Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
416  structures 8286  species 0  interactions 52050  sequences 4000  architectures

Family: Ketoacyl-synt_C (PF02801)

Summary: Beta-ketoacyl synthase, C-terminal domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

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

Beta-ketoacyl-ACP synthase Edit Wikipedia article

3-oxoacyl-ACP synthase, mitochondrial
Identifiers
SymbolOXSM
NCBI gene54995
HGNC26063
OMIM610324
RefSeqNM_017897
UniProtQ9NWU1
Other data
EC number2.3.1.41
LocusChr. 3 p24.2

Beta-ketoacyl-ACP synthase is an enzyme involved in fatty acid synthesis. It results in the formation of acetoacetyl ACP. FattyAcid-MB-Condensation.png

External links

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

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

  1. 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

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR014031

Beta-ketoacyl-ACP synthase EC (KAS) [ PUBMED:3076376 ] is the enzyme that catalyses 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 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 [ 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 between 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...

Loading domain graphics...

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 14 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 KAsynt_C_assoc ketoacyl-synt Ketoacyl-synt_2 Ketoacyl-synt_C SpoVAD Thiolase_C Thiolase_N

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

View options

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
(79)
Full
(52050)
Representative proteomes UniProt
(212926)
RP15
(5616)
RP35
(21947)
RP55
(50208)
RP75
(88170)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

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

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(79)
Full
(52050)
Representative proteomes UniProt
(212926)
RP15
(5616)
RP35
(21947)
RP55
(50208)
RP75
(88170)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

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
(79)
Full
(52050)
Representative proteomes UniProt
(212926)
RP15
(5616)
RP35
(21947)
RP55
(50208)
RP75
(88170)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Dotter
Previous IDs: ketoacyl-synt_C;
Type: Domain
Sequence Ontology: SO:0000417
Author: Sonnhammer ELL , Griffiths-Jones SR
Number in seed: 79
Number in full: 52050
Average length of the domain: 115.3 aa
Average identity of full alignment: 34 %
Average coverage of the sequence by the domain: 8.99 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.8 20.8
Trusted cut-off 20.8 20.8
Noise cut-off 20.7 20.7
Model length: 119
Family (HMM) version: 25
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

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 416 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 sequence.

Loading structure mapping...

AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A044TXS3 View 3D Structure Click here
A0A067XNI2 View 3D Structure Click here
A0A075TRC0 View 3D Structure Click here
A0A077YWM3 View 3D Structure Click here
A0A077Z0J0 View 3D Structure Click here
A0A084R1H6 View 3D Structure Click here
A0A089QRB9 View 3D Structure Click here
A0A098D6U0 View 3D Structure Click here
A0A098D8A0 View 3D Structure Click here
A0A0A0RM07 View 3D Structure Click here
A0A0A2JW91 View 3D Structure Click here
A0A0A2V1U3 View 3D Structure Click here
A0A0D2D9I2 View 3D Structure Click here
A0A0D2DQN8 View 3D Structure Click here
A0A0D2GG68 View 3D Structure Click here
A0A0D2HLU5 View 3D Structure Click here
A0A0D2YG10 View 3D Structure Click here
A0A0H3GLG4 View 3D Structure Click here
A0A0H3GR90 View 3D Structure Click here
A0A0H3GTQ4 View 3D Structure Click here
A0A0H4ADX3 View 3D Structure Click here
A0A0J9XWP5 View 3D Structure Click here
A0A0K0DSY1 View 3D Structure Click here
A0A0K0EHK0 View 3D Structure Click here
A0A0K0ELX4 View 3D Structure Click here
A0A0K0ESV2 View 3D Structure Click here
A0A0N4UAQ1 View 3D Structure Click here
A0A0N4UH23 View 3D Structure Click here
A0A0R0GE20 View 3D Structure Click here
A0A158N7W9 View 3D Structure Click here
A0A175VMR7 View 3D Structure Click here
A0A175VQW4 View 3D Structure Click here
A0A175VSS8 View 3D Structure Click here
A0A175VTR7 View 3D Structure Click here
A0A175VUA5 View 3D Structure Click here
A0A175VVT3 View 3D Structure Click here
A0A175VXF2 View 3D Structure Click here
A0A175VY08 View 3D Structure Click here
A0A175VZ44 View 3D Structure Click here
A0A175VZ76 View 3D Structure Click here