Summary: Hydrogenase maturation protease
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Hydrogenase maturation protease family Edit Wikipedia article
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|Hydrogenase maturation protease|
hydrogenase maturating endopeptidase hybd from e. coli
The large subunit of [NiFe]-hydrogenase, as well as other nickel metalloenzymes, is synthesized as a precursor devoid of the metalloenzyme active site. This precursor undergoes a complex post-translational maturation process that requires a number of accessory proteins. At one step of this process, after nickel incorporation, each hydrogenase isoenzyme is processed by proteolytic cleavage at the C-terminal end by the corresponding hydrogenase maturation endopeptidase. For example, Escherichia coli HycI is involved in processing of pre-HycE (the large subunit of hydrogenase 3),; HybD is involved in processing of pre-HybC (the large subunit of hydrogenase 2); and HyaD is assumed to be involved in processing of the large subunit of hydrogenase 1.
The cleavage site is after a His or an Arg, liberating a short peptide. This cleavage occurs only in the presence of nickel, and the endopeptidase probably uses the metal in the large subunit of [NiFe]-hydrogenases as a recognition motif. There is no direct evidence for the active site or substrate-binding site, but there are predictions based on an available structure.
Nomenclature note: the following names are used in different organisms for members of this family: HycI, HybD, HyaD, HoxM, HoxW, HupD, HynC, HupM, VhoD, VhtD. Gene/protein names are sometimes used interchangeably to designate various "hydrogenase cluster" proteins unrelated to each other in various organisms. For example, the following names are used for members of this group, but also for unrelated proteins: HupD is used in Azotobacter chroococcum and Anabaena species to designate an unrelated hydrogenase maturation factor; HydD is used to designate hydrogenase structural genes in Thermococcus litoralis, Pyrococcus abyssi, and other species.
- Casalot L, Rousset M (May 2001). "Maturation of the [NiFe] hydrogenases". Trends Microbiol. 9 (5): 228–37. doi:10.1016/S0966-842X(01)02009-1. PMID 11336840.
- Blokesch M, Paschos A, Theodoratou E, Bauer A, Hube M, Huth S, Bock A (August 2002). "Metal insertion into NiFe-hydrogenases". Biochem. Soc. Trans. 30 (4): 674–80. doi:10.1042/bst0300674. PMID 12196162.
- Maroney MJ (April 1999). "Structure/function relationships in nickel metallobiochemistry". Curr Opin Chem Biol. 3 (2): 188–99. doi:10.1016/S1367-5931(99)80032-5. PMID 10226043.
- Theodoratou E, Paschos A, Magalon A, Fritsche E, Huber R, Bock A (April 2000). "Nickel serves as a substrate recognition motif for the endopeptidase involved in hydrogenase maturation". Eur. J. Biochem. 267 (7): 1995–9. doi:10.1046/j.1432-1327.2000.01202.x. PMID 10727938.
- Rossmann R, Sauter M, Lottspeich F, Bock A (March 1994). "Maturation of the large subunit (HYCE) of Escherichia coli hydrogenase 3 requires nickel incorporation followed by C-terminal processing at Arg537". Eur. J. Biochem. 220 (2): 377–84. doi:10.1111/j.1432-1033.1994.tb18634.x. PMID 8125094.
- Theodoratou E, Paschos A, Mintz-Weber, Bock A (February 2000). "Analysis of the cleavage site specificity of the endopeptidase involved in the maturation of the large subunit of hydrogenase 3 from Escherichia coli". Arch. Microbiol. 173 (2): 110–6. doi:10.1007/s002039900116. PMID 10795682.
- Fritsche E, Paschos A, Beisel HG, Bock A, Huber R (May 1999). "Crystal structure of the hydrogenase maturating endopeptidase HYBD from Escherichia coli". J. Mol. Biol. 288 (5): 989–98. doi:10.1006/jmbi.1999.2719. PMID 10331925.
