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253  structures 2229  species 3  interactions 10916  sequences 71  architectures

Family: Thiolase_C (PF02803)

Summary: Thiolase, C-terminal domain

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This is the Wikipedia entry entitled "Beta-ketoacyl-ACP synthase". More...

Beta-ketoacyl-ACP synthase Edit Wikipedia article

3-oxoacyl-ACP synthase, mitochondrial
Identifiers
Symbol OXSM
Entrez 54995
HUGO 26063
OMIM 610324
RefSeq NM_017897
UniProt Q9NWU1
Other data
EC number 2.3.1.41
Locus Chr. 3 p24.2
Beta-ketoacyl synthase, N-terminal domain
PDB 1oxh EBI.jpg
the crystal structure of beta-ketoacyl-[acyl carrier protein] synthase ii from streptococcus pneumoniae, triclinic form
Identifiers
Symbol ketoacyl-synt
Pfam PF00109
Pfam clan CL0046
InterPro IPR014030
PROSITE PDOC00529
SCOP 1kas
SUPERFAMILY 1kas
Beta-ketoacyl synthase, C-terminal domain
PDB 2ix4 EBI.jpg
arabidopsis thaliana mitochondrial beta-ketoacyl acp synthase hexanoic acid complex
Identifiers
Symbol Ketoacyl-synt_C
Pfam PF02801
Pfam clan CL0046
InterPro IPR014031
PROSITE PDOC00529
SCOP 1kas
SUPERFAMILY 1kas

In molecular biology, Beta-ketoacyl-ACP synthase EC 2.3.1.41, is an enzyme involved in fatty acid synthesis. It results in the formation of acetoacetyl ACP.

FattyAcid-MB-Condensation.png

Beta-ketoacyl-ACP synthase is a highly conserved enzyme that is found in almost all life on earth as a domain in fatty acid synthase (FAS). FAS has two types, aptly named type I and II. Type I is found in animals, fungi, and “lower eukaryotes.” Type II is found in prokaryotes, plastids, and mitochondria.[1] Beta-ketoacyl-ACP synthase III, perhaps the most well known of this family of enzymes, catalyzes a Claisen condensation between acetyl CoA and malonyl ACP. The image below reveals how CoA fits in the active site as a substrate of synthase III.

Proposed active site of beta-ketoacyl-ACP synthase III

Beta-ketoacyl-ACP synthases I and II only catalyze acyl-ACP reactions with malonyl ACP. Synthases I and II are capable of producing long-chain acyl-ACPs. Both are efficient up to acyl-ACPs with a 14 carbon chain, at which point synthase II is the more efficient choice for further carbon additions. Type I FAS catalyzes all the reactions necessary to create palmitic acid, which is a necessary function in animals for metabolic processes, one of which includes the formation of sphingosines.[2]

Beta-ketoacyl-ACP synthase is found as a component of a number of enzymatic systems, including fatty acid synthetase (FAS); the multi-functional 6-methysalicylic acid synthase (MSAS) from Penicillium patulum,[3] which is involved in the biosynthesis of a polyketide antibiotic; polyketide antibiotic synthase enzyme systems; Emericella nidulans multifunctional protein Wa, which is involved in the biosynthesis of conidial green pigment; Rhizobium nodulation protein nodE, which probably acts as a beta-ketoacyl synthase in the synthesis of the nodulation Nod factor fatty acyl chain; and yeast mitochondrial protein CEM1.

Structure

Beta-ketoacyl synthase contains two protein domains. The active site is located between the N- and C-terminal domains. The N-terminal domain contains most of the structures involved in dimer formation and also the active site cysteine. Residues from both domains contribute to substrate binding and catalysis[4]

In animals and in prokaryotes, beta-ketoacyl-ACP synthase is a domain on type I FAS, which is a large enzyme complex that has multiple domains to catalyze multiple different reactions. Analogously, beta-ketoacyl-ACP synthase in plants is found in type II FAS; note that synthases in plants have been documented to have a range of substrate specificities.[2] The presence of similar ketoacyl synthases present in all living organisms point to a common ancestor.[5] Further examination of beta-ketoacyl-ACP synthases I and II of E. coli revealed that both are homodimeric, but synthase II is slightly larger. However, even though they are both involved in fatty acid metabolism, they also have highly divergent primary structure.[6] In synthase II, each subunit consists of a five-stranded beta pleated sheet surrounded by multiple alpha helices, shown in the image below.

