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125  structures 8121  species 0  interactions 18535  sequences 134  architectures

Family: Orn_Arg_deC_N (PF02784)

Summary: Pyridoxal-dependent decarboxylase, pyridoxal binding domain

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This is the Wikipedia entry entitled "Group IV pyridoxal-dependent decarboxylases". More...

Group IV pyridoxal-dependent decarboxylases Edit Wikipedia article

Pyridoxal-dependent decarboxylase, pyridoxal binding domain
PDB 1ko0 EBI.jpg
crystal structure of a d,l-lysine complex of diaminopimelate decarboxylase
Identifiers
SymbolOrn_Arg_deC_N
PfamPF02784
Pfam clanCL0036
InterProIPR022644
PROSITEPDOC00685
SCOPe1qu4 / SUPFAM
Pyridoxal-dependent decarboxylase, C-terminal sheet domain
PDB 1szr EBI.jpg
a dimer interface mutant of ornithine decarboxylase reveals structure of gem diamine intermediate
Identifiers
SymbolOrn_DAP_Arg_deC
PfamPF00278
InterProIPR022643
PROSITEPDOC00685
SCOPe1qu4 / SUPFAM

In molecular biology, group IV pyridoxal-dependent decarboxylases are a family of enzymes comprising ornithine decarboxylase EC 4.1.1.17, lysine decarboxylase EC 4.1.1.18, arginine decarboxylase EC 4.1.1.19 and diaminopimelate decarboxylaseEC 4.1.1.20.[1] It is also known as the Orn/Lys/Arg decarboxylase class-II family.

Pyridoxal-5'-phosphate-dependent amino acid decarboxylases can be divided into four groups based on amino acid sequence. Group IV comprises eukaryotic ornithine and lysine decarboxylase and the prokaryotic biosynthetic type of arginine decarboxylase and diaminopimelate decarboxylase.[1]

Members of this family while most probably evolutionary related, do not share extensive regions of sequence similarities. The proteins contain a conserved lysine residue which is known, in mouse ODC to be the site of attachment of the pyridoxal-phosphate group.[2] The proteins also contain a stretch of three consecutive glycine residues and has been proposed to be part of a substrate-binding region.[3]

See also

References

  1. ^ a b Sandmeier E, Hale TI, Christen P (May 1994). "Multiple evolutionary origin of pyridoxal-5'-phosphate-dependent amino acid decarboxylases". Eur. J. Biochem. 221 (3): 997–1002. doi:10.1111/j.1432-1033.1994.tb18816.x. PMID 8181483.
  2. ^ Poulin R, Lu L, Ackermann B, Bey P, Pegg AE (January 1992). "Mechanism of the irreversible inactivation of mouse ornithine decarboxylase by alpha-difluoromethylornithine. Characterization of sequences at the inhibitor and coenzyme binding sites". J. Biol. Chem. 267 (1): 150–8. PMID 1730582.
  3. ^ Moore RC, Boyle SM (August 1990). "Nucleotide sequence and analysis of the speA gene encoding biosynthetic arginine decarboxylase in Escherichia coli". J. Bacteriol. 172 (8): 4631–40. PMC 213298. PMID 2198270.
This article incorporates text from the public domain Pfam and InterPro: IPR022643
This article incorporates text from the public domain Pfam and InterPro: IPR022644

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.

Pyridoxal-dependent decarboxylase, pyridoxal binding domain Provide feedback

These pyridoxal-dependent decarboxylases acting on ornithine, lysine, arginine and related substrates This domain has a TIM barrel fold.

