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608  structures 8554  species 0  interactions 73114  sequences 447  architectures

Family: Amidohydro_1 (PF01979)

Summary: Amidohydrolase family

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Amidohydrolase family Provide feedback

This family of enzymes are a a large metal dependent hydrolase superfamily [1]. The family includes Adenine deaminase EC:3.5.4.2 that hydrolyses adenine to form hypoxanthine and ammonia. Adenine deaminases reaction is important for adenine utilisation as a purine and also as a nitrogen source [2]. This family also includes dihydroorotase and N-acetylglucosamine-6-phosphate deacetylases, EC:3.5.1.25 These enzymes catalyse the reaction N-acetyl-D-glucosamine 6-phosphate + H2O <=> D-glucosamine 6-phosphate + acetate. This family includes the catalytic domain of urease alpha subunit [3]. Dihydroorotases ( EC:3.5.2.3) are also included [4-5].

Literature references

  1. Holm L, Sander C; , Proteins 1997;28:72-82.: An evolutionary treasure: unification of a broad set of amidohydrolases related to urease. PUBMED:9144792 EPMC:9144792

  2. Nygaard P, Duckert P, Saxild HH; , J Bacteriol 1996;178:846-853.: Role of adenine deaminase in purine salvage and nitrogen metabolism and characterization of the ade gene in Bacillus subtilis. PUBMED:8550522 EPMC:8550522

  3. 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

  4. Gao G, Nara T, Nakajima-Shimada J, Aoki T; , J Mol Biol 1999;285:149-161.: Novel organization and sequences of five genes encoding all six enzymes for de novo pyrimidine biosynthesis in Trypanosoma cruzi. PUBMED:9878395 EPMC:9878395

  5. Lollier M, Jaquet L, Nedeva T, Lacroute F, Potier S, Souciet JL; , Curr Genet 1995;28:138-149.: As in Saccharomyces cerevisiae, aspartate transcarbamoylase is assembled on a multifunctional protein including a dihydroorotase-like cryptic domain in Schizosaccharomyces pombe. PUBMED:8590465 EPMC:8590465


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006680

Proteins containing this domain are enzymes from a large metal dependent hydrolase superfamily [ PUBMED:9144792 ]. The family includes adenine deaminase ( EC ) that hydrolyses adenine to form hypoxanthine and ammonia. This reaction is important for adenine utilisation as a purine and also as a nitrogen source [ PUBMED:8550522 ]. The family also includes dihydroorotase and N-acetylglucosamine-6-phosphate deacetylases ( EC ). The domain is also found in the urease alpha subunit, where it is the catalytic domain [ 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 17 members:

A_deaminase Amidohydro_1 Amidohydro_2 Amidohydro_3 AMP_deaminase CpsB_CapC DHOase DUF3604 DUF6282 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 (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.

  Seed
(57)
Full
(73114)
Representative proteomes UniProt
(314411)
RP15
(8656)
RP35
(32847)
RP55
(71165)
RP75
(120374)
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

  Seed
(57)
Full
(73114)
Representative proteomes UniProt
(314411)
RP15
(8656)
RP35
(32847)
RP55
(71165)
RP75
(120374)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(57)
Full
(73114)
Representative proteomes UniProt
(314411)
RP15
(8656)
RP35
(32847)
RP55
(71165)
RP75
(120374)
Raw Stockholm Download   Download   Download   Download   Download      
Gzipped 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...

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: Bateman A
Previous IDs: Adenine_deam;
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A , Eberhardt R
Number in seed: 57
Number in full: 73114
Average length of the domain: 321.50 aa
Average identity of full alignment: 14 %
Average coverage of the sequence by the domain: 67.98 %

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 21.6 21.6
Trusted cut-off 21.6 21.6
Noise cut-off 21.5 21.5
Model length: 344
Family (HMM) version: 22
Download: download the raw HMM for this family

Species distribution

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Selections

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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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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 Amidohydro_1 domain has been found. There are 608 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.

