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94  structures 6011  species 0  interactions 10873  sequences 80  architectures

Family: Metalloenzyme (PF01676)

Summary: Metalloenzyme superfamily

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

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.

Metalloenzyme superfamily Provide feedback

This family includes phosphopentomutase P07651 and 2,3-bisphosphoglycerate-independent phosphoglycerate mutase, P37689. This family is also related to PF00245 [1]. The alignment contains the most conserved residues that are probably involved in metal binding and catalysis.

Literature references

  1. Galperin MY, Bairoch A, Koonin EV; , Protein Sci 1998;7:1829-1835.: A superfamily of metalloenzymes unifies phosphopentomutase and cofactor- independent phosphoglycerate mutase with alkaline phosphatases and sulfatases. PUBMED:10082381 EPMC:10082381


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006124

This domain unites alkaline phosphatase, N-acetylgalactosamine-4-sulphatase, and cerebroside sulphatase, enzymes with known three-dimensional structures, with phosphopentomutase, 2,3-bisphosphoglycerate-independent phosphoglycerate mutase, phosphoglycerol transferase, phosphonate monoesterase, streptomycin-6-phosphate phosphatase, alkaline phosphodiesterase/nucleotide pyrophosphatase PC-1, and several closely related sulphatases. This domain is also related to alkaline phosphatase INTERPRO [ PUBMED:10082381 ]. The most conserved residues are probably involved in metal binding and catalysis.

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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Pfam Clan

This family is a member of clan Alk_phosphatase (CL0088), which has the following description:

The members of this clan all share a common structure of their catalytic domains, which contain conserved metal binding residues [1].

The clan contains the following 10 members:

Alk_phosphatase DUF1501 DUF229 DUF4976 Metalloenzyme PglZ Phosphodiest Phosphoesterase Sulfatase Sulfatase_C

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...

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
(28)
Full
(10873)
Representative proteomes UniProt
(54941)
RP15
(1931)
RP35
(5956)
RP55
(10848)
RP75
(17421)
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, x not generated, not available.

Format an alignment

  Seed
(28)
Full
(10873)
Representative proteomes UniProt
(54941)
RP15
(1931)
RP35
(5956)
RP55
(10848)
RP75
(17421)
Alignment:
Format:
Order:
Sequence:
Gaps:
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
(28)
Full
(10873)
Representative proteomes UniProt
(54941)
RP15
(1931)
RP35
(5956)
RP55
(10848)
RP75
(17421)
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: Pfam-B_1926 (release 4.1)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Bateman A
Number in seed: 28
Number in full: 10873
Average length of the domain: 429.20 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 93.59 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null --hand HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 24.3 24.3
Trusted cut-off 24.3 24.3
Noise cut-off 24.2 24.2
Model length: 248
Family (HMM) version: 21
Download: download the raw HMM for this family

Species distribution

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Selections

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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 Metalloenzyme domain has been found. There are 94 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
A0A0R0F2Z4 View 3D Structure Click here
A0A1D6DVL7 View 3D Structure Click here
A0A1D6G993 View 3D Structure Click here
A0A1D6K1T6 View 3D Structure Click here
A0A1D6MXQ4 View 3D Structure Click here
A0A1D6N8I0 View 3D Structure Click here
A0B6L2 View 3D Structure Click here
A0KPE2 View 3D Structure Click here
A0LDF3 View 3D Structure Click here
A0PYP3 View 3D Structure Click here
A0PYX6 View 3D Structure Click here
A1AXW7 View 3D Structure Click here
A1B4Z9 View 3D Structure Click here
A1S1L6 View 3D Structure Click here
A1S476 View 3D Structure Click here
A1SYK3 View 3D Structure Click here
A1SZI3 View 3D Structure Click here
A2SR62 View 3D Structure Click here
A3CNA8 View 3D Structure Click here
A3DBQ2 View 3D Structure Click here
A3DD83 View 3D Structure Click here
A3QGT1 View 3D Structure Click here
A3QJM4 View 3D Structure Click here
A4I3V2 View 3D Structure Click here
A4VWC5 View 3D Structure Click here
A4Y077 View 3D Structure Click here
A4YIX4 View 3D Structure Click here
A4YPV1 View 3D Structure Click here
A5N2N6 View 3D Structure Click here
A5N7K3 View 3D Structure Click here
A5VHR0 View 3D Structure Click here
A6H1H2 View 3D Structure Click here
A6L050 View 3D Structure Click here
A6LFB1 View 3D Structure Click here
A6TR59 View 3D Structure Click here
A6UTF2 View 3D Structure Click here
A6VM02 View 3D Structure Click here
A7H8W4 View 3D Structure Click here
A8AC98 View 3D Structure Click here
A8AXN8 View 3D Structure Click here