1EBL dimer

The active sites are relatively close, only about 25 angstroms apart, and consist of a mostly hydrophobic pocket.[4] Certain experiments have also suggested the presence of “fatty acid transport tunnels” within the beta-ketoacyl-ACP synthase domain that lead to one of many “fatty acid cavities”, which essentially acts as the active site.[7]

Mechanism

Beta-ketoacyl-synthase’s mechanism is a topic of debate among chemists. Many agree that Cys171 of the active site attacks acetyl ACP's carbonyl, and, like most enzymes, stabilizes the intermediate with other residues in the active site. ACP is subsequently eliminated, and it deprotonates His311 in the process. A thioester is then regenerated with the cysteine in the active site. Decarboxylation of a malonyl CoA that is also in the active site initially creates an enolate, which is stabilized by His311 and His345. The enolate tautomerizes to a carbanion that attacks the thioester of the acetyl-enzyme complex.[8] Some sources speculate that an activated water molecule also resides in the active site as a means of hydrating the CO2oreleasedr of attacking C3 of malonyl CoA. Another proposed mechanism considers the creation of a tetrahedral transition state.[2] The driving force of the reaction comes from the decarboxylation of malonyl ACP; the energy captured in that bond technically comes from ATP, which is what is initially used to carboxylate acetyl CoA to malonyl CoA.[9]

Beta ketoacyl synthase mechanism

Biological function

The main function of beta-ketoacyl-ACP synthase is to produce fatty acids of various lengths for use by the organism. These uses include energy storage and creation of cell membranes. Fatty acids can also be used to synthesize prostaglandins, phospholipids, and vitamins, among many other things. Further, palmitic acid, which is created by the beta-ketoacyl-synthases on type I FAS, is used in a number of biological capacities. It is a precursor of both stearic and palmitoleic acids. Palmitoleic can subsequently be used to create a number of other fatty acids.[10] Palmitic acid is also used to synthesize sphingosines, which play a role in cell membranes.[2]

Clinical significance

The different types of beta-ketoacyl-ACP synthases in type II FAS are called FabB, FabF, and FabH synthases. FabH catalyzes the quintessential ketoacyl synthase reaction with malonyl ACP and acetyl CoA. FabB and FabF catalyze other related reactions. Given that their function is necessary for proper biological function surrounding lipoprotein, phospholipid, and lipopolysaccharide synthesis, they have become a target in antibacterial drug creation. Bacteria has the ability to adapt to its environment; bacteria can alter the phospholipid composition of its membrane to best suit the environment, so inhibiting this pathway is integral in disrupting bacterial proliferation.[11] By studying Yersinia pestis, which causes bubonic, pneumonic, and septicaemic plagues, researchers have shown that FabB, FabF, and FabH can theoretically all be inhibited by the same drug due to similarities in their binding sites. However, such a drug has not yet been developed.[12] Cerulenin, a molecule that appears to inhibit by mimicking the “condensation transition state” can only inhibit B or F, but not H. Another molecule, thiolactomycin, which mimics malonyl ACP in the active site, can ony inhibit FabB.[13] Lastly, platensimycin also has possible antibiotic use due to its inhibition of FabF.[14]

These types of drugs are highly relevant. For example, Y. pestis was the main agent in the Justinian Plague, Black Death, and the modern plague. Even within the last five years, China, Peru, and Madagascar all experienced an outbreak of infection by Y. pestis. If it is not treated within 24 hours, it normally results in death. Furthermore, there is worry that it can now be used as a possible biological warfare weapon.[12]

