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6  structures 467  species 1  interaction 1158  sequences 13  architectures

Family: Allantoicase (PF03561)

Summary: Allantoicase repeat

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This is the Wikipedia entry entitled "Allantoicase". More...

Allantoicase Edit Wikipedia article

allantoicase
Identifiers
EC number 3.5.3.4
CAS number 9025-21-2
Databases
IntEnz IntEnz view
BRENDA BRENDA entry
ExPASy NiceZyme view
KEGG KEGG entry
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum
Gene Ontology AmiGO / EGO
Allantoicase
PDB 1sg3 EBI.jpg
structure of allantoicase
Identifiers
Symbol Allantoicase
Pfam PF03561
Pfam clan CL0202
InterPro IPR015908
SCOP 1sg3
SUPERFAMILY 1sg3

In enzymology, an allantoicase (EC 3.5.3.4) is an enzyme that catalyzes the chemical reaction

allantoate + H2O \rightleftharpoons (S)-ureidoglycolate + urea

Thus, the two substrates of this enzyme are allantoate and H2O, whereas its two products are (S)-ureidoglycolate and urea.

This enzyme belongs to the family of hydrolases, those acting on carbon-nitrogen bonds other than peptide bonds, specifically in linear amidines. The systematic name of this enzyme class is allantoate amidinohydrolase. This enzyme participates in purine metabolism by facilitating the utilization of purines as secondary nitrogen sources under nitrogen-limiting conditions. While purine degradation converges to uric acid in all vertebrates, its further degradation varies from species to species. Uric acid is excreted by birds, reptiles, and some mammals that do not have a functional uricase gene, whereas other mammals produce allantoin. Amphibians and microorganisms produce ammonia and carbon dioxide using the uricolytic pathway. Allantoicase performs the second step in this pathway catalyzing the conversion of allantoate into ureidoglycolate and urea.

Structural studies[edit]

As of late 2007, two structures have been solved for this class of enzymes, with PDB accession codes 1O59 and 1SG3.

The structure of allantoicase is best described as being composed of two repeats (the allantoicase repeats: AR1 and AR2), which are connected by a flexible linker. The crystal structure, resolved at 2.4A resolution, reveals that AR1 has a very similar fold to AR2, both repeats being jelly-roll motifs, composed of four-stranded and five-stranded antiparallel beta-sheets.[1] Each jelly-roll motif has two conserved surface patches that probably constitute the active site.[2]

References[edit]

  1. ^ Xu Q, Schwarzenbacher R, Page R, Sims E, Abdubek P, Ambing E, Biorac T, Brinen LS, Cambell J, Canaves JM, Chiu HJ, Dai X, Deacon AM, DiDonato M, Elsliger MA, Floyd R, Godzik A, Grittini C, Grzechnik SK, Hampton E, Jaroszewski L, Karlak C, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, Levin I, McMullan D, McPhillips TM, Miller MD, Morse A, Moy K, Ouyang J, Quijano K, Reyes R, Rezezadeh F, Robb A, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, von Delft F, Wang X, West B, Wolf G, Hodgson KO, Wooley J, Wilson IA (August 2004). "Crystal structure of an allantoicase (YIR029W) from Saccharomyces cerevisiae at 2.4 A resolution". Proteins 56 (3): 619–24. doi:10.1002/prot.20164. PMID 15229895. 
  2. ^ Leulliot N, Quevillon-Cheruel S, Sorel I, Graille M, Meyer P, Liger D, Blondeau K, Janin J, van Tilbeurgh H (May 2004). "Crystal structure of yeast allantoicase reveals a repeated jelly roll motif". J. Biol. Chem. 279 (22): 23447–52. doi:10.1074/jbc.M401336200. PMID 15020593. 

