Summary: Orn/Lys/Arg decarboxylase, major domain

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Wikipedia: Group III pyridoxal-dependent decarboxylases
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Group III pyridoxal-dependent decarboxylases Edit Wikipedia article

Orn/Lys/Arg decarboxylase, N-terminal domain

crystallographic structure of a plp-dependent ornithine decarboxylase from lactobacillus 30a to 3.1 angstroms resolution

Identifiers

Symbol

OKR_DC_1_N

Pfam clan

1ord / SCOPe / SUPFAM

Available protein structures:
Pfam Â	structures / ECOD Â
PDB	RCSB PDB; PDBe; PDBj
PDBsum	structure summary

Orn/Lys/Arg decarboxylase, major domain

crystallographic structure of a plp-dependent ornithine decarboxylase from lactobacillus 30a to 3.1 angstroms resolution

Identifiers

Symbol

OKR_DC_1

Pfam clan

1ord / SCOPe / SUPFAM

Available protein structures:
Pfam Â	structures / ECOD Â
PDB	RCSB PDB; PDBe; PDBj
PDBsum	structure summary

Orn/Lys/Arg decarboxylase, C-terminal domain

crystallographic structure of a plp-dependent ornithine decarboxylase from lactobacillus 30a to 3.1 angstroms resolution

Identifiers

Symbol

OKR_DC_1_C

1ord / SCOPe / SUPFAM

Available protein structures:
Pfam Â	structures / ECOD Â
PDB	RCSB PDB; PDBe; PDBj
PDBsum	structure summary

In molecular biology, group III pyridoxal-dependent decarboxylases are a family of bacterial enzymes comprising ornithine decarboxylase EC 4.1.1.17, lysine decarboxylase EC 4.1.1.18 and arginine decarboxylase EC 4.1.1.19.^[1]

Structure

These enzymes consist of several conserved domains. The N-terminal domain has a flavodoxin-like fold, and is termed the "wing" domain because of its position in the overall 3D structure. Ornithine decarboxylase from Lactobacillus 30a (L30a OrnDC) is representative of the large, pyridoxal-5'-phosphate-dependent decarboxylases that act on lysine, arginine or ornithine. The crystal structure of the L30a OrnDC has been solved to 3.0 A resolution. Six dimers related by C6 symmetry compose the enzymatically active dodecamer (approximately 10⁶ Da). Each monomer of L30a OrnDC can be described in terms of five sequential folding domains. The amino-terminal domain, residues 1 to 107, consists of a five-stranded beta-sheet termed the "wing" domain. Two wing domains of each dimer project inward towards the centre of the dodecamer and contribute to dodecamer stabilisation.^[2] The major domain contains a conserved lysine residue, which is the site of attachment of the pyridoxal-phosphate group.^[2]

References

^ Sandmeier E, Hale TI, Christen P (1994). "Multiple evolutionary origin of pyridoxal-5'-phosphate-dependent amino acid decarboxylases". Eur. J. Biochem. 221 (3): 997â€“1002. PMIDÂ 8181483. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
^ ^a ^b Momany C, Ernst S, Ghosh R, Chang NL, Hackert ML (1995). "Crystallographic structure of a PLP-dependent ornithine decarboxylase from Lactobacillus 30a to 3.0 A resolution". J. Mol. Biol. 252 (5): 643â€“55. doi:10.1006/jmbi.1995.0526. PMIDÂ 7563080. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link) Cite error: The named reference "pmid7563080" was defined multiple times with different content (see the help page).

This article incorporates text from the public domain Pfam and InterPro: IPR000310

This article incorporates text from the public domain Pfam and InterPro: IPR005308

This article incorporates text from the public domain Pfam and InterPro: IPR008286

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.

Orn/Lys/Arg decarboxylase, major domain Provide feedback

No Pfam abstract.

Literature references

Momany C, Ernst S, Ghosh R, Chang NL, Hackert ML; , J Mol Biol 1995;252:643-655.: Crystallographic structure of a PLP-dependent ornithine decarboxylase from Lactobacillus 30a to 3.0 A resolution. PUBMED:7563080 EPMC:7563080

Internal database links

SCOOP:	Aminotran_1_2 Aminotran_5 Beta_elim_lyase Cys_Met_Meta_PP DegT_DnrJ_EryC1 GDC-P Pyridoxal_deC SepSecS SHMT
Similarity to PfamA using HHSearch:	Aminotran_1_2 Aminotran_5 Pyridoxal_deC DegT_DnrJ_EryC1 Beta_elim_lyase

External database links

PROSITE:	PDOC00585
SCOP:	1ord

This tab holds annotation information from the InterPro database.