Unfortunately, many drugs that target prokaryotic beta-ketoacyl-synthases carry many side effects. Given the similarities between prokaryotic ketoacyl synthases and mitochondrial ones, these types of drugs tend to unintentionally also act upon mitochondrial synthases, leading to many biological consequences for humans.[1]

Industrial applications

Recent efforts in bioengineering include engineering of FAS proteins, which includes beta-ketoacyl-ACP synthase domains, in order to favor the synthesis of branched carbon chains as a renewable energy source. Branched carbon chains contain more energy and can be used in colder temperatures because of their lower freezing point. Using E. coli as the organism of choice, engineers have replaced the endogenous FabH domain on FAS, which favors unbranched chains, with FabH versions that favor branching due to their high substrate specificity for branched acyl-ACPs.[15]

See also

References

  1. ^ a b Christensen, Caspar Elo; Kragelund, Birthe B.; von Wettstein-Knowles, Penny; Henriksen, Anette (2007-02-01). "Structure of the human β-ketoacyl [ACP] synthase from the mitochondrial type II fatty acid synthase". Protein Science : A Publication of the Protein Society 16 (2): 261–272. doi:10.1110/ps.062473707. ISSN 0961-8368. PMC 2203288. PMID 17242430. 
  2. ^ a b c d Witkowski, Andrzej; Joshi, Anil K.; Smith, Stuart. "Mechanism of the β-Ketoacyl Synthase Reaction Catalyzed by the Animal Fatty Acid Synthase †". Biochemistry 41 (35): 10877–10887. doi:10.1021/bi0259047. 
  3. ^ Beck J, Ripka S, Siegner A, Schiltz E, Schweizer E (Sep 1990). "The multifunctional 6-methylsalicylic acid synthase gene of Penicillium patulum. Its gene structure relative to that of other polyketide synthases". European Journal of Biochemistry / FEBS 192 (2): 487–98. doi:10.1111/j.1432-1033.1990.tb19252.x. PMID 2209605. 
  4. ^ a b Huang W, Jia J, Edwards P, Dehesh K, Schneider G, Lindqvist Y (Mar 1998). "Crystal structure of beta-ketoacyl-acyl carrier protein synthase II from E.coli reveals the molecular architecture of condensing enzymes". The EMBO Journal 17 (5): 1183–91. doi:10.1093/emboj/17.5.1183. PMC 1170466. PMID 9482715. 
  5. ^ Beld, Joris; Blatti, Jillian L.; Behnke, Craig; Mendez, Michael; Burkart, Michael D. (2014-08-01). "Evolution of acyl-ACP-thioesterases and β-ketoacyl-ACP-synthases revealed by protein-protein interactions". Journal of applied phycology 26 (4): 1619–1629. doi:10.1007/s10811-013-0203-4. ISSN 0921-8971. PMC 4125210. PMID 25110394. 
  6. ^ Garwin, J. L.; Klages, A. L.; Cronan, J. E. (1980-12-25). "Structural, enzymatic, and genetic studies of beta-ketoacyl-acyl carrier protein synthases I and II of Escherichia coli.". Journal of Biological Chemistry 255 (24): 11949–11956. ISSN 0021-9258. PMID 7002930. 
  7. ^ Cui, Wei; Liang, Yan; Tian, Weixi; Ji, Mingjuan; Ma, Xiaofeng (2016-03-01). "Regulating effect of β-ketoacyl synthase domain of fatty acid synthase on fatty acyl chain length in de novo fatty acid synthesis". Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids 1861 (3): 149–155. doi:10.1016/j.bbalip.2015.12.002. 
  8. ^ Lee, Wook; Engels, Bernd. "The Protonation State of Catalytic Residues in the Resting State of KasA Revisited: Detailed Mechanism for the Activation of KasA by Its Own Substrate". Biochemistry 53 (5): 919–931. doi:10.1021/bi401308j. 
  9. ^ Tymoczko, John; Berg; Stryer (2013). Biochemistry A Short Course. United States of America: W.H. Freeman and Company. ISBN 1-4292-8360-2. 
  10. ^ "Palmitic acid, a saturated fatty acid, in Cell Culture". Sigma-Aldrich. Retrieved 2016-02-29. 
  11. ^ Zhang, Yong-Mei; Rock, Charles O. (2008-03-01). "Membrane lipid homeostasis in bacteria". Nature Reviews Microbiology 6 (3): 222–233. doi:10.1038/nrmicro1839. ISSN 1740-1526. 
  12. ^ a b Nanson, Jeffrey D.; Himiari, Zainab; Swarbrick, Crystall M. D.; Forwood, Jade K. (2015-10-15). "Structural Characterisation of the Beta-Ketoacyl-Acyl Carrier Protein Synthases, FabF and FabH, of Yersinia pestis". Scientific Reports 5. doi:10.1038/srep14797. PMC 4606726. PMID 26469877. 
  13. ^ Price, Allen C.; Choi, Keum-Hwa; Heath, Richard J.; Li, Zhenmei; White, Stephen W.; Rock, Charles O. (2001-03-02). "Inhibition of β-Ketoacyl-Acyl Carrier Protein Synthases by Thiolactomycin and Cerulenin STRUCTURE AND MECHANISM". Journal of Biological Chemistry 276 (9): 6551–6559. doi:10.1074/jbc.M007101200. ISSN 0021-9258. PMID 11050088. 
  14. ^ Wright, H Tonie; Reynolds, Kevin A (2007-10-01). "Antibacterial targets in fatty acid biosynthesis". Current Opinion in Microbiology. Antimicrobials/Genomics 10 (5): 447–453. doi:10.1016/j.mib.2007.07.001. PMC 2271077. PMID 17707686. 
  15. ^ Jiang, Wen; Jiang, Yanfang; Bentley, Gayle J.; Liu, Di; Xiao, Yi; Zhang, Fuzhong (2015-08-01). "Enhanced production of branched-chain fatty acids by replacing β-ketoacyl-(acyl-carrier-protein) synthase III (FabH)". Biotechnology and Bioengineering 112 (8): 1613–1622. doi:10.1002/bit.25583. ISSN 1097-0290. 