Protein Predicted structure External Information
A0A0G2K8Y5 View 3D Structure Click here
A0A0R0FXA5 View 3D Structure Click here
A0A0R0IJW2 View 3D Structure Click here
A0A0R0IJW2 View 3D Structure Click here
A0A0R0IV26 View 3D Structure Click here
A0A0R0JV11 View 3D Structure Click here
A0A0R4IYX8 View 3D Structure Click here
A0A1D6FAC8 View 3D Structure Click here
A0A1D6FAC8 View 3D Structure Click here
A0A1D6JI69 View 3D Structure Click here
A0A1D6MTX1 View 3D Structure Click here
A0A1D6MTX2 View 3D Structure Click here
A0A1D8PQG3 View 3D Structure Click here
A0A1D8PQQ8 View 3D Structure Click here
A0A2R8Q5K7 View 3D Structure Click here
A0A2R8Q6T7 View 3D Structure Click here
A0A2R8QFM8 View 3D Structure Click here
A2BG14 View 3D Structure Click here
A4HWV7 View 3D Structure Click here
A4I4E1 View 3D Structure Click here
A4ICY4 View 3D Structure Click here
B1H1J6 View 3D Structure Click here
B2RQC6 View 3D Structure Click here
B4FQJ2 View 3D Structure Click here
B6U6Z4 View 3D Structure Click here
B9FDB8 View 3D Structure Click here
B9GCH9 View 3D Structure Click here
C6TEN9 View 3D Structure Click here
D4A8A0 View 3D Structure Click here
D4AAV1 View 3D Structure Click here
F1QR62 View 3D Structure Click here
F1RB68 View 3D Structure Click here
I1JIW1 View 3D Structure Click here
I1K3K3 View 3D Structure Click here
I1M259 View 3D Structure Click here
I1M261 View 3D Structure Click here
I1MDY5 View 3D Structure Click here
I1MEH3 View 3D Structure Click here
I1NJF1 View 3D Structure Click here
K7LU89 View 3D Structure Click here
O00084 View 3D Structure Click here
O04904 View 3D Structure Click here
O08553 View 3D Structure Click here
O14057 View 3D Structure Click here
O14531 View 3D Structure Click here
O35098 View 3D Structure Click here
O53382 View 3D Structure Click here
O53619 View 3D Structure Click here
P05020 View 3D Structure Click here
P05990 View 3D Structure Click here
P08298 View 3D Structure Click here
P0AF18 View 3D Structure Click here
P20054 View 3D Structure Click here
P27708 View 3D Structure Click here
P31441 View 3D Structure Click here
P32375 View 3D Structure Click here
P34480 View 3D Structure Click here
P39377 View 3D Structure Click here
P40896 View 3D Structure Click here
P42906 View 3D Structure Click here
P47942 View 3D Structure Click here
P76641 View 3D Structure Click here
P77671 View 3D Structure Click here
P97427 View 3D Structure Click here
P9WFF1 View 3D Structure Click here
P9WHL3 View 3D Structure Click here
P9WL23 View 3D Structure Click here
Q01630 View 3D Structure Click here
Q07729 View 3D Structure Click here
Q0JJD1 View 3D Structure Click here
Q14117 View 3D Structure Click here
Q14194 View 3D Structure Click here
Q14195 View 3D Structure Click here
Q16555 View 3D Structure Click here
Q18677 View 3D Structure Click here
Q18990 View 3D Structure Click here
Q20166 View 3D Structure Click here
Q21773 View 3D Structure Click here
Q22419 View 3D Structure Click here
Q2FVT6 View 3D Structure Click here
Q2FZ74 View 3D Structure Click here
Q2G2K5 View 3D Structure Click here
Q2G2U0 View 3D Structure Click here
Q2QRA2 View 3D Structure Click here
Q46806 View 3D Structure Click here
Q46812 View 3D Structure Click here
Q4CLJ4 View 3D Structure Click here
Q4CRZ4 View 3D Structure Click here
Q4CSV8 View 3D Structure Click here
Q4CVT7 View 3D Structure Click here
Q4D711 View 3D Structure Click here
Q4DBC4 View 3D Structure Click here
Q4DUS4 View 3D Structure Click here
Q52PJ5 View 3D Structure Click here
Q54N71 View 3D Structure Click here
Q54SV3 View 3D Structure Click here
Q55C91 View 3D Structure Click here
Q55CY3 View 3D Structure Click here
Q55DL0 View 3D Structure Click here
Q58110 View 3D Structure Click here
Q58854 View 3D Structure Click here
Q58885 View 3D Structure Click here
Q58936 View 3D Structure Click here
Q5A7L5 View 3D Structure Click here
Q5A7L5 View 3D Structure Click here
Q5BJY6 View 3D Structure Click here
Q5RGY8 View 3D Structure Click here
Q62188 View 3D Structure Click here
Q62950 View 3D Structure Click here
Q62951 View 3D Structure Click here
Q62952 View 3D Structure Click here
Q63150 View 3D Structure Click here
Q6P0U0 View 3D Structure Click here
Q7SXK5 View 3D Structure Click here
Q86AW9 View 3D Structure Click here
Q8IPQ2 View 3D Structure Click here
Q8JZV7 View 3D Structure Click here
Q92342 View 3D Structure Click here
Q949H4 View 3D Structure Click here
Q94AP0 View 3D Structure Click here
Q94J90 View 3D Structure Click here
Q96NU7 View 3D Structure Click here
Q9BPU6 View 3D Structure Click here
Q9DBA8 View 3D Structure Click here
Q9EQF5 View 3D Structure Click here
Q9EQF6 View 3D Structure Click here
Q9FMP3 View 3D Structure Click here
Q9JHU0 View 3D Structure Click here
Q9R111 View 3D Structure Click here
Q9SR52 View 3D Structure Click here
Q9UTI0 View 3D Structure Click here
Q9VMY9 View 3D Structure Click here
Q9VR81 View 3D Structure Click here
Q9VWW1 View 3D Structure Click here
Q9WTT6 View 3D Structure Click here
Q9Y2T3 View 3D Structure Click here
Q9Y303 View 3D Structure Click here
U3JAV8 View 3D Structure Click here