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56  structures 4927  species 3  interactions 12833  sequences 36  architectures

Family: PGM_PMM_IV (PF00408)

Summary: Phosphoglucomutase/phosphomannomutase, C-terminal domain

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Phosphoglucomutase/phosphomannomutase, C-terminal domain Provide feedback

No Pfam abstract.

Literature references

  1. Dai JB, Liu Y, Ray WJ Jr, Konno M; , J Biol Chem 1992;267:6322-6337.: The crystal structure of muscle phosphoglucomutase refined at 2.7-angstrom resolution. PUBMED:1532581 EPMC:1532581


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR005843

The alpha-D-phosphohexomutase superfamily is composed of four related enzymes, each of which catalyses a phosphoryl transfer on their sugar substrates: phosphoglucomutase (PGM), phosphoglucomutase/phosphomannomutase (PGM/PMM), phosphoglucosamine mutase (PNGM), and phosphoacetylglucosamine mutase (PAGM) [PUBMED:10506283]. PGM (EC) converts D-glucose 1-phosphate into D-glucose 6-phosphate, and participates in both the breakdown and synthesis of glucose [PUBMED:15299905]. PGM/PMM (EC; EC) are primarily bacterial enzymes that use either glucose or mannose as substrate, participating in the biosynthesis of a variety of carbohydrates such as lipopolysaccharides and alginate [PUBMED:16595672, PUBMED:14725765]. Both PNGM (EC) and PAGM (EC) are involved in the biosynthesis of UDP-N-acetylglucosamine [PUBMED:10913078, PUBMED:11004509].

Despite differences in substrate specificity, these enzymes share a similar catalytic mechanism, converting 1-phospho-sugars to 6-phospho-sugars via a biphosphorylated 1,6-phospho-sugar. The active enzyme is phosphorylated at a conserved serine residue and binds one magnesium ion; residues around the active site serine are well conserved among family members. The reaction mechanism involves phosphoryl transfer from the phosphoserine to the substrate to create a biophosphorylated sugar, followed by a phosphoryl transfer from the substrate back to the enzyme [PUBMED:15238632].

The structures of PGM and PGM/PMM have been determined, and were found to be very similar in topology. These enzymes are both composed of four domains and a large central active site cleft, where each domain contains residues essential for catalysis and/or substrate recognition. Domain I contains the catalytic phosphoserine, domain II contains a metal-binding loop to coordinate the magnesium ion, domain III contains the sugar-binding loop that recognises the two different binding orientations of the 1- and 6-phospho-sugars, and domain IV contains a phosphate-binding site required for orienting the incoming phospho-sugar substrate.

This entry represents the C-terminal domain alpha-D-phosphohexomutase enzymes.

Gene Ontology

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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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics 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
(112)
Full
(12833)
Representative proteomes NCBI
(9608)
Meta
(4242)
RP15
(1056)
RP35
(2051)
RP55
(2778)
RP75
(3279)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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Format an alignment

  Seed
(112)
Full
(12833)
Representative proteomes NCBI
(9608)
Meta
(4242)
RP15
(1056)
RP35
(2051)
RP55
(2778)
RP75
(3279)
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
(112)
Full
(12833)
Representative proteomes NCBI
(9608)
Meta
(4242)
RP15
(1056)
RP35
(2051)
RP55
(2778)
RP75
(3279)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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: PGM_PMM;
Type: Family
Author: Bateman A, Finn RD, Griffiths-Jones SR
Number in seed: 112
Number in full: 12833
Average length of the domain: 81.50 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 16.51 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 23.1 23.1
Trusted cut-off 23.1 23.1
Noise cut-off 23.0 23.0
Model length: 73
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

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Interactions

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

PGM_PMM_II PGM_PMM_I PGM_PMM_III

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 PGM_PMM_IV domain has been found. There are 56 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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