spacer
spacer

PDBsum entry 1q4u

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Hydrolase PDB id
1q4u
Jmol
Contents
Protein chains
140 a.a. *
Ligands
4CA ×2
EDO
Waters ×301
* Residue conservation analysis
PDB id:
1q4u
Name: Hydrolase
Title: Crystal structure of 4-hydroxybenzoyl coa thioesterase from arthrobacter sp. Strain su complexed with 4-hydroxybenzyl c
Structure: Thioesterase. Chain: a, b. Synonym: fcbc2, 4-chlorobenzoate thioesterase. Engineered: yes
Source: Arthrobacter sp.. Organism_taxid: 71255. Strain: su. Gene: fcbc. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PDB file)
Resolution:
1.60Å     R-factor:   0.175     R-free:   0.213
Authors: J.B.Thoden,Z.Zhuang,D.Dunaway-Mariano,H.M.Holden
Key ref:
J.B.Thoden et al. (2003). The structure of 4-hydroxybenzoyl-CoA thioesterase from arthrobacter sp. strain SU. J Biol Chem, 278, 43709-43716. PubMed id: 12907670 DOI: 10.1074/jbc.M308198200
Date:
04-Aug-03     Release date:   23-Sep-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q04416  (4HBT_ARTSP) -  4-hydroxybenzoyl-CoA thioesterase
Seq:
Struc:
151 a.a.
140 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.1.2.23  - 4-hydroxybenzoyl-CoA thioesterase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 4-hydroxybenzoyl-CoA + H2O = 4-hydroxybenzoate + CoA
4-hydroxybenzoyl-CoA
Bound ligand (Het Group name = 4CA)
matches with 98.25% similarity
+ H(2)O
= 4-hydroxybenzoate
+ CoA
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   1 term 
  Biochemical function     hydrolase activity     2 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M308198200 J Biol Chem 278:43709-43716 (2003)
PubMed id: 12907670  
 
 
The structure of 4-hydroxybenzoyl-CoA thioesterase from arthrobacter sp. strain SU.
J.B.Thoden, Z.Zhuang, D.Dunaway-Mariano, H.M.Holden.
 
  ABSTRACT  
 
The 4-chlorobenzoyl-CoA dehalogenation pathway in certain Arthrobacter and Pseudomonas bacterial species contains three enzymes: a ligase, a dehalogenase, and a thioesterase. Here we describe the high resolution x-ray crystallographic structure of the 4-hydroxybenzoyl-CoA thioesterase from Arthrobacter sp. strain SU. The tetrameric enzyme is a dimer of dimers with each subunit adopting the so-called "hot dog fold" composed of six strands of anti-parallel beta-sheet flanked on one side by a rather long alpha-helix. The dimers come together to form the tetramer with their alpha-helices facing outwards. This quaternary structure is in sharp contrast to that previously observed for the 4-hydroxybenzoyl-CoA thioesterase from Pseudomonas species strain CBS-3, whereby the dimers forming the tetramer pack with their alpha-helices projecting toward the interfacial region. In the Arthrobacter thioesterase, each of the four active sites is formed by three of the subunits of the tetramer. On the basis of both structural and kinetic data, it appears that Glu73 is the active site base in the Arthrobacter thioesterase. Remarkably, this residue is located on the opposite side of the substrate-binding pocket compared with that observed for the Pseudomonas enzyme. Although these two bacterial thioesterases demonstrate equivalent catalytic efficiencies, substrate specificities, and metabolic functions, their quaternary structures, CoA-binding sites, and catalytic platforms are decidedly different.
 