External links

Further reading

  • Jiang W, Jiang Y, Bentley GJ, Liu D, Xiao Y, Zhang F (Aug 2015). "Enhanced production of branched-chain fatty acids by replacing β-ketoacyl-(acyl-carrier-protein) synthase III (FabH)". Biotechnology and Bioengineering 112 (8): 1613–22. doi:10.1002/bit.25583. PMID 25788017. 
  • Witkowski A, Joshi AK, Smith S (Sep 2002). "Mechanism of the beta-ketoacyl synthase reaction catalyzed by the animal fatty acid synthase". Biochemistry 41 (35): 10877–87. doi:10.1021/bi0259047. PMID 12196027. 
  • Christensen CE, Kragelund BB, von Wettstein-Knowles P, Henriksen A (Feb 2007). "Structure of the human beta-ketoacyl [ACP] synthase from the mitochondrial type II fatty acid synthase". Protein Science 16 (2): 261–72. doi:10.1110/ps.062473707. PMID 17242430. 
  • Lee W, Engels B (Feb 2014). "The protonation state of catalytic residues in the resting state of KasA revisited: detailed mechanism for the activation of KasA by its own substrate". Biochemistry 53 (5): 919–31. doi:10.1021/bi401308j. PMID 24479625. 

This article incorporates text from the public domain Pfam and InterPro IPR014030 This article incorporates text from the public domain Pfam and InterPro IPR014031

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Thiolase, C-terminal domain Provide feedback

Thiolase is reported to be structurally related to beta-ketoacyl synthase (PF00109), and also chalcone synthase.

