Summary: UreD urease accessory protein
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UreD urease accessory protein Provide feedback
UreD is a urease accessory protein. Urease PF00449 hydrolyses urea into ammonia and carbamic acid [2]. UreD is involved in activation of the urease enzyme via the UreD-UreF-UreG-urease complex [1] and is required for urease nickel metallocenter assembly [3]. See also UreF PF01730 UreG PF01495.
Literature references
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Moncrief MB, Hausinger RP; , J Bacteriol 1997;179:4081-4086.: Characterization of UreG, identification of a UreD-UreF-UreG complex, and evidence suggesting that a nucleotide-binding site in UreG is required for in vivo metallocenter assembly of Klebsiella aerogenes urease. PUBMED:9209019 EPMC:9209019
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Neyrolles O, Ferris S, Behbahani N, Montagnier L, Blanchard A; , J Bacteriol 1996;178:647-655.: Organization of Ureaplasma urealyticum urease gene cluster and expression in a suppressor strain of Escherichia coli. PUBMED:8550495 EPMC:8550495
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Park IS, Carr MB, Hausinger RP; , Proc Natl Acad Sci U S A 1994;91:3233-3237.: In vitro activation of urease apoprotein and role of UreD as a chaperone required for nickel metallocenter assembly. PUBMED:7909161 EPMC:7909161
This tab holds annotation information from the InterPro database.
InterPro entry IPR002669
UreD is a urease accessory protein. Urease hydrolyses urea into ammonia and carbamic acid [ PUBMED:8550495 ]. UreD is involved in activation of the urease enzyme via the UreD-UreF-UreG-urease complex [ PUBMED:9209019 ] and is required for urease nickel metallocentre assembly [ PUBMED:7909161 ]. This entry includes UreH from Helicobacter pylori, which is an orthologue of UreD [ PUBMED:24115911 ].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Molecular function | nickel cation binding (GO:0016151) |
Biological process | nitrogen compound metabolic process (GO:0006807) |
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 (355) |
Full (4079) |
Representative proteomes | UniProt (17037) |
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RP15 (415) |
RP35 (1743) |
RP55 (3984) |
RP75 (7191) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
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Seed (355) |
Full (4079) |
Representative proteomes | UniProt (17037) |
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RP15 (415) |
RP35 (1743) |
RP55 (3984) |
RP75 (7191) |
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Raw Stockholm | |||||||
Gzipped |
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
Seed source: | Pfam-B_1109 (release 4.2) |
Previous IDs: | none |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Bashton M |
Number in seed: | 355 |
Number in full: | 4079 |
Average length of the domain: | 208.5 aa |
Average identity of full alignment: | 22 % |
Average coverage of the sequence by the domain: | 71.25 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 213 | ||||||||||||
Family (HMM) version: | 20 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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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 UreD domain has been found. There are 4 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.
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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.