  Selected figure(s)  
 
Figure 1.
FIG. 1. Ribbon representation of the Arthrobacter thioesterase monomer. The bound ligands, 4-hydroxybenzoate and CoA, are shown in ball-and-stick representations.
Figure 4.
FIG. 4. Inhibitor binding to the Arthrobacter thioesterase. A superposition of the two inhibitors, 4-hydroxybenzyl-CoA (pink) and 4-hydroxyphenacyl-CoA (blue) onto the bound hydrolysis products, 4-hydroxybenzoate and CoA (gray).
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 43709-43716) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20882276 B.E.Alber (2011).
Biotechnological potential of the ethylmalonyl-CoA pathway.
  Appl Microbiol Biotechnol, 89, 17-25.  
20506386 D.C.Cantu, Y.Chen, and P.J.Reilly (2010).
Thioesterases: a new perspective based on their primary and tertiary structures.
  Protein Sci, 19, 1281-1295.  
20430898 M.V.Dias, F.Huang, D.Y.Chirgadze, M.Tosin, D.Spiteller, E.F.Dry, P.F.Leadlay, J.B.Spencer, and T.L.Blundell (2010).
Structural basis for the activity and substrate specificity of fluoroacetyl-CoA thioesterase FlK.
  J Biol Chem, 285, 22495-22504.
PDB codes: 3kuv 3kuw 3kv7 3kv8 3kvi 3kvu 3kvz 3kw1 3kx7 3kx8
19453107 H.Zhao, B.M.Martin, M.Bisoffi, and D.Dunaway-Mariano (2009).
The Akt C-terminal modulator protein is an acyl-CoA thioesterase of the Hotdog-Fold family.
  Biochemistry, 48, 5507-5509.  
19170545 J.Cao, H.Xu, H.Zhao, W.Gong, and D.Dunaway-Mariano (2009).
The mechanisms of human hotdog-fold thioesterase 2 (hTHEM2) substrate recognition and catalysis illuminated by a structure and function based analysis.
  Biochemistry, 48, 1293-1304.
PDB code: 3f5o
19473548 L.S.Pidugu, K.Maity, K.Ramaswamy, N.Surolia, and K.Suguna (2009).
Analysis of proteins with the 'hot dog' fold: prediction of function and identification of catalytic residues of hypothetical proteins.
  BMC Struct Biol, 9, 37.  
19357082 M.Kotaka, R.Kong, I.Qureshi, Q.S.Ho, H.Sun, C.W.Liew, L.P.Goh, P.Cheung, Y.Mu, J.Lescar, and Z.X.Liang (2009).
Structure and catalytic mechanism of the thioesterase CalE7 in enediyne biosynthesis.
  J Biol Chem, 284, 15739-15749.
PDB code: 2w3x
19622860 T.Hosaka, K.Murayama, M.Kato-Murayama, A.Urushibata, R.Akasaka, T.Terada, M.Shirouzu, S.Kuramitsu, and S.Yokoyama (2009).
Structure of the putative thioesterase protein TTHA1846 from Thermus thermophilus HB8 complexed with coenzyme A and a zinc ion.
  Acta Crystallogr D Biol Crystallogr, 65, 767-776.
PDB code: 2cye
19303060 T.Yokoyama, K.J.Choi, A.M.Bosch, and H.J.Yeo (2009).
Structure and function of a Campylobacter jejuni thioesterase Cj0915, a hexameric hot dog fold enzyme.
  Biochim Biophys Acta, 1794, 1073-1081.
PDB code: 3d6l
19635449 Z.Li, F.Song, Z.Zhuang, D.Dunaway-Mariano, and K.S.Anderson (2009).
Monitoring enzyme catalysis in the multimeric state: direct observation of Arthrobacter 4-hydroxybenzoyl-coenzyme A thioesterase catalytic complexes using time-resolved electrospray ionization mass spectrometry.
  Anal Biochem, 394, 209-216.  
18338382 A.Angelini, L.Cendron, S.Goncalves, G.Zanotti, and L.Terradot (2008).
Structural and enzymatic characterization of HP0496, a YbgC thioesterase from Helicobacter pylori.
  Proteins, 72, 1212-1221.
PDB code: 2pzh
