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12  structures 2091  species 0  interactions 2948  sequences 47  architectures

Family: ARD (PF03079)

Summary: ARD/ARD' family

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ARD/ARD' family Provide feedback

The two acireductone dioxygenase enzymes (ARD and ARD', previously known as E-2 and E-2') from Klebsiella pneumoniae share the same amino acid sequence Q9ZFE7 but bind different metal ions: ARD binds Ni2+, ARD' binds Fe2+. ARD and ARD' can be experimentally interconverted by removal of the bound metal ion and reconstitution with the appropriate metal ion. The two enzymes share the same substrate, 1,2-dihydroxy-3-keto-5-(methylthio)pentene, but yield different products. ARD' yields the alpha-keto precursor of methionine (and formate), thus forming part of the ubiquitous methionine salvage pathway that converts 5'-methylthioadenosine (MTA) to methionine. This pathway is responsible for the tight control of the concentration of MTA, which is a powerful inhibitor of polyamine biosynthesis and transmethylation reactions [1,2]. ARD yields methylthiopropanoate, carbon monoxide and formate, and thus prevents the conversion of MTA to methionine. The role of the ARD catalysed reaction is unclear: methylthiopropanoate is cytotoxic, and carbon monoxide can activate guanylyl cyclase, leading to increased intracellular cGMP levels [1,2]. This family also contains other members, whose functions are not well characterised.

Literature references

  1. Dai Y, Pochapsky TC, Abeles RH; , Biochemistry 2001;40:6379-6387.: Mechanistic Studies of Two Dioxygenases in the Methionine Salvage Pathway of Klebsiella pneumoniae(,). PUBMED:11371200 EPMC:11371200

  2. Dai Y, Wensink PC, Abeles RH; , J Biol Chem 1999;274:1193-1195.: One protein, two enzymes. PUBMED:9880484 EPMC:9880484


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004313

The two acireductone dioxygenase enzymes (ARD and ARD', previously known as E-2 and E-2') from Klebsiella pneumoniae share the same amino acid sequence SWISSPROT , but bind different metal ions: ARD binds Ni2+, ARD' binds Fe2+ [ PUBMED:9880484 ]. ARD and ARD' can be experimentally interconverted by removal of the bound metal ion and reconstitution with the appropriate metal ion. The two enzymes share the same substrate, 1,2-dihydroxy-3-keto-5-(methylthio)pentene, but yield different products. ARD' yields the alpha-keto precursor of methionine (and formate), thus forming part of the ubiquitous methionine salvage pathway that converts 5'-methylthioadenosine (MTA) to methionine. This pathway is responsible for the tight control of the concentration of MTA, which is a powerful inhibitor of polyamine biosynthesis and transmethylation reactions [ PUBMED:11371200 ]. ARD yields methylthiopropanoate, carbon monoxide and formate, and thus prevents the conversion of MTA to methionine. The role of the ARD catalysed reaction is unclear: methylthiopropanoate is cytotoxic, and carbon monoxide can activate guanylyl cyclase, leading to increased intracellular cGMP levels [ PUBMED:11371200 , PUBMED:9880484 ].

Eukaryotic aci-reductone dioxygenase (ARD), also known as 1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase, acts in the methionine salvage pathway [ PUBMED:15938715 ]. Several homologous ARD genes have been identified in plants [ PUBMED:16297065 ].

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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Alignments

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  Seed
(10)
Full
(2948)
Representative proteomes UniProt
(9137)
RP15
(526)
RP35
(1456)
RP55
(2583)
RP75
(4113)
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PP/heatmap 1 View           

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

Key: ✓ available, x not generated, not available.

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  Seed
(10)
Full
(2948)
Representative proteomes UniProt
(9137)
RP15
(526)
RP35
(1456)
RP55
(2583)
RP75
(4113)
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
(10)
Full
(2948)
Representative proteomes UniProt
(9137)
RP15
(526)
RP35
(1456)
RP55
(2583)
RP75
(4113)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

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.

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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: Pfam-B_2276 (release 6.4)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Mifsud W
Number in seed: 10
Number in full: 2948
Average length of the domain: 148.00 aa
Average identity of full alignment: 32 %
Average coverage of the sequence by the domain: 75.68 %

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 21.0 21.0
Trusted cut-off 21.0 21.0
Noise cut-off 20.9 20.9
Model length: 157
Family (HMM) version: 16
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 ARD domain has been found. There are 12 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
A0A0R0I5N9 View 3D Structure Click here
A0A0R0J2E3 View 3D Structure Click here
A0A0R0J2E3 View 3D Structure Click here
A0A1D6EHD0 View 3D Structure Click here
A0A1D6GLE7 View 3D Structure Click here
A0A1D6H377 View 3D Structure Click here
A0A1D6HUW8 View 3D Structure Click here
A0A1D6J506 View 3D Structure Click here
A0A1D6JPD5 View 3D Structure Click here
A0A1D6MU53 View 3D Structure Click here
A0A1D6Q6Z2 View 3D Structure Click here
A1L4T4 View 3D Structure Click here
A4HYT9 View 3D Structure Click here
A4IAL2 View 3D Structure Click here
B6U3W8 View 3D Structure Click here
I1LE06 View 3D Structure Click here
I1NGJ7 View 3D Structure Click here
I1NGJ8 View 3D Structure Click here
O48707 View 3D Structure Click here
O94286 View 3D Structure Click here
P91416 View 3D Structure Click here
Q03677 View 3D Structure Click here
Q09407 View 3D Structure Click here
Q10RE5 View 3D Structure Click here
Q20340 View 3D Structure Click here
Q4CVG3 View 3D Structure Click here
Q4DFX2 View 3D Structure Click here
Q4DQC4 View 3D Structure Click here
Q54ER6 View 3D Structure Click here
Q562C9 View 3D Structure Click here
Q59WJ5 View 3D Structure Click here
Q6AWN0 View 3D Structure Click here
Q6PBX5 View 3D Structure Click here
Q7XEJ5 View 3D Structure Click here
Q7XNS7 View 3D Structure Click here
Q8GXE2 View 3D Structure Click here
Q8H185 View 3D Structure Click here
Q8W108 View 3D Structure Click here
Q99JT9 View 3D Structure Click here
Q9BV57 View 3D Structure Click here