Summary: Beta-ketoacyl synthase, C-terminal domain

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

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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
Locus	Chr. 3 p24.2

Beta-ketoacyl synthase, N-terminal domain

the crystal structure of beta-ketoacyl-[acyl carrier protein] synthase ii from streptococcus pneumoniae, triclinic form

Identifiers

Symbol

ketoacyl-synt

Pfam clan

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe; PDBj
PDBsum	structure summary

Beta-ketoacyl synthase, C-terminal domain

arabidopsis thaliana mitochondrial beta-ketoacyl acp synthase hexanoic acid complex

Identifiers

Symbol

Ketoacyl-synt_C

Pfam clan

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe; PDBj
PDBsum	structure summary

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.

It is the enzyme that catalyses the condensation of malonyl-ACP with the growing fatty acid chain.^[1] It is found as a component of a number of enzymatic systems, including fatty acid synthetase (FAS), which catalyses the formation of long-chain fatty acids from acetyl-CoA, malonyl-CoA and NADPH; the multi-functional 6-methysalicylic acid synthase (MSAS) from Penicillium patulum,^[2] 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. The condensation reaction is a two step process, first the acyl component of an activated acyl primer is transferred to a cysteine residue of the enzyme and is then condensed with an activated malonyl donor with the concomitant release of carbon dioxide.

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^[3]

External links

beta Ketoacyl ACP Synthase at the US National Library of Medicine Medical Subject Headings (MeSH)

References

^ Kauppinen S, Siggaard-Andersen M, von Wettstein-Knowles P (1988). "beta-Ketoacyl-ACP synthase I of Escherichia coli: nucleotide sequence of the fabB gene and identification of the cerulenin binding residue". Carlsberg Res. Commun. 53 (6): 357–70. doi:10.1007/bf02983311. PMID 3076376.
^ Beck J, Ripka S, Siegner A, Schiltz E, Schweizer E (September 1990). "The multifunctional 6-methylsalicylic acid synthase gene of Penicillium patulum. Its gene structure relative to that of other polyketide synthases". Eur. J. Biochem. 192 (2): 487–98. doi:10.1111/j.1432-1033.1990.tb19252.x. PMID 2209605.
^ Huang W, Jia J, Edwards P, Dehesh K, Schneider G, Lindqvist Y (1998). "Crystal structure of beta-ketoacyl-acyl carrier protein synthase II from E.coli reveals the molecular architecture of condensing enzymes.". EMBO J 17 (5): 1183–91. doi:10.1093/emboj/17.5.1183. PMC 1170466. PMID 9482715.

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

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

Transferases: acyltransferases (EC 2.3)

2.3.1: other than amino-acyl groups

2.3.2: Aminoacyltransferases

2.3.3: converted into alkyl on transfer

B
enzm
1.1
- 2
- 3
- 4
- 5
- 6
- 7
- 8
- 10
- 11
- 13
- 14
- 15-18
2.1
- 2
- 3
- 4
- 5
- 6
- 7
  - 2.7.10
  - 11-12
- 8
3.1
- - 3.1.3.48
- 2
- 3
- 4
  - 3.4.21
  - 22
  - 23
  - 24
- 5
- 6
- 7
4.1
- 2
- 3
- 4
- 5
- 6
5.1
- 2
- 3
- 4
- 99
6.1-3
- 4
- 5-6

Metabolism: lipid metabolism / fatty acid metabolism, triglyceride and fatty acid enzymes

Synthesis

Malonyl-CoA synthesis	ATP citrate lyase Acetyl-CoA carboxylase

Fatty acid synthesis/ Fatty acid synthase	Beta-ketoacyl-ACP synthase Β-Ketoacyl ACP reductase 3-Hydroxyacyl ACP dehydrase Enoyl ACP reductase

Fatty acid desaturases	Stearoyl-CoA desaturase-1

Triacyl glycerol	Glycerol-3-phosphate dehydrogenase Thiokinase

Degradation

Acyl transport

Beta oxidation

General	Acyl CoA dehydrogenase (ACADL ACADM ACADS ACADVL ACADSB) Enoyl-CoA hydratase MTP: HADH HADHA HADHB Acetyl-CoA C-acyltransferase

Unsaturated	Enoyl CoA isomerase 2,4 Dienoyl-CoA reductase

Odd chain	Propionyl-CoA carboxylase

Other	Hydroxyacyl-Coenzyme A dehydrogenase

To acetyl-CoA

Malonyl-CoA decarboxylase

Aldehydes

Long-chain-aldehyde dehydrogenase

M: MET

mt, k, c/g/r/p/y/i, f/h/s/l/o/e, a/u, n, m

k, cgrp/y/i, f/h/s/l/o/e, au, n, m, epon

m (A16/C10), i (k, c/g/r/p/y/i, f/h/s/o/e, a/u, n, m)

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Beta-ketoacyl synthase, C-terminal domain Provide feedback

The structure of beta-ketoacyl synthase is similar to that of the thiolase family (PF00108) and also chalcone synthase. The active site of beta-ketoacyl synthase is located between the N and C-terminal domains.

