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116  structures 1268  species 3  interactions 1294  sequences 5  architectures

Family: PyrI_C (PF02748)

Summary: Aspartate carbamoyltransferase regulatory chain, metal binding domain

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Aspartate carbamoyltransferase regulatory chain, metal binding domain Provide feedback

The regulatory chain is involved in allosteric regulation of aspartate carbamoyltransferase. The C-terminal metal binding domain has a rubredoxin-like fold and provides the interface with the catalytic chain.

Literature references

  1. Monaco HL, Crawford JL, Lipscomb WN; , Proc Natl Acad Sci U S A 1978;75:5276-5280.: Three-dimensional structures of aspartate carbamoyltransferase from Escherichia coli and of its complex with cytidine triphosphate. PUBMED:364472 EPMC:364472

  2. Jin L, Stec B, Lipscomb WN, Kantrowitz ER; , Proteins 1999;37:729-742.: Insights into the mechanisms of catalysis and heterotropic regulation of Escherichia coli aspartate transcarbamoylase based upon a structure of the enzyme complexed with the bisubstrate analogue N-phosphonacetyl-L-aspartate at 2.1 A. PUBMED:10651286 EPMC:10651286


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR020542

Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) EC is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity [PUBMED:11323717]. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme [PUBMED:7791626]. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies.

A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme [PUBMED:10651286]. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold.

ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation [PUBMED:10600394].

This entry represents the C-terminal domain.

Domain organisation

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Alignments

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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
(70)
Full
(1294)
Representative proteomes NCBI
(677)
Meta
(90)
RP15
(70)
RP35
(143)
RP55
(195)
RP75
(241)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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Format an alignment

  Seed
(70)
Full
(1294)
Representative proteomes NCBI
(677)
Meta
(90)
RP15
(70)
RP35
(143)
RP55
(195)
RP75
(241)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(70)
Full
(1294)
Representative proteomes NCBI
(677)
Meta
(90)
RP15
(70)
RP35
(143)
RP55
(195)
RP75
(241)
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: Enright A
Previous IDs: none
Type: Domain
Author: Enright A, Ouzounis C, Bateman A, Griffiths-Jones SR
Number in seed: 70
Number in full: 1294
Average length of the domain: 51.10 aa
Average identity of full alignment: 47 %
Average coverage of the sequence by the domain: 31.64 %

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 21.8 21.8
Trusted cut-off 21.8 23.1
Noise cut-off 21.7 21.7
Model length: 52
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

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Interactions

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

OTCace PyrI OTCace_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 PyrI_C domain has been found. There are 116 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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