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48  structures 1537  species 2  interactions 1905  sequences 17  architectures

Family: Urease_alpha (PF00449)

Summary: Urease alpha-subunit, N-terminal domain

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Urease alpha-subunit, N-terminal domain Provide feedback

The N-terminal domain is a composite domain and plays a major trimer stabilising role by contacting the catalytic domain of the symmetry related alpha-subunit.

Literature references

  1. Jabri E, Carr MB, Hausinger RP, Karplus PA; , Science 1995;268:998-1004.: The crystal structure of urease from Klebsiella aerogenes. PUBMED:7754395 EPMC:7754395


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR011612

Urease (urea amidohydrolase, EC) catalyses the hydrolysis of urea to form ammonia and carbamate. The subunit composition of urease from different sources varies [PUBMED:7565414], but each holoenzyme consists of four structural domains [PUBMED:7754395]: three structural domains and a nickel-binding catalytic domain common to amidohydrolases [PUBMED:9144792]. Urease is unique among nickel metalloenzymes in that it catalyses a hydrolysis rather than a redox reaction. In Helicobacter pylori, the gamma and beta domains are fused and called the alpha subunit (INTERPRO). The catalytic subunit (called beta or B) has the same organisation as the Klebsiella alpha subunit. Jack bean (Canavalia ensiformis) urease has a fused gamma-beta-alpha organisation (INTERPRO).

The N-terminal domain is a composite domain and plays a major trimer stabilising role by contacting the catalytic domain of the symmetry related alpha-subunit [PUBMED:7754395].

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...

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Pfam Clan

This family is a member of clan Amidohydrolase (CL0034), which has the following description:

This family includes a large family of metal dependent amidohydrolase enzymes [1].

The clan contains the following 16 members:

A_deaminase Amidohydro_1 Amidohydro_2 Amidohydro_3 Amidohydro_4 Amidohydro_5 DHOase DUF3604 Peptidase_M19 PHP PHP_C PTE RNase_P_p30 TatD_DNase Urease_alpha UxaC

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
(117)
Full
(1905)
Representative proteomes NCBI
(1638)
Meta
(555)
RP15
(139)
RP35
(288)
RP55
(388)
RP75
(464)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(117)
Full
(1905)
Representative proteomes NCBI
(1638)
Meta
(555)
RP15
(139)
RP35
(288)
RP55
(388)
RP75
(464)
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
(117)
Full
(1905)
Representative proteomes NCBI
(1638)
Meta
(555)
RP15
(139)
RP35
(288)
RP55
(388)
RP75
(464)
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.

Pfam alignments:

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: Prosite
Previous IDs: urease;
Type: Domain
Author: Finn RD, Griffiths-Jones SR
Number in seed: 117
Number in full: 1905
Average length of the domain: 117.10 aa
Average identity of full alignment: 58 %
Average coverage of the sequence by the domain: 20.98 %

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 21.8
Noise cut-off 21.7 21.7
Model length: 121
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

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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...

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Interactions

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

Urease_beta Amidohydro_1

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 Urease_alpha domain has been found. There are 48 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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