Literature references

Huang W, Jia J, Edwards P, Dehesh K, Schneider G, Lindqvist Y; , EMBO J 1998;17:1183-1191.: Crystal structure of beta-ketoacyl-acyl carrier protein synthase II from E.coli reveals the molecular architecture of condensing enzymes. PUBMED:9482715 EPMC:9482715

Internal database links

Similarity to PfamA using HHSearch:

Thiolase_C

External database links

PANDIT:	PF02801
PROSITE:	PDOC00529
Pseudofam:	PF02801
SCOP:	1kas
SYSTERS:	Ketoacyl-synt_C

This tab holds annotation information from the InterPro database.

InterPro entry IPR014031

Beta-ketoacyl-ACP synthase EC (KAS) [PUBMED:3076376] is the enzyme that catalyzes the condensation of malonyl-ACP with the growing fatty acid chain. It is found as a component of a number of enzymatic systems, including fatty acid synthetase (FAS), which catalyzes the formation of long-chain fatty acids from acetyl-CoA, malonyl-CoA and NADPH; the multi-functional 6-methysalicylic acid synthase (MSAS) from Penicillium patulum [PUBMED:2209605], 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. The condensation reaction is a two step process, first the acyl component of an activated acyl primer is transferred to a cysteine residue of the enzyme and is then condensed with an activated malonyl donor with the concomitant release of carbon dioxide.

This entry represents the C-terminal domain of beta-ketoacyl-ACP synthases. The active site is contained in a cleft betweeen N- and C-terminal domains, with residues from both domains contributing to substrate binding and catalysis [PUBMED:11152607].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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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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There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.

Alignment types

We make a range of alignments for each Pfam-A family:

seed: the curated alignment from which the HMM for the family is built
full: the alignment generated by searching the sequence database using the HMM
RP15/RP35/RP55/RP75: Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
NCBI: alignment generated by searching the NCBI sequence database using the family HMM
meta: alignment generated by searching the metagenomics sequence database using the family HMM

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

	Seed (165)	Full (23531)	Representative proteomes				NCBI (21515)	Meta (3921)
	Seed (165)	Full (23531)	RP15 (1709)	RP35 (3766)	RP55 (5251)	RP75 (6174)	NCBI (21515)	Meta (3921)
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PP/heatmap	₁		View	View
Pfam viewer	View	View

¹Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: available, not generated, — not available.

Format an alignment

	Seed (165)	Full (23531)	Representative proteomes				NCBI (21515)	Meta (3921)
	Seed (165)	Full (23531)	RP15 (1709)	RP35 (3766)	RP55 (5251)	RP75 (6174)	NCBI (21515)	Meta (3921)
Alignment:
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	Download View

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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

	Seed (165)	Full (23531)	Representative proteomes				NCBI (21515)	Meta (3921)
	Seed (165)	Full (23531)	RP15 (1709)	RP35 (3766)	RP55 (5251)	RP75 (6174)	NCBI (21515)	Meta (3921)
Raw Stockholm	Download	Download	Download	Download	Download	Download	Download	Download
Gzipped	Download	Download	Download	Download	Download	Download	Download	Download

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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Curation and family details

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Curation

Seed source:

Dotter

Previous IDs:

ketoacyl-synt_C;

Type:

Domain

Author:

Sonnhammer ELL, Griffiths-Jones SR

Number in seed:

165

Number in full:

23531

Average length of the domain:

108.60 aa

Average identity of full alignment:

35 %

Average coverage of the sequence by the domain:

10.85 %

HMM information

HMM build commands:

build method: hmmbuild -o /dev/null HMM SEED

search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq

Model details:

Parameter	Sequence	Domain
Gathering cut-off	20.7	20.7
Trusted cut-off	20.7	20.7
Noise cut-off	20.6	20.6

Model length:

119

Family (HMM) version:

17

Download:

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Species distribution

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Interactive tree

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Interactions

There are 2 interactions for this family. More...

Ketoacyl-synt_C ketoacyl-synt

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 Ketoacyl-synt_C domain has been found. There are 190 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.

Loading structure mapping...

Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: Ketoacyl-synt_C (PF02801)

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Summary: Beta-ketoacyl synthase, C-terminal domain

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Beta-ketoacyl-ACP synthase Edit Wikipedia article

See also

External links

References

Beta-ketoacyl synthase, C-terminal domain Provide feedback

Literature references

Internal database links

External database links

InterPro entry IPR014031

Domain organisation

Pfam Clan

Alignments

Alignment types

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Downloading

View options

Format an alignment

Download options

External links

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Curation and family details

Curation

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Species distribution

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How the sunburst is generated

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Interactions

Structures