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.
113  structures 4650  species 5  interactions 10242  sequences 97  architectures

Family: Biotin_carb_C (PF02785)

Summary: Biotin carboxylase 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 "Biotin carboxylase". More...

Biotin carboxylase Edit Wikipedia article

biotin carboxylase
Identifiers
EC number 6.3.4.14
CAS number 9075-71-2
Databases
IntEnz IntEnz view
BRENDA BRENDA entry
ExPASy NiceZyme view
KEGG KEGG entry
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum
Gene Ontology AmiGO / EGO
Biotin carboxylase C-terminal domain
PDB 1w96 EBI.jpg
crystal structure of biotin carboxylase domain of acetyl-coenzyme a carboxylase from saccharomyces cerevisiae in complex with soraphen a
Identifiers
Symbol Biotin_carb_C
Pfam PF02785
InterPro IPR005482
SCOP 1dv1
SUPERFAMILY 1dv1

In enzymology, a biotin carboxylase (EC 6.3.4.14) is an enzyme that catalyzes the chemical reaction

ATP + biotin-carboxyl-carrier protein + CO2 \rightleftharpoons ADP + phosphate + carboxybiotin-carboxyl-carrier protein

The 3 substrates of this enzyme are ATP, biotin-carboxyl-carrier protein, and CO2, whereas its 3 products are ADP, phosphate, and carboxybiotin-carboxyl-carrier protein.

This enzyme belongs to the family of ligases, specifically those forming generic carbon-nitrogen bonds. The systematic name of this enzyme class is biotin-carboxyl-carrier-protein:carbon-dioxide ligase (ADP-forming). This enzyme is also called biotin carboxylase (component of acetyl CoA carboxylase). This enzyme participates in fatty acid biosynthesis.

A C-terminal conserved domain within this enzyme contains most of the active site residues.[1]

Structural studies[edit]

As of late 2007, 5 structures have been solved for this class of enzymes, with PDB accession codes 1BNC, 1DV1, 1DV2, 2GPS, and 2GPW.

References[edit]

  1. ^ Waldrop, G. L.; Rayment, I.; Holden, H. M. (1994). "Three-dimensional structure of the biotin carboxylase subunit of acetyl-CoA carboxylase". Biochemistry 33 (34): 10249–10256. doi:10.1021/bi00200a004. PMID 7915138.  edit

Further reading[edit]

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.

Biotin carboxylase C-terminal domain Provide feedback

Biotin carboxylase is a component of the acetyl-CoA carboxylase multi-component enzyme which catalyses the first committed step in fatty acid synthesis in animals, plants and bacteria. Most of the active site residues reported in reference [1] are in this C-terminal domain.

Literature references

  1. Waldrop GL, Rayment I, Holden HM; , Biochemistry 1994;33:10249-10256.: Three-dimensional structure of the biotin carboxylase subunit. of acetyl-CoA carboxylase. PUBMED:7915138 EPMC:7915138


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR005482

Acetyl-CoA carboxylase is found in all animals, plants, and bacteria and catalyzes the first committed step in fatty acid synthesis. It is a multicomponent enzyme containing a biotin carboxylase activity, a biotin carboxyl carrier protein, and a carboxyltransferase functionality. The "B-domain" extends from the main body of the subunit where it folds into two alpha-helical regions and three strands of beta-sheet. Following the excursion into the B-domain, the polypeptide chain folds back into the body of the protein where it forms an eight-stranded antiparallel beta-sheet. In addition to this major secondary structural element, the C-terminal domain also contains a smaller three-stranded antiparallel beta-sheet and seven alpha-helices [PUBMED:7915138].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

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

Loading domain graphics...

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics 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
(109)
Full
(10242)
Representative proteomes NCBI
(8078)
Meta
(3751)
RP15
(942)
RP35
(1879)
RP55
(2586)
RP75
(3077)
Jalview View  View  View  View  View  View  View  View 
HTML View    View  View  View  View     
PP/heatmap 1   View  View  View  View     
Pfam viewer View  View             

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

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

Format an alignment

  Seed
(109)
Full
(10242)
Representative proteomes NCBI
(8078)
Meta
(3751)
RP15
(942)
RP35
(1879)
RP55
(2586)
RP75
(3077)
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
(109)
Full
(10242)
Representative proteomes NCBI
(8078)
Meta
(3751)
RP15
(942)
RP35
(1879)
RP55
(2586)
RP75
(3077)
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.

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: ref [1]
Previous IDs: none
Type: Domain
Author: Griffiths-Jones SR
Number in seed: 109
Number in full: 10242
Average length of the domain: 106.20 aa
Average identity of full alignment: 38 %
Average coverage of the sequence by the domain: 14.54 %

HMM information View help on HMM parameters

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 20.3
Model length: 107
Family (HMM) version: 14
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Show

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.

Interactions

There are 5 interactions for this family. More...

CPSase_L_chain CPSase_L_D2 Biotin_lipoyl PYC_OADA Biotin_carb_C

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 Biotin_carb_C domain has been found. There are 113 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...