19898606 M.Chruszcz, M.D.Zimmerman, S.Wang, K.D.Koclega, H.Zheng, E.Evdokimova, M.Kudritska, M.Cymborowski, A.Savchenko, A.Edwards, and W.Minor (2008).
Function-biased choice of additives for optimization of protein crystallization - the case of the putative thioesterase PA5185 from Pseudomonas aeruginosa PAO1.
  Cryst Growth Des, 8, 4054-4061.
PDB codes: 2av9 2o5u 2o6b 2o6t 2o6u
18835274 T.Yokoyama, S.Paek, C.P.Ewing, P.Guerry, and H.J.Yeo (2008).
Structure of a sigma28-regulated nonflagellar virulence protein from Campylobacter jejuni.
  J Mol Biol, 384, 364-376.
PDB code: 3bnv
18361456 Y.Li, P.Bahti, N.Shaw, G.Song, S.Chen, X.Zhang, M.Zhang, C.Cheng, J.Yin, J.Y.Zhu, H.Zhang, D.Che, H.Xu, A.Abbas, B.C.Wang, and Z.J.Liu (2008).
Crystal structure of a novel non-Pfam protein AF1514 from Archeoglobus fulgidus DSM 4304 solved by S-SAD using a Cr X-ray source.
  Proteins, 71, 2109-2113.
PDB code: 3c0f
17384944 F.Radice, V.Orlandi, V.Massa, V.Battini, G.Bertoni, W.Reineke, and P.Barbieri (2007).
Cloning of the Arthrobacter sp. FG1 dehalogenase genes and construction of hybrid pathways in Pseudomonas putida strains.
  Appl Microbiol Biotechnol, 75, 1111-1118.  
17524985 F.Wang, R.Langley, G.Gulten, L.Wang, and J.C.Sacchettini (2007).
Identification of a type III thioesterase reveals the function of an operon crucial for Mtb virulence.
  Chem Biol, 14, 543-551.
PDB code: 2pfc
17563367 J.K.Forwood, A.S.Thakur, G.Guncar, M.Marfori, D.Mouradov, W.Meng, J.Robinson, T.Huber, S.Kellie, J.L.Martin, D.A.Hume, and B.Kobe (2007).
Structural basis for recruitment of tandem hotdog domains in acyl-CoA thioesterase 7 and its role in inflammation.
  Proc Natl Acad Sci U S A, 104, 10382-10387.
PDB codes: 2q2b 2v1o
16932747 G.E.Schujman, M.Guerin, A.Buschiazzo, F.Schaeffer, L.I.Llarrull, G.Reh, A.J.Vila, P.M.Alzari, and D.de Mendoza (2006).
Structural basis of lipid biosynthesis regulation in Gram-positive bacteria.
  EMBO J, 25, 4074-4083.
PDB codes: 2f3x 2f41
16763992 K.H.Chin, C.C.Chou, A.H.Wang, and S.H.Chou (2006).
Crystal structure of a putative acyl-CoA thioesterase from Xanthomonas campestris (XC229) adopts a tetrameric hotdog fold of epsilongamma mode.
  Proteins, 64, 823-826.
PDB code: 2fuj
15987908 A.Castell, P.Johansson, T.Unge, T.A.Jones, and K.Bäckbro (2005).
Rv0216, a conserved hypothetical protein from Mycobacterium tuberculosis that is essential for bacterial survival during infection, has a double hotdog fold.
  Protein Sci, 14, 1850-1862.
PDB code: 2bi0
16021630 D.Liger, S.Quevillon-Cheruel, I.Sorel, M.Bremang, K.Blondeau, I.Aboulfath, J.Janin, H.van Tilbeurgh, and N.Leulliot (2005).
Crystal structure of YHI9, the yeast member of the phenazine biosynthesis PhzF enzyme superfamily.
  Proteins, 60, 778-786.
PDB code: 1ym5
15231793 M.A.Warren, L.M.Kucharski, A.Veenstra, L.Shi, P.F.Grulich, and M.E.Maguire (2004).
The CorA Mg2+ transporter is a homotetramer.
  J Bacteriol, 186, 4605-4612.  
15307895 S.C.Dillon, and A.Bateman (2004).
The Hotdog fold: wrapping up a superfamily of thioesterases and dehydratases.
  BMC Bioinformatics, 5, 109.  
14997554 Y.Tajika, N.Sakai, Y.Tanaka, M.Yao, N.Watanabe, and I.Tanaka (2004).
Crystal structure of conserved protein PH1136 from Pyrococcus horikoshii.
  Proteins, 55, 210-213.
PDB code: 1ixl
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.