InterPro entry IPR000310

Pyridoxal-dependent decarboxylases are bacterial proteins acting on ornithine, lysine, arginine and related substrates [ PUBMED:8181483 ]. One of the regions of sequence similarity contains a conserved lysine residue, which is the site of attachment of the pyridoxal-phosphate group. Ornithine decarboxylase is a dodecamer composed of six homodimers and catalyzes the decarboxylation of tryptophan. Arginine decarboxylase catalyzes the decarboxylation of arginine and lysine decarboxylase catalyzes the decarboxylation of lysine. Members of this family are widely found in all three forms of life [ PUBMED:8181483 , PUBMED:7663340 , PUBMED:9405048 , PUBMED:9063963 , PUBMED:8112347 , PUBMED:7748903 , PUBMED:10586514 , PUBMED:17504214 , PUBMED:17109392 , PUBMED:10223296 , PUBMED:9914259 , PUBMED:10800595 , PUBMED:11933250 , PUBMED:10673430 ].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Molecular function

catalytic activity (GO:0003824)

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 PLP_aminotran (CL0061), which has the following description:

This superfamily contains a variety of PLP-dependent enzymes.

The clan contains the following 16 members:

Alliinase_C Aminotran_1_2 Aminotran_3 Aminotran_5 Asp_aminotransf Beta_elim_lyase ComK Cys_Met_Meta_PP DegT_DnrJ_EryC1 GDC-P Met_gamma_lyase OKR_DC_1 Pyridoxal_deC SelA SepSecS SHMT

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...

There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.

Alignment types

We make a range of alignments for each Pfam-A family:

seed: the curated alignment from which the HMM for the family is built
full: the alignment generated by searching the sequence database using the HMM
RP15/RP35/RP55/RP75: Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
UniProt: alignment generated by searching the UniProtKB sequence database using the family HMM

Viewing

You can see the alignments as HTML or in three different sequence viewers:

jalview: a Java applet developed at the University of Dundee. You will need Java installed before running jalview
HTML: an HTML page showing the whole alignment.Please note: full Pfam alignments can be very large. These HTML views are extremely large and often cause problems for browsers. Please use either jalview or the Pfam viewer if you have trouble viewing the HTML version
PP/Heatmap: an HTML-based representation of the alignment, coloured according to the posterior-probability (PP) values from the HMM. As for the standard HTML view, heatmap alignments can also be very large and slow to render.

Reformatting

You can download (or view in your browser) a text representation of a Pfam alignment in various formats:

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Stockholm
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You can also change the order in which sequences are listed in the alignment, change how insertions are represented, alter the characters that are used to represent gaps in sequences and, finally, choose whether to download the alignment or to view it in your browser directly.

Downloading

You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.

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 (8)	Full (5324)	Representative proteomes				UniProt (30301)
	Seed (8)	Full (5324)	RP15 (646)	RP35 (2668)	RP55 (5436)	RP75 (10024)	UniProt (30301)
Jalview	View	View	View	View	View	View	View
HTML	View
PP/heatmap	₁

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

Key: available, not generated, — not available.

Format an alignment

	Seed (8)	Full (5324)	Representative proteomes				UniProt (30301)
	Seed (8)	Full (5324)	RP15 (646)	RP35 (2668)	RP55 (5436)	RP75 (10024)	UniProt (30301)
Alignment:
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	Download View

Download options

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 (8)	Full (5324)	Representative proteomes				UniProt (30301)
	Seed (8)	Full (5324)	RP15 (646)	RP35 (2668)	RP55 (5436)	RP75 (10024)	UniProt (30301)
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

Seed source:

Prosite

Previous IDs:

none

Type:

Domain

Sequence Ontology:

SO:0000417

Author:

Finn RD

, Bateman A

, Griffiths-Jones SR

Number in seed:

8

Number in full:

5324

Average length of the domain:

341.3 aa

Average identity of full alignment:

29 %

Average coverage of the sequence by the domain:

61.55 %

HMM information

HMM build commands:

build method: hmmbuild -o /dev/null HMM SEED

search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq

Model details:

Parameter	Sequence	Domain
Gathering cut-off	27.0	27.0
Trusted cut-off	27.0	27.0
Noise cut-off	26.9	26.9

Model length:

417

Family (HMM) version:

23

Download:

download the raw HMM for this family

Species distribution

Sunburst
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Colour assignments

Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Selections

Align selected sequences to HMM

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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...

