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13  structures 581  species 1  interaction 596  sequences 3  architectures

# Summary: IMP cyclohydrolase-like protein

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This is the Wikipedia entry entitled "IMP cyclohydrolase". More...

# IMP cyclohydrolase

IMP cyclohydrolase
Identifiers
EC number3.5.4.10
CAS number9013-81-4
Databases
IntEnzIntEnz view
BRENDABRENDA entry
ExPASyNiceZyme view
KEGGKEGG entry
MetaCycmetabolic pathway
PRIAMprofile
PDB structures
Gene Ontology
IMP cyclohydrolase-like protein
crystal structure of puro from methanothermobacter thermoautotrophicus
Identifiers
SymbolIMP_cyclohyd
PfamPF07826
InterProIPR020600

In enzymology, an IMP cyclohydrolase (EC 3.5.4.10) is an enzyme that catalyzes the chemical reaction

IMP + H2O ${\displaystyle \rightleftharpoons }$ 5-formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide

Thus, the two substrates of this enzyme are IMP and H2O, whereas its product is 5-formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide.

This enzyme belongs to the family of hydrolases, those acting on carbon-nitrogen bonds other than peptide bonds, specifically in cyclic amidines. The systematic name of this enzyme class is IMP 1,2-hydrolase (decyclizing). Other names in common use include inosinicase, and inosinate cyclohydrolase. This enzyme catalyses the cyclisation of 5-formylamidoimidazole-4-carboxamide ribonucleotide to IMP, a reaction which is important in de novo purine biosynthesis in archaeal species.[1]

## Structural studies

In most cases this single-domain protein is arranged to form an overall fold that consists of a four-layered alpha-beta-beta-alpha core structure. The two antiparallel beta-sheets pack against each other and are covered by alpha-helices on one face of the molecule. The protein is structurally similar to members of the N-terminal nucleophile (NTN) hydrolase superfamily. A deep pocket was in fact found on the surface of IMP cyclohydrolase in a position equivalent to that of active sites of NTN-hydrolases, but an N-terminal nucleophile could not be found. Therefore, it is thought that this enzyme is structurally but not functionally similar to members of the NTN-hydrolase family.[2]

As of late 2007, 14 structures have been solved for this class of enzymes, with PDB accession codes 1G8M, 1M9N, 1OZ0, 1P4R, 1PKX, 1PL0, 1THZ, 2B1G, 2B1I, 2IU0, 2IU3, 2NTK, 2NTL, and 2NTM.

## References

1. ^ Graupner M, Xu H, White RH (March 2002). "New class of IMP cyclohydrolases in Methanococcus jannaschii". J. Bacteriol. 184 (5): 1471â€“3. doi:10.1128/jb.184.5.1471-1473.2002. PMC 134845. PMID 11844782.
2. ^ Saridakis V, Christendat D, Thygesen A, Arrowsmith CH, Edwards AM, Pai EF (July 2002). "Crystal structure of Methanobacterium thermoautotrophicum conserved protein MTH1020 reveals an NTN-hydrolase fold". Proteins. 48 (1): 141â€“3. doi:10.1002/prot.10147. PMID 12012346.

• FLAKS JG, ERWIN MJ, BUCHANAN JM (1957). "Biosynthesis of the purines. XVIII 5-Amino-1-ribosyl-4-imidazolecarboxamide 5'-phosphate transformylase and inosinicase". J. Biol. Chem. 229 (2): 603â€“12. PMID 13502325.
This article incorporates text from the public domain Pfam and InterPro: IPR020600

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

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

# IMP cyclohydrolase-like protein

This enzyme (O27099) is may catalyse the cyclization of 5-formylamidoimidazole-4-carboxamide ribonucleotide to inosine monophosphate (IMP), a reaction which is important in de novo purine biosynthesis in archaeal species. This single domain protein is arranged to form an overall fold that consists of a four-layered alpha-beta-beta-alpha core structure. The two antiparallel beta-sheets pack against each other and are covered by alpha-helices on one face of the molecule. The protein is structurally similar to members of the N-terminal nucleophile (NTN) hydrolase superfamily. A deep pocket was in fact found on the surface of IMP cyclohydrolase in a position equivalent to that of active sites of NTN-hydrolases, but an N-terminal nucleophile could not be found. Therefore, it is thought that this enzyme is structurally but not functionally similar to members of the NTN-hydrolase family [1].