Literature references

  1. Mathieu M, Modis Y, Zeelen JP, Engel CK, Abagyan RA, Ahlberg A, Rasmussen B, Lamzin VS, Kunau WH, Wierenga RK; , J Mol Biol 1997;273:714-728.: The 1.8 A crystal structure of the dimeric peroxisomal 3-ketoacyl-CoA thiolase of Saccharomyces cerevisiae: implications for substrate binding and reaction mechanism. PUBMED:9402066 EPMC:9402066


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR020617

Two different types of thiolase [PUBMED:1755959, PUBMED:2191949, PUBMED:1354266] are found both in eukaryotes and in prokaryotes: acetoacetyl-CoA thiolase (EC) and 3-ketoacyl-CoA thiolase (EC). 3-ketoacyl-CoA thiolase (also called thiolase I) has a broad chain-length specificity for its substrates and is involved in degradative pathways such as fatty acid beta-oxidation. Acetoacetyl-CoA thiolase (also called thiolase II) is specific for the thiolysis of acetoacetyl-CoA and involved in biosynthetic pathways such as poly beta-hydroxybutyrate synthesis or steroid biogenesis.

In eukaryotes, there are two forms of 3-ketoacyl-CoA thiolase: one located in the mitochondrion and the other in peroxisomes.

There are two conserved cysteine residues important for thiolase activity. The first located in the N-terminal section of the enzymes is involved in the formation of an acyl-enzyme intermediate; the second located at the C-terminal extremity is the active site base involved in deprotonation in the condensation reaction.

Mammalian nonspecific lipid-transfer protein (nsL-TP) (also known as sterol carrier protein 2) is a protein which seems to exist in two different forms: a 14 Kd protein (SCP-2) and a larger 58 Kd protein (SCP-x). The former is found in the cytoplasm or the mitochondria and is involved in lipid transport; the latter is found in peroxisomes. The C-terminal part of SCP-x is identical to SCP-2 while the N-terminal portion is evolutionary related to thiolases [PUBMED:1755959].

Gene Ontology

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Domain organisation

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Pfam Clan

This family is a member of clan Thiolase (CL0046), which has the following description:

Thiolases are ubiquitous and form a large superfamily. Thiolases can function either degradatively, in the beta-oxidation pathway of fatty acids, or biosynthetically. Biosynthetic thiolases catalyse the formation of acetoacetyl-CoA from two molecules of acetyl-CoA . This is one of the fundamental categories of carbon skeletal assembly patterns in biological systems and is the first step in a wide range of biosynthetic pathways [1]. Thiolase are usually dimeric or tetrameric enzymes. Within each monomer there are two similar domains related by pseudo dyad. The N-terminal of these two domains contains a large insertion of about 100 amino acids.

The clan contains the following 13 members:

ACP_syn_III ACP_syn_III_C Chal_sti_synt_C Chal_sti_synt_N FAE1_CUT1_RppA HMG_CoA_synt_C HMG_CoA_synt_N ketoacyl-synt Ketoacyl-synt_2 Ketoacyl-synt_C SpoVAD Thiolase_C Thiolase_N

Alignments

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  Seed
(21)
Full
(10916)
Representative proteomes UniProt
(45414)
NCBI
(67025)
Meta
(4432)
RP15
(2329)
RP35
(7223)
RP55
(13984)
RP75
(22772)
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  Seed
(21)
Full
(10916)
Representative proteomes UniProt
(45414)
NCBI
(67025)
Meta
(4432)
RP15
(2329)
RP35
(7223)
RP55
(13984)
RP75
(22772)
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  Seed
(21)
Full
(10916)
Representative proteomes UniProt
(45414)
NCBI
(67025)
Meta
(4432)
RP15
(2329)
RP35
(7223)
RP55
(13984)
RP75
(22772)
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Curation and family details

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Seed source: Prosite
Previous IDs: thiolase_C;
Type: Domain
Author: Sonnhammer ELL, Griffiths-Jones SR
Number in seed: 21
Number in full: 10916
Average length of the domain: 124.70 aa
Average identity of full alignment: 37 %
Average coverage of the sequence by the domain: 30.93 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.6 20.6
Trusted cut-off 20.6 20.6
Noise cut-off 20.5 20.5
Model length: 123
Family (HMM) version: 16
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Species distribution

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Interactions

There are 3 interactions for this family. More...

Thiolase_N ECH_1 Thiolase_N

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Thiolase_C domain has been found. There are 253 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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