Summary: Creatinase/Prolidase N-terminal domain

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Creatinase Edit Wikipedia article

creatinase

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Creatinase/Prolidase N-terminal domain

The Crystal Structure of the Creatinase/Prolidase N-terminal domain of an X-PRO dipeptidase from Streptococcus pyogenes to 1.85A ^[1]

Identifiers

Symbol

Creatinase_N

1chm / SUPFAM

Available protein structures:
Pfam	structures / ECOD
PDB	RCSB PDB; PDBe; PDBj
PDBsum	structure summary
PDB	1wn1B:2-131 1chmA:27-158 1kp0B:27-157 1pv9B:4-124 1wy2B:7-127

In enzymology, a creatinase (EC 3.5.3.3) is an enzyme that catalyzes the chemical reaction

creatine + H₂O

\rightleftharpoons

sarcosine + urea

Thus, the two substrates of this enzyme are creatine and H₂O, whereas its two products are sarcosine and urea.

The native enzyme was shown to be made up of two subunit monomers via SDS-polyacrylamide gel electrophoresis. The molecular weights of these subunits was estimated to be 47,000 g/mol.^[2] The enzyme works as a homodimer, and is induced by choline chloride. Each monomer of creatinase has two clearly defined domains, a small N-terminal domain, and a large C-terminal domain. Each of the two active sites is made by residues of the large domain of one monomer and some residues of the small domain of the other monomer. It has been suggested that a sulfhydryl group is located on or near the active site of the enzyme following inhibition experiments.^[2] Creatinase has been found to be most active at pH 8 and is most stable between ph 6-8 for 24 hrs. at 37 degrees.^[2]

This enzyme belongs to the family of hydrolases, those acting on carbon-nitrogen bonds other than peptide bonds, specifically in linear amidines. The systematic name of this enzyme class is creatine amidinohydrolase. This enzyme participates in arginine and proline metabolism.

Structural studies

As of late 2007, two structures have been solved for this class of enzymes, with PDB accession codes 1CHM and 1KP0.

References

"RCSB Protein Data Bank - Structure Summary for 3O5V - The Crystal Structure of the Creatinase/Prolidase N-terminal domain of an X-PRO dipeptidase from Streptococcus pyogenes to 1.85A".

^ "RCSB Protein Data Bank - Structure Summary for 3O5V - The Crystal Structure of the Creatinase/Prolidase N-terminal domain of an X-PRO dipeptidase from Streptococcus pyogenes to 1.85A".
^ ^a ^b ^c Yoshimoto T, Oka I, Tsuru D (June 1976). "Purification, crystallization, and some properties of creatine amidinohydrolase from Pseudomonas putida". J. Biochem. 79 (6): 1381â€“3. PMID 8443.

ROCHE J, LACOMBE G, GIRARD H (1950). "[On the specificity of certain bacterial deguanidases generating urea and on arginindihydrolase.]". Biochim. Biophys. Acta. 6 (1): 210â€“6. doi:10.1016/0006-3002(50)90093-x. PMID 14791411.

v t e Hydrolases: carbon-nitrogen non-peptide (EC 3.5)
3.5.1: Linear amides / Amidohydrolases	Asparaginase Glutaminase Urease Biotinidase Aspartoacylase Ceramidase Aspartylglucosaminidase Fatty acid amide hydrolase Histone deacetylase Sirtuin
3.5.2: Cyclic amides/ Amidohydrolases	Barbiturase Beta-lactamase Dihydroorotase
3.5.3: Linear amidines/ Ureohydrolases	Arginase Agmatinase Protein-arginine deiminase
3.5.4: Cyclic amidines/ Aminohydrolases	Guanine deaminase Adenosine deaminase AMP deaminase Inosine monophosphate synthase DCMP deaminase GTP cyclohydrolase I Cytidine deaminase AICDA Activation-induced cytidine deaminase
3.5.5: Nitriles/ Aminohydrolases	Nitrilase
3.5.99: Other	Riboflavinase Thiaminase II

v t e Enzymes
Activity	Active site Binding site Catalytic triad Oxyanion hole Enzyme promiscuity Catalytically perfect enzyme Coenzyme Cofactor Enzyme catalysis
Regulation	Allosteric regulation Cooperativity Enzyme inhibitor Enzyme activator
Classification	EC number Enzyme superfamily Enzyme family List of enzymes
Kinetics	Enzyme kinetics Eadieâ€“Hofstee diagram Hanesâ€“Woolf plot Lineweaverâ€“Burk plot Michaelisâ€“Menten kinetics
Types	EC1 Oxidoreductases (list) EC2 Transferases (list) EC3 Hydrolases (list) EC4 Lyases (list) EC5 Isomerases (list) EC6 Ligases (list) EC7 Translocases (list)

This EC 3.5 enzyme-related article is a stub. You can help Wikipedia by expanding it.