Literature references

  1. Kern AD, Oliveira MA, Coffino P, Hackert ML; , Structure Fold Des 1999;7:567-581.: Structure of mammalian ornithine decarboxylase at 1.6 A resolution: stereochemical implications of PLP-dependent amino acid decarboxylases. PUBMED:10378276 EPMC:10378276


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR022644

These enzymes are collectively known as group IV decarboxylases [ PUBMED:8181483 ]. Pyridoxal-dependent decarboxylases acting on ornithine, lysine, arginine and related substrates can be classified into two different families on the basis of sequence similarities [ PUBMED:3143046 , PUBMED:8181483 ]. Members of this family while most probably evolutionary related, do not share extensive regions of sequence similarities. The proteins contain a conserved lysine residue which is known, in mouse ODC [ PUBMED:1730582 ], to be the site of attachment of the pyridoxal-phosphate group. The proteins also contain a stretch of three consecutive glycine residues and has been proposed to be part of a substrate- binding region [ PUBMED:2198270 ].

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

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...

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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
(15)
Full
(18535)
Representative proteomes UniProt
(81931)
RP15
(2523)
RP35
(8496)
RP55
(18172)
RP75
(30565)
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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
(15)
Full
(18535)
Representative proteomes UniProt
(81931)
RP15
(2523)
RP35
(8496)
RP55
(18172)
RP75
(30565)
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
(15)
Full
(18535)
Representative proteomes UniProt
(81931)
RP15
(2523)
RP35
(8496)
RP55
(18172)
RP75
(30565)
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.

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: Prosite
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD , Griffiths-Jones SR
Number in seed: 15
Number in full: 18535
Average length of the domain: 241.80 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 53.40 %

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 23.4 23.4
Trusted cut-off 23.4 23.4
Noise cut-off 23.3 23.3
Model length: 247
Family (HMM) version: 18
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

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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 Orn_Arg_deC_N domain has been found. There are 125 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
A0A0P0W6G1 View 3D Structure Click here
A0A0P0XPU2 View 3D Structure Click here
A0A1D6DQM6 View 3D Structure Click here
A0A1D6F6Q5 View 3D Structure Click here
A0A1D6IA25 View 3D Structure Click here
B4FT32 View 3D Structure Click here
B4G076 View 3D Structure Click here
B7ZYV4 View 3D Structure Click here
C6TA11 View 3D Structure Click here
D4A693 View 3D Structure Click here
E9AGB5 View 3D Structure Click here
F1LVE6 View 3D Structure Click here
F1QZN2 View 3D Structure Click here
I1JSI5 View 3D Structure Click here
I1K723 View 3D Structure Click here
I1LZ51 View 3D Structure Click here
I1NA94 View 3D Structure Click here
K7LHL6 View 3D Structure Click here
K7LHL6 View 3D Structure Click here
K7W734 View 3D Structure Click here
O01579 View 3D Structure Click here
O14977 View 3D Structure Click here
O23141 View 3D Structure Click here
O35484 View 3D Structure Click here
P00860 View 3D Structure Click here
P00861 View 3D Structure Click here
P08432 View 3D Structure Click here
P09057 View 3D Structure Click here
P11926 View 3D Structure Click here
P21170 View 3D Structure Click here
P40807 View 3D Structure Click here
P40808 View 3D Structure Click here
P41931 View 3D Structure Click here
P78599 View 3D Structure Click here
P9WIU7 View 3D Structure Click here
Q2FYN4 View 3D Structure Click here
Q2G1M6 View 3D Structure Click here
Q39827 View 3D Structure Click here
Q3UNZ2 View 3D Structure Click here
Q54UF3 View 3D Structure Click here
Q55CY1 View 3D Structure Click here
Q58497 View 3D Structure Click here
Q63764 View 3D Structure Click here
Q6K2K1 View 3D Structure Click here
Q6ZG77 View 3D Structure Click here
Q70MR5 View 3D Structure Click here
Q70MR6 View 3D Structure Click here
Q75JL7 View 3D Structure Click here
Q7XRA1 View 3D Structure Click here
Q801V3 View 3D Structure Click here
Q8BVM4 View 3D Structure Click here
Q8IJ77 View 3D Structure Click here
Q949X7 View 3D Structure Click here
Q94A94 View 3D Structure Click here
Q96A70 View 3D Structure Click here
Q9DGJ4 View 3D Structure Click here
Q9SI64 View 3D Structure Click here
Q9SNN0 View 3D Structure Click here
Q9UQW9 View 3D Structure Click here