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139  structures 2116  species 1  interaction 2760  sequences 3  architectures

Family: Tautomerase (PF01361)

Summary: Tautomerase enzyme

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This is the Wikipedia entry entitled "4-Oxalocrotonate tautomerase". More...

4-Oxalocrotonate tautomerase Edit Wikipedia article

4-oxalocrotonate tautomerase
Identifiers
Symbol Taut
Pfam PF01361
InterPro IPR004370
CDD cd00491

4-Oxalocrotonate tautomerase (EC 5.3.2.-4-OT) is an enzyme that converts 2-hydroxymuconate to the αβ-unsaturated ketone, 2-oxo-3-hexenedioate.[1] This enzyme forms part of a bacterial metabolic pathway that oxidatively catabolizes toluene, o-xylene, 3-ethyltoluene, and 1,2,4-trimethylbenzene into intermediates of the citric acid cycle. With a monomer size of just 62 amino acid residues, the 4-Oxalocrotonate tautomerase is one of the smallest enzyme subunits known.[2] However, in solution, the enzyme forms a hexamer of six identical subunits, so the active site may be formed by amino acid residues from several subunits.[3] This enzyme is also unusual in that it uses a proline residue at the amino terminus as an active site residue.

[edit] References

  1. ^ Chen LH, Kenyon GL, Curtin F, Harayama S, Bembenek ME, Hajipour G, Whitman CP (1992). "4-Oxalocrotonate tautomerase, an enzyme composed of 62 amino acid residues per monomer". J. Biol. Chem. 267 (25): 17716–21. PMID 1339435.
  2. ^ Whitman CP (2002). "The 4-oxalocrotonate tautomerase family of enzymes: how nature makes new enzymes using a beta-alpha-beta structural motif". Arch. Biochem. Biophys. 402 (1): 1–13. doi:10.1016/S0003-9861(02)00052-8. PMID 12051677.
  3. ^ Subramanya HS, Roper DI, Dauter Z, Dodson EJ, Davies GJ, Wilson KS, Wigley DB. Enzymatic ketonization of 2-hydroxymuconate: specificity and mechanism investigated by the crystal structures of two isomerases. (1996) Biochemistry. 35(3):792-802. PMID 8547259


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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.

Tautomerase enzyme Provide feedback

This family includes the enzyme 4-oxalocrotonate tautomerase Q01468 that catalyses the ketonisation of 2-hydroxymuconate to 2-oxo-3-hexenedioate.

Literature references

  1. Roper DI, Subramanya HS, Shingler V, Wigley DB; , J Mol Biol 1994;243:799-801.: Preliminary crystallographic analysis of 4-oxalocrotonate tautomerase reveals the oligomeric structure of the enzyme. PUBMED:7966298 EPMC:7966298


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004370

4-Oxalocrotonate tautomerase (4-OT) catalyzes the isomerisation of beta,gamma-unsaturated enones to their alpha,beta-isomers. The enzyme is part of a plasmid-encoded pathway, which enables bacteria harbouring the plasmid to use various aromatic hydrocarbons as their sole sources of carbon and energy. The enzyme is a barrel-shaped hexamer, which can be viewed as a trimer of dimers. The hexamer contains a hydrophobic core formed by three beta-sheets and surrounded by three pairs of alpha-helices. Each 4-OT monomer of 62 amino acids has a relatively simple beta-alpha-beta fold as described by the structure of the enzyme from Pseudomonas putida [PUBMED:12051677]. The monomer begins with a conserved proline at the start of a beta-strand, followed by an alpha-helix and a 310 helix preceding a second parallel beta-strand, and ends with a beta-hairpin near the C terminus. The dimer results from antiparallel interactions between the beta-sheets and alpha-helices of the two monomers, forming a four-stranded beta-sheet with antiparallel alpha-helices on one side, creating two active sites, one at each end of the beta-sheet. Three dimers further associate to form a hexamer by the interactions of the strands of the C-terminal beta-hairpin loops with the edges of the four-stranded beta-sheets of neighbouring dimers, creating a series of cross-links that stabilise the hexamer

Pro-1 of the mature protein functions as the general base while Arg-39 and an ordered water molecule each provide a hydrogen bond to the C-2 oxygen of substrate. Arg-39 plays an additional role in the binding of the C-1 carboxylate group. Arg-11 participates both in substrate binding and in catalysis. It interacts with the C-6 carboxylate group, thereby holding the substrate in place and drawing electron density to the C-5 position. The hydrophobic nature of the active site, which lowers the pKa of Pro-1 and provides a favourable environment for catalysis, is largely maintained by Phe-50.

Because several Arg residues located near the active site are not conserved among all members of this family and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.

Gene Ontology

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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 MIF (CL0082), which has the following description:

This clan groups 5-(carboxymethyl)-2-hydroxymuconate isomerase (CHMI) and 4-oxalocrotonate tautomerase (4-OT) with macrophage inhibitory factor (MIF). Interestingly they all share an amino-terminal proline. Members of this clan for homotrimers [1].

The clan contains the following 6 members:

CHMI DUF1904 MIF Tautomerase Tautomerase_2 Tautomerase_3

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.

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(28)
Full
(2760)
Representative proteomes NCBI
(2083)
Meta
(293)
RP15
(159)
RP35
(365)
RP55
(504)
RP75
(636)
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  Seed
(28)
Full
(2760)
Representative proteomes NCBI
(2083)
Meta
(293)
RP15
(159)
RP35
(365)
RP55
(504)
RP75
(636)
Alignment:
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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
(28)
Full
(2760)
Representative proteomes NCBI
(2083)
Meta
(293)
RP15
(159)
RP35
(365)
RP55
(504)
RP75
(636)
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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:

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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.

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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: none
Type: Domain
Author: Finn RD
Number in seed: 28
Number in full: 2760
Average length of the domain: 59.20 aa
Average identity of full alignment: 29 %
Average coverage of the sequence by the domain: 84.64 %

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 20.7 20.7
Trusted cut-off 20.7 20.7
Noise cut-off 20.6 20.6
Model length: 60
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

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Interactions

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

Tautomerase

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 Tautomerase domain has been found. There are 139 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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