Phosphatase Subfamily MTMR5

Phosphatase Classification: Fold CC1: Superfamily CC1: Family Myotubularin: Subfamily MTMR5 (SBF)

MTMR5 is an inactive phosphatase (pseudophosphatase), which regulates the active phosphatase MTMR2.

Evolution

MTMR5 is found throughout metazoa. It has two human members, MTMR5 (SBF1) and MTMR13 (SBF2), and single members in Drosophila (Sbf) and C. elegans (mtm-5).

Domain structure

The MTMR5s of most metazoa except chordates have a domain combination of DENN, GRAM, phosphatase, coiled coil, C1 and PH. Vertebrate MTMR5s lost C1 domain (see technical notes below).

The DENN domain interacts with Rab family small GTPases and functions enzymatically as a Rab-specific guanine nucleotide exchange factor (GEF). Human MTMR5 and MTMR13 have GEF activity toward Rab28, a poorly characterized and divergent member of the Rab superfamily [1]. Drosophila Sbf regulates Rab21, which specifies an endosomal pathway and cortical control.

A coiled-coil domain mediates the interactions of MTMR5 and MTMR13 with MTMR2, which results in the increase of enzymatic activity of MTMR2 [2, 3].

Catalytic activity and functions

All MTMR5 members are predicted to be catalytically inactive pseudophosphatases. Human MTMR5 interacts with MTMR2 (see MTMR1 subfamily) via its coiled-coil domain and mutations in the coiled-coil domain of either MTMR2 or MTMR5 abrogate this interaction. Through this interaction, MTMR5 increases the enzymatic activity of MTMR2 and dictates its subcellular localization [2]. This is a good example of inactive phosphatase functions as regulator of active phosphatase.

The interaction between MTMR5 and MTMR1 subfamilies is also observed in Drosophila. In addition, fruit fly Sbf has been reported as a critical coordinator of PI(3)P and Rab21 regulation, which specifies an endosomal pathway and cortical control [4],.

Diseases

Mice deficient for MTMR5 exhibit male infertility characterized by azoospermia [5].

Charcot-Marie-Tooth disease type 4B (CMT4B) is a severe, demyelinating peripheral neuropathy caused by mutations in either MTMR13, MTMR5 or their binding partner, MTMR2 [3, 6, 7, 8]. In addition, loss of Mtmr13 in mice leads to a peripheral neuropathy with many of the key features of CMT4B.

References

1. Yoshimura S, Gerondopoulos A, Linford A, Rigden DJ, and Barr FA. Family-wide characterization of the DENN domain Rab GDP-GTP exchange factors. J Cell Biol. 2010 Oct 18;191(2):367-81. DOI:10.1083/jcb.201008051 |
2. Kim SA, Vacratsis PO, Firestein R, Cleary ML, and Dixon JE. Regulation of myotubularin-related (MTMR)2 phosphatidylinositol phosphatase by MTMR5, a catalytically inactive phosphatase. Proc Natl Acad Sci U S A. 2003 Apr 15;100(8):4492-7. DOI:10.1073/pnas.0431052100 |
3. Robinson FL and Dixon JE. The phosphoinositide-3-phosphatase MTMR2 associates with MTMR13, a membrane-associated pseudophosphatase also mutated in type 4B Charcot-Marie-Tooth disease. J Biol Chem. 2005 Sep 9;280(36):31699-707. DOI:10.1074/jbc.M505159200 |
4. Jean S, Cox S, Schmidt EJ, Robinson FL, and Kiger A. Sbf/MTMR13 coordinates PI(3)P and Rab21 regulation in endocytic control of cellular remodeling. Mol Biol Cell. 2012 Jul;23(14):2723-40. DOI:10.1091/mbc.E12-05-0375 |
5. Firestein R, Nagy PL, Daly M, Huie P, Conti M, and Cleary ML. Male infertility, impaired spermatogenesis, and azoospermia in mice deficient for the pseudophosphatase Sbf1. J Clin Invest. 2002 May;109(9):1165-72. DOI:10.1172/JCI12589 |
6. Chen M, Wu J, Liang N, Tang L, Chen Y, Chen H, Wei W, Wei T, Huang H, Yi X, and Qi M. Identification of a novel SBF2 frameshift mutation in charcot-marie-tooth disease type 4B2 using whole-exome sequencing. Genomics Proteomics Bioinformatics. 2014 Oct;12(5):221-7. DOI:10.1016/j.gpb.2014.09.003 |
7. Robinson FL, Niesman IR, Beiswenger KK, and Dixon JE. Loss of the inactive myotubularin-related phosphatase Mtmr13 leads to a Charcot-Marie-Tooth 4B2-like peripheral neuropathy in mice. Proc Natl Acad Sci U S A. 2008 Mar 25;105(12):4916-21. DOI:10.1073/pnas.0800742105 |
8. Nakhro K, Park JM, Hong YB, Park JH, Nam SH, Yoon BR, Yoo JH, Koo H, Jung SC, Kim HL, Kim JY, Choi KG, Choi BO, and Chung KW. SET binding factor 1 (SBF1) mutation causes Charcot-Marie-Tooth disease type 4B3. Neurology. 2013 Jul 9;81(2):165-73. DOI:10.1212/WNL.0b013e31829a3421 |

Technical notes

C1 domain lost in vertebrates

We noticed that sea urchin, Drosophila melanogaster, C. elegans, and sponge have a C1 domain adjacent to C-terminal PH domain. To study the presence and absence of C1 domain in MTMR5 subfamily, we carried out the following analyses:

1. We searched the presence of C1 domain in MTMR5 orthologs in internal orthology database. The C1 domain is present in most metazoa except vertebrates. Among three chordates in internal orthology database, lancet has the typical domain combination, but the two Ciona genomes do not contain the C1 domain. Nematostella has a very weak-scoring PH domain due to poor gene prediction - the homologous sequence from the Cnidarian Exaiptasia pallida (gb|KXJ12124.1|) fills in a gap in the gene model and encodes a strong C1 domain, indicating that it is also present in Nematostella
2. We searched the C1 domain against protein NR dataset of human and vertebrates. We obtained the C1 domain sequence from D. melanogaster based upon its alignment to Pfam C1_1 domain (see below). Then, BLAST the sequence against human protein NR dataset. The best hit is from PKC, followed by the hits from other proteins involved in cell signaling. But, neither human MTMR5 or MTMR13 is among the hits (E-value threshold e^-5. We then searched against chordates NR dataset, and did not find MTMR5 and MTMR13, either.
3. We then searched the full sequence of C1-containing MTMR5, the Drosophila melanogaster Sbf against protein NR dataset against vertebrates, and then investigated the conserved domain among the top hits. We did not find C1 domain among the top hits in chordates. We looked into the region of C1 domain in the alignment. We found it is either badly aligned with many gaps and very low number of identical residues, or did not align at all.

Here is the sequence of C1 domain of Drosophila melanogaster:

HRFEKHPYTTPTNCNHCTKLLWGPVGYRCMDCGNSYHEKCTEHSMKNCT