Further reading[edit]

  • Florkin M and Duchateau-Bosson G (1940). "Microdosage photometrique de l'allantoine en solutions pures et dans l'urine". Enzymologia 9: 5–9. 
  • Trijbels F, Vogels GD (1966). "Allantoicase and ureidoglycolase in Pseudomonas and Penicillium species". Biochim. Biophys. Acta. 118 (2): 387–95. doi:10.1016/S0926-6593(66)80047-4. PMID 4960174. 
  • Probst C, Grotz M, Krettek C, Pape HC (2005). "Impact of hypothermia on the immunologic response after trauma and elective surgery". Surg. Technol. Int. 14: 41–50. PMID 16525953. 
  • s'Gravenmade EJ, van der Drift C and Vogels GD (1971). "Hydrolysis, racemization and absolute configuration of ureidoglycolate, a substrate of allantoicase". Biochim. Biophys. Acta 198 (3): 569–582. doi:10.1016/0005-2744(70)90134-8. PMID 4314237. 


This article incorporates text from the public domain Pfam and InterPro IPR015908

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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Allantoicase repeat Provide feedback

This family is found in pairs in Allantoicases, forming the majority of the protein. These proteins allow the use of purines as secondary nitrogen sources in nitrogen-limiting conditions through the reaction: allantoate + H(2)0 = (-)-ureidoglycolate + urea.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR015908

Allantoicase (also known as allantoate amidinohydrolase) is involved in purine degradation, facilitating the utilization of purines as secondary nitrogen sources under nitrogen-limiting conditions. While purine degradation converges to uric acid in all vertebrates, its further degradation varies from species to species. Uric acid is excreted by birds, reptiles, and some mammals that do not have a functional uricase gene, whereas other mammals produce allantoin. Amphibians and microorganisms produce ammonia and carbon dioxide using the uricolytic pathway. Allantoicase performs the second step in this pathway catalyzing the conversion of allantoate into ureidoglycolate and urea.

allantoate + H(2)0 = (S)-ureidoglycolate + urea

The structure of allantoicase is best described as being composed of two repeats (the allantoicase repeats: AR1 and AR2), which are connected by a flexible linker. The crystal structure, resolved at 2.4A resolution, reveals that AR1 has a very similar fold to AR2, both repeats being jelly-roll motifs, composed of four-stranded and five-stranded antiparallel beta-sheets [PUBMED:15229895]. Each jelly-roll motif has two conserved surface patches that probably constitute the active site [PUBMED:15020593].

The mammalian proteins matched by this entry are thought to be non-functional as mammals do not appear to possess allantoicase activity [PUBMED:11054555].

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 GBD (CL0202), which has the following description:

This large superfamily contains beta sandwich domains with a jelly roll topology. Many of these families are involved in carbohydrate recognition. Despite sharing little sequence similarity they do share a weak sequence motif, with a conserved bulge in the C-terminal beta sheet. The probable role of this bulge is in bending of the beta sheet that contains the bulge. This enables the curvature of the sheet forming the sugar binding site [1].

The clan contains the following 27 members:

Allantoicase APC10 Bac_rhamnosid_N BetaGal_dom4_5 CBM_11 CBM_15 CBM_17_28 CBM_4_9 CBM_6 CIA30 Cleaved_Adhesin DUF642 Endotoxin_C Ephrin_lbd F5_F8_type_C FBA Glyco_hydro_2_N Laminin_N Lyase_N MAM Muskelin_N P_proprotein PA-IL PepX_C PITH Sad1_UNC XRCC1_N

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...

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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
(13)
Full
(1158)
Representative proteomes NCBI
(1098)
Meta
(1048)
RP15
(146)
RP35
(279)
RP55
(433)
RP75
(534)
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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
(13)
Full
(1158)
Representative proteomes NCBI
(1098)
Meta
(1048)
RP15
(146)
RP35
(279)
RP55
(433)
RP75
(534)
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
(13)
Full
(1158)
Representative proteomes NCBI
(1098)
Meta
(1048)
RP15
(146)
RP35
(279)
RP55
(433)
RP75
(534)
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: Yeats C
Previous IDs: none
Type: Family
Author: Finn RD, Yeats C
Number in seed: 13
Number in full: 1158
Average length of the domain: 143.30 aa
Average identity of full alignment: 39 %
Average coverage of the sequence by the domain: 75.20 %

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 21.6 21.6
Trusted cut-off 30.6 23.8
Noise cut-off 19.1 20.5
Model length: 152
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

Allantoicase

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 Allantoicase domain has been found. There are 6 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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