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.
170  structures 7956  species 0  interactions 26957  sequences 278  architectures

Family: Biotin_carb_N (PF00289)

Summary: Biotin carboxylase, N-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
EC number6.3.4.14
CAS number9075-71-2
IntEnzIntEnz view
ExPASyNiceZyme view
MetaCycmetabolic pathway
PDB structuresRCSB PDB PDBe PDBsum
Gene OntologyAmiGO / QuickGO
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

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

ATP + biotin-carboxyl-carrier protein + CO2 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

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


  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.

Further reading

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, N-terminal domain Provide feedback

This domain is structurally related to the PreATP-grasp domain. The family contains the N-terminus of biotin carboxylase enzymes [1,3], and propionyl-CoA carboxylase A chain [2].

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

  2. Tran TH, Hsiao YS, Jo J, Chou CY, Dietrich LE, Walz T, Tong L;, Nature. 2015;518:120-124.: Structure and function of a single-chain, multi-domain long-chain acyl-CoA carboxylase. PUBMED:25383525 EPMC:25383525

  3. Healy S, McDonald MK, Wu X, Yue WW, Kochan G, Oppermann U, Gravel RA;, Biochemistry. 2010;49:4687-4694.: Structural impact of human and Escherichia coli biotin carboxyl carrier proteins on biotin attachment. PUBMED:20443544 EPMC:20443544

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR005481

This domain is structurally related to the PreATP-grasp domain. It is found at the N terminus of biotin carboxylase enzymes [ PUBMED:7915138 , PUBMED:20443544 , PUBMED:18725455 ], and propionyl-CoA carboxylase A chain [ PUBMED:25383525 ].

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 PreATP-grasp (CL0483), which has the following description:

This superfamily is characterised by bein g the copies of the domain that precedes the ATP-grasp domain common to all superfamily members, and it can contain a substrate-binding function.

The clan contains the following 11 members:

Biotin_carb_N Dala_Dala_lig_N DUF1246 GARS_N GSH-S_N GSH_synth_ATP GSH_synthase Ins134_P3_kin_N PPIP5K2_N Rimk_N Synapsin


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.

Representative proteomes UniProt
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

Representative proteomes UniProt

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.

Representative proteomes UniProt
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...


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: Prosite
Previous IDs: CPSase;
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD , Griffiths-Jones SR
Number in seed: 89
Number in full: 26957
Average length of the domain: 109.70 aa
Average identity of full alignment: 47 %
Average coverage of the sequence by the domain: 12.81 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.5 24.5
Trusted cut-off 26.0 24.8
Noise cut-off 25.4 24.4
Model length: 110
Family (HMM) version: 24
Download: download the raw HMM for this family

Species distribution

Sunburst controls


Weight segments by...

Change the size of the sunburst


Colour assignments

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


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


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


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.


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_N domain has been found. There are 170 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...