## Literature references

1. Saridakis V, Christendat D, Thygesen A, Arrowsmith CH, Edwards AM, Pai EF; , Proteins 2002;48:141-143.: Crystal structure of Methanobacterium thermoautotrophicum conserved protein MTH1020 reveals an NTN-hydrolase fold. PUBMED:12012346 EPMC:12012346

This tab holds annotation information from the InterPro database.

# InterPro entry IPR020600

This entry represents inosine monophosphate (IMP) cyclohydrolase family, found in archaeal species, as well as some bacterial proteins of unknown function.

IMP cyclohydrolase catalyses the cyclisation of 5-formylamidoimidazole-4-carboxamide ribonucleotide to IMP, a reaction which is important in de novo purine biosynthesis in archaeal species [PUBMED:11844782]. This single domain protein is arranged to form an overall fold that consists of a four-layered alpha-beta-beta-alpha core structure. The two antiparallel beta-sheets pack against each other and are covered by alpha-helices on one face of the molecule. The protein is structurally similar to members of the N-terminal nucleophile (NTN) hydrolase superfamily. A deep pocket was in fact found on the surface of IMP cyclohydrolase in a position equivalent to that of active sites of NTN-hydrolases, but an N-terminal nucleophile could not be found. Therefore, it is thought that this enzyme is structurally but not functionally similar to members of the NTN-hydrolase family [PUBMED:12012346].

In bacteria this step is catalysed by a bifunctional enzyme (purH).

### 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...

# Pfam Clan

This family is a member of clan NTN (CL0052), which has the following description:

In the N-terminal nucleophile aminohydrolases (Ntn hydrolases) the N-terminal residue provides two catalytic groups, nucleophile and proton donor. These enzymes use the side chain of the amino-terminal residue, incorporated in a beta-sheet, as the nucleophile in the catalytic attack at the carbonyl carbon. The nucleophile is cysteine in GAT, serine in penicillin acylase, and threonine in the proteasome. All the enzymes share an unusual fold in which the nucleophile and other catalytic groups occupy equivalent sites. This fold provides both the capacity for nucleophilic attack and the possibility of autocatalytic processing [1].

The clan contains the following 16 members:

IMP_cyclohyd

# 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, the UniProtKB sequence database, 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
(56)
Full
(596)
Representative proteomes UniProt
(2230)
NCBI
(2080)
Meta
(29)
RP15
(92)
RP35
(361)
RP55
(576)
RP75
(965)
Jalview View  View  View  View  View  View  View  View  View
HTML View  View
PP/heatmap 1 View

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: available, not generated, not available.

## Format an alignment

Seed
(56)
Full
(596)
Representative proteomes UniProt
(2230)
NCBI
(2080)
Meta
(29)
RP15
(92)
RP35
(361)
RP55
(576)
RP75
(965)
Alignment:
Format:
Order:
Sequence:
Gaps:

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
(56)
Full
(596)
Representative proteomes UniProt
(2230)
NCBI
(2080)
Meta
(29)
RP15
(92)
RP35
(361)
RP55
(576)
RP75
(965)

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_50235 (release 14.0) Previous IDs: none Type: Domain Sequence Ontology: SO:0000417 Author: Fenech M Number in seed: 56 Number in full: 596 Average length of the domain: 203.10 aa Average identity of full alignment: 46 % Average coverage of the sequence by the domain: 88.98 %

## HMM information

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 28.1 28.1
Trusted cut-off 28.4 28.3
Noise cut-off 27.5 27.2
Model length: 194
Family (HMM) version: 12

# Species distribution

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### Colour assignments

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