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.

Creatinase/Prolidase N-terminal domain Provide feedback

This family includes the N-terminal non-catalytic domains from creatinase and prolidase. The exact function of this domain is uncertain.

Literature references

Coll M, Knof SH, Ohga Y, Messerschmidt A, Huber R, Moellering H, Russmann L, Schumacher G; , J Mol Biol 1990;214:597-610.: Enzymatic mechanism of creatine amidinohydrolase as deduced from crystal structures. PUBMED:1696320 EPMC:1696320
Maher MJ, Ghosh M, Grunden AM, Menon AL, Adams MW, Freeman HC, Guss JM; , Biochemistry. 2004;43:2771-2783.: Structure of the prolidase from Pyrococcus furiosus. PUBMED:15005612 EPMC:15005612

Internal database links

SCOOP:	AMP_N Creatinase_N_2
Similarity to PfamA using HHSearch:	Creatinase_N_2

External database links

SCOP:

1chm

This tab holds annotation information from the InterPro database.

InterPro entry IPR000587

Creatinase or creatine amidinohydrolase (EC) catalyses the conversion of creatine and water to sarcosine and urea. The enzyme works as a homodimer, and is induced by choline chloride. Each monomer of creatinase has two clearly defined domains, a small N-terminal domain, and a large C-terminal domain.

The structure of the C-terminal region represents the "pita-bread" fold. The fold contains both alpha helices and an anti-parallel beta sheet within two structurally similar domains that are thought to be derived from an ancient gene duplication. The active site, where conserved, is located between the two domains. The fold is common to methionine aminopeptidase (EC), aminopeptidase P (EC), prolidase (EC), agropine synthase and creatinase (EC). Though many of these peptidases require a divalent cation, creatinase is not a metal-dependent enzyme [PUBMED:8146141, PUBMED:12136144, PUBMED:8471602].

Gene Ontology

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

Molecular function

hydrolase activity (GO:0016787)

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 AMP_N-like (CL0356), which has the following description:

Bacterial amino-peptidases and creatinases, where the fold is a ribonuclease H-like motif, are grouped in this superfamily.

The clan contains the following 4 members:

AMP_N Creatinase_N Creatinase_N_2 FACT-Spt16_Nlob

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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics 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
NCBI: alignment generated by searching the NCBI sequence database using the family HMM
meta: alignment generated by searching the metagenomics 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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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 (91)	Full (13257)	Representative proteomes				UniProt (58494)	NCBI (84338)	Meta (3532)
	Seed (91)	Full (13257)	RP15 (1603)	RP35 (6055)	RP55 (12736)	RP75 (21806)	UniProt (58494)	NCBI (84338)	Meta (3532)
Jalview	View	View	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 (91)	Full (13257)	Representative proteomes				UniProt (58494)	NCBI (84338)	Meta (3532)
	Seed (91)	Full (13257)	RP15 (1603)	RP35 (6055)	RP55 (12736)	RP75 (21806)	UniProt (58494)	NCBI (84338)	Meta (3532)
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 (91)	Full (13257)	Representative proteomes				UniProt (58494)	NCBI (84338)	Meta (3532)
	Seed (91)	Full (13257)	RP15 (1603)	RP35 (6055)	RP55 (12736)	RP75 (21806)	UniProt (58494)	NCBI (84338)	Meta (3532)
Raw Stockholm	Download	Download	Download	Download	Download	Download	Download	Download	Download
Gzipped	Download	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.

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:

Bateman A

Previous IDs:

none

Type:

Domain

Sequence Ontology:

SO:0000417

Author:

Finn RD

, Bateman A

Number in seed:

91

Number in full:

13257

Average length of the domain:

135.90 aa

Average identity of full alignment:

18 %

Average coverage of the sequence by the domain:

29.34 %

HMM information

HMM build commands:

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

search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq

Model details:

Parameter	Sequence	Domain
Gathering cut-off	22.0	22.0
Trusted cut-off	22.0	22.0
Noise cut-off	21.9	21.9

Model length:

131

Family (HMM) version:

19

Download:

download the raw HMM for this family

Species distribution

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Archea	Eukaryota
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Viroids	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...

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.

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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
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Interactions

There are 3 interactions for this family. More...

Creatinase_N Peptidase_M24 Peptidase_M24

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 Creatinase_N domain has been found. There are 71 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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Family: Creatinase_N (PF01321)

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Summary: Creatinase/Prolidase N-terminal domain

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Creatinase Edit Wikipedia article

Structural studies

References

Creatinase/Prolidase N-terminal domain Provide feedback

Literature references

Internal database links

External database links

InterPro entry IPR000587

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

Interactions

Structures

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