- Menon NK, Robbins J, Der Vartanian M, Patil D, Peck HD, Menon AL, Robson RL, Przybyla AE (September 1993). "Carboxy-terminal processing of the large subunit of [NiFe] hydrogenases". FEBS Lett. 331 (1-2): 91–5. doi:10.1016/0014-5793(93)80303-C. PMID 8405419.
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.
Hydrogenase maturation protease Provide feedback
The family consists of hydrogenase maturation proteases. In E. coli HypI the hydrogenase maturation protease is involved in processing of HypE the large subunit of hydrogenases 3, by cleavage of its C-terminal .
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR000671
This group represents metallopeptidases of the MEROPS peptidase family A31 (HybD endopeptidase family). Peptidase family A31 includes endopeptidases involved in hydrogenase maturation. HycI (hydrogenase 3 maturation protease) is a protease involved in the C-terminal processing of HycE, the large subunit of hydrogenase 3 [PUBMED:8125094, PUBMED:10795682, PUBMED:7851435]. HybD is involved in processing of pre-HybC (the large subunit of hydrogenase 2) [PUBMED:10331925]; and HyaD is assumed to be involved in processing of the large subunit of hydrogenase 1.
The large subunit of [NiFe]-hydrogenase, as well as other nickel metalloenzymes, is synthesized as a precursor devoid of the metalloenzyme active site. This precursor undergoes a complex post-translational maturation process that requires a number of accessory proteins [PUBMED:11336840, PUBMED:12196162, PUBMED:10226043]. At one step of this process, after nickel incorporation, each hydrogenase isoenzyme is processed by proteolytic cleavage at the C-terminal end by the corresponding hydrogenase maturation endopeptidase [PUBMED:10727938]. The cleavage site is after a His or an Arg, liberating a short peptide [PUBMED:8405419, PUBMED:8125094]. This cleavage occurs only in the presence of nickel, and the endopeptidase probably uses the metal in the large subunit of [NiFe]-hydrogenases as a recognition motif [PUBMED:10727938]. There is no direct evidence for the active site or substrate-binding site, but there are predictions based on an available structure [PUBMED:10331925].
Nomenclature note: the following names are used in different organisms for members of this group: HycI, HybD, HyaD, HoxM, HoxW, HupD, HynC, HupM, VhoD, VhtD [PUBMED:11336840]. Gene/protein names are sometimes used interchangeably to designate various "hydrogenase cluster" proteins unrelated to each other in various organisms. For example, the following names are used for members of this group, but also for unrelated proteins: HupD is used in Azotobacter chroococcum and Anabaena species to designate an unrelated hydrogenase maturation factor; HydD is used to designate hydrogenase structural genes in Thermococcus litoralis, Pyrococcus abyssi, and other species.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||peptidase activity (GO:0008233)|
|enzyme activator activity (GO:0008047)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:
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a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
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This clan contains HybD-like domains. HybD is a nickel binding endopeptidase. Structural and sequences analyses have highlighted the presence of two highly conserved motifs that are shared with germination proteases and HybD . Members of this clan adopt an alpha/beta fold, comprised of a central beta sheet, surrounded by alpha helices.
The clan contains the following 3 members:DUF1256 HycI Peptidase_A25
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...
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We make a range of alignments for each Pfam-A family:
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- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the UniProtKB sequence database using the family HMM
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- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
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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.
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
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.
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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.
|Seed source:||Pfam-B_548 (release 4.2)|
|Author:||Bashton M, Bateman A|
|Number in seed:||19|
|Number in full:||1363|
|Average length of the domain:||125.50 aa|
|Average identity of full alignment:||22 %|
|Average coverage of the sequence by the domain:||72.07 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||17|
|Download:||download the raw HMM for this family|
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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 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:
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.
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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".
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.
The tree shows the occurrence of this domain across different species. More...
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.
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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.
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There is 1 interaction for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 HycI domain has been found. There are 11 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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