKKSMDLRDC-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain DA [auth G] Focus chain HA [auth H] Focus chain J [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain T [auth D] Focus chain W [auth E] Interactions & Density Focus chain AA [auth F] Focus chain DA [auth G] Focus chain HA [auth H] Focus chain J [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain T [auth D] Focus chain W [auth E]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain Z [auth F] SDF format, chain V [auth E] SDF format, chain S [auth D] SDF format, chain O [auth C] SDF format, chain I [auth A] SDF format, chain GA [auth H] SDF format, chain CA [auth G] MOL2 format, chain Z [auth F] MOL2 format, chain V [auth E] MOL2 format, chain S [auth D] MOL2 format, chain O [auth C] MOL2 format, chain I [auth A] MOL2 format, chain GA [auth H] MOL2 format, chain CA [auth G] mmCIF format, chain Z [auth F] mmCIF format, chain V [auth E] mmCIF format, chain S [auth D] mmCIF format, chain O [auth C] mmCIF format, chain I [auth A] mmCIF format, chain GA [auth H] mmCIF format, chain CA [auth G]	CA [auth G] GA [auth H] I [auth A] O [auth C] S [auth D] CA [auth G], GA [auth H], I [auth A], O [auth C], S [auth D], V [auth E], Z [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain CA [auth G] Focus chain GA [auth H] Focus chain I [auth A] Focus chain O [auth C] Focus chain S [auth D] Focus chain V [auth E] Focus chain Z [auth F] Interactions & Density Focus chain CA [auth G] Focus chain GA [auth H] Focus chain I [auth A] Focus chain O [auth C] Focus chain S [auth D] Focus chain V [auth E] Focus chain Z [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.237 (Depositor), 0.236 (DCC)
R-Value Work: 0.199 (Depositor), 0.197 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.032	α = 90
b = 110.632	β = 90
c = 119.819	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-08-18

Deposition Author(s):

Xu, H.

Gong, W.

Revision History (Full details and data files)

Version 1.0: 2009-08-18
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description

3F5O | pdb_00003f5o

Crystal Structure of hTHEM2(undecan-2-one-CoA) complex

Literature

The mechanisms of human hotdog-fold thioesterase 2 (hTHEM2) substrate recognition and catalysis illuminated by a structure and function based analysis

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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