This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.

How the sunburst is generated

The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.

In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:

superkingdom
kingdom
phylum
class
order
family
genus
species

Colouring and labels

Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.

As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.

Anomalies in the taxonomy tree

There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.

Missing taxonomic levels

Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.

Unmapped species names

The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.

So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".

Sub-species

Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.

Too many species/sequences

For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.

Loading sunburst data...

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The tree shows the occurrence of this domain across different species. More...

Species trees

We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.

Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.

If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.

Interactive tree

For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.

We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.

Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.

We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.

You can use the tree controls to manipulate how the interactive tree is displayed:

show/hide the summary boxes
highlight species that are represented in the seed alignment
expand/collapse the tree or expand it to a given depth
select a sub-tree or a set of species within the tree and view them graphically or as an alignment
save a plain text representation of the tree

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Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

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 OKR_DC_1 domain has been found. There are 117 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.

Loading structure mapping...

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
A0A077ZAX2	View 3D Structure	Click here
A0A077ZE87	View 3D Structure	Click here
A0A077ZMB4	View 3D Structure	Click here
A0A0H3GMX3	View 3D Structure	Click here
A0A0H3GPD9	View 3D Structure	Click here
A0A0H3GYC4	View 3D Structure	Click here
A0A1D6ELE7	View 3D Structure	Click here
A0A1D6ISZ9	View 3D Structure	Click here
A0A1D6LBV0	View 3D Structure	Click here
I1LQA4	View 3D Structure	Click here
I6X4K0	View 3D Structure	Click here
K0F2G7	View 3D Structure	Click here
P0A1Z0	View 3D Structure	Click here
P0A9H3	View 3D Structure	Click here
P0A9H4	View 3D Structure	Click here
P21169	View 3D Structure	Click here
P21885	View 3D Structure	Click here
P24169	View 3D Structure	Click here
P28629	View 3D Structure	Click here
P37536	View 3D Structure	Click here
P44317	View 3D Structure	Click here
P52095	View 3D Structure	Click here
Q2G232	View 3D Structure	Click here
Q329J7	View 3D Structure	Click here
Q32C34	View 3D Structure	Click here
Q819L4	View 3D Structure	Click here
Q81MS2	View 3D Structure	Click here
Q8DQ73	View 3D Structure	Click here
Q8I1X1	View 3D Structure	Click here
Q8ZKE3	View 3D Structure	Click here
Q8ZM37	View 3D Structure	Click here
Q8ZQW6	View 3D Structure	Click here
Q8ZRN7	View 3D Structure	Click here
Q9CCR8	View 3D Structure	Click here
Q9I2S7	View 3D Structure	Click here
Q9I3Z8	View 3D Structure	Click here
Q9K9K5	View 3D Structure	Click here
X8FD45	View 3D Structure	Click here

Showing 38 matches

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Family: OKR_DC_1 (PF01276)

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Summary: Orn/Lys/Arg decarboxylase, major domain

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Group III pyridoxal-dependent decarboxylases Edit Wikipedia article

Structure

References

Orn/Lys/Arg decarboxylase, major domain Provide feedback

Literature references

Internal database links

External database links

InterPro entry IPR000310

Gene Ontology

Domain organisation

Pfam Clan

Alignments

Alignment types

Viewing

Reformatting

Downloading

View options

Format an alignment

Download options

HMM logo

Trees

Curation and family details

Curation

HMM information

Species distribution

Sunburst controls

Weight segments by...

Change the size of the sunburst

Colour assignments

Selections

Currently selected:

How the sunburst is generated

Colouring and labels

Anomalies in the taxonomy tree

Missing taxonomic levels

Unmapped species names

Sub-species

Too many species/sequences

Tree controls

Annotation

Download tree

Selected sequences

Species trees

Interactive tree

Structures

AlphaFold Structure Predictions

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