Phosphatase Subfamily MTMR5 - Revision history

Gerard at 18:25, 14 March 2017

2017-03-14T18:25:08Z

Gerard at 18:20, 14 March 2017

2017-03-14T18:20:51Z

Gerard at 06:00, 9 March 2016

2016-03-09T06:00:38Z

Gerard at 05:46, 9 March 2016

2016-03-09T05:46:20Z

Gerard: /* C1 domain lost in vertebrates */

2015-10-21T00:28:29Z

‎C1 domain lost in vertebrates

Mark at 05:37, 2 October 2015

2015-10-02T05:37:51Z

Mark: /* C1 domain lost in vertebrates */

2015-06-25T19:55:48Z

‎C1 domain lost in vertebrates

Mark at 17:57, 25 June 2015

2015-06-25T17:57:21Z

Mark: /* C1 domain lost in chordates */

2015-06-25T17:56:21Z

‎C1 domain lost in chordates

Mark: /* C1 domain lost in chordates */

2015-06-25T17:42:20Z

‎C1 domain lost in chordates

@@ Line 8: / Line 8: @@
 ===Domain structure===
-The MTMR5s of most metazoa except chordates have a domain combination of DENN, GRAM, phosphatase, coiled coil, [[Protein_Domain#C1|C1 domain]] and PH. Vertebrate MTMR5s lost C1 domain (see technical notes below).
+The MTMR5s of most metazoa except chordates have a domain combination of DENN, GRAM, phosphatase, coiled coil, [[Protein_Domain#C1|C1]] and PH. Vertebrate MTMR5s lost C1 domain (see technical notes below).
-The DENN domain interacts directly with members of the Rab family of 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 distant member of the Rab superfamily <cite>yashimura10</cite>. Drosophila Sbf regulates Rab21, which specifies an endosomal pathway and cortical control.
+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 <cite>yashimura10</cite>. 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 <cite>kim03, robinson05</cite>.
@@ Line 17: / Line 17: @@
 All MTMR5 members are predicted to be catalytically inactive [[pseudophosphatase]]s. Human MTMR5 interacts with MTMR2 (see [[Phosphatase_Subfamily_MTMR1|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 <cite>kim03</cite>. 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, which indicates the conservation of the this regulatory mechanism. 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 <cite>jean12</cite>,.
+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 <cite>jean12</cite>,.
 ===Diseases===

@@ Line 39: / Line 39: @@
 ===== 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:
-# We searched the presence of C1 domain in MTMR5 orthologs in [http://resdev.gene.com/gOrtholog/view/cluster/MC0003324/sequence/fasta 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 does not have C1 domain, either.
+# We searched the presence of C1 domain in MTMR5 orthologs in [http://resdev.gene.com/gOrtholog/view/cluster/MC0003324/sequence/fasta 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
 # 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<sup>-5</sup>. We then searched against chordates NR dataset, and did not find MTMR5 and MTMR13, either.
 # 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.

@@ Line 1: / Line 1: @@
 [[Phosphatase classification|Phosphatase Classification]]: [[Phosphatase_Fold_CC1|Fold CC1]]: [[Phosphatase_Superfamily_CC1|Superfamily CC1]]:  [[Phosphatase_Family_Myotubularin|Family Myotubularin]]: [[Phosphatase_Subfamily_MTMR5|Subfamily MTMR5]] (SBF)
@@ Line 4: / Line 5: @@
 ===Evolution===
-MTMR5 subfamily is found throughout metazoa. It consists of two members in human, MTMR5 and MTMR13, also called SBF1 and SBF2, respectively. In Drosophila and C. elegans, a single copy is found.
+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===
@@ Line 16: / Line 17: @@
 All MTMR5 members are predicted to be catalytically inactive [[pseudophosphatase]]s. Human MTMR5 interacts with MTMR2 (see [[Phosphatase_Subfamily_MTMR1|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 <cite>kim03</cite>. This is a good example of inactive phosphatase functions as regulator of active phosphatase.
-The interaction between MTMR5 subfamily and MTMR1 subfamily is also observed in fruit fly, which indicates the conservation of the this regulatory mechanism. 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 <cite>jean12</cite>,.
+The interaction between MTMR5 and MTMR1 subfamilies is also observed in Drosophila, which indicates the conservation of the this regulatory mechanism. 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 <cite>jean12</cite>,.
 ===Diseases===
 Mice deficient for MTMR5 exhibit male infertility characterized by azoospermia <cite>firestein02</cite>.
-Deleterious mutations in human MTMR13 (SBF2) causes Charcot-Marie-Tooth disease type 4B (CMT4B),  which is a severe, demyelinating peripheral neuropathy characterized by slowed nerve conduction velocity, axon loss, and distinctive myelin outfolding and infolding <cite>Chen14</cite>. In addition, loss of Mtmr13 in mice leads to a peripheral neuropathy with many of the key features of CMT4B. It worthy pointing out that recessive mutations in either MTMR2 or MTMR13 lead to nearly indistinguishable forms of CMT4B <cite>robinson08</cite>. MTMR5 mutations cause CMT4B, as well <cite>nakhro13</cite>.
+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   <cite>Chen14, robinson05, robinson08, nakhro13</cite>. In addition, loss of Mtmr13 in mice leads to a peripheral neuropathy with many of the key features of CMT4B.
 ===References===

@@ Line 1: / Line 1: @@
 [[Phosphatase classification|Phosphatase Classification]]: [[Phosphatase_Fold_CC1|Fold CC1]]: [[Phosphatase_Superfamily_CC1|Superfamily CC1]]:  [[Phosphatase_Family_Myotubularin|Family Myotubularin]]: [[Phosphatase_Subfamily_MTMR5|Subfamily MTMR5]] (SBF)
-MTMR5 subfamily is an inactive phosphatase (pseudophosphatase), which major function is regulating active phosphatase MTMR2 via interactions.
+MTMR5 is an inactive phosphatase (pseudophosphatase), which regulates the active phosphatase MTMR2.
 ===Evolution===
-MTMR5 subfamily is found throughout metazoan. It consists of two members in human, MTMR5 and MTMR13, also called SBF1 and SBF2, respectively. In fruit fly and C elegans, a single copy is found.
+MTMR5 subfamily is found throughout metazoa. It consists of two members in human, MTMR5 and MTMR13, also called SBF1 and SBF2, respectively. In Drosophila and C. elegans, a single copy is found.
 ===Domain structure===
 The MTMR5s of most metazoa except chordates have a domain combination of DENN, GRAM, phosphatase, coiled coil, [[Protein_Domain#C1|C1 domain]] and PH. Vertebrate MTMR5s lost C1 domain (see technical notes below).
-The DENN domain of the MTMR5 subfamily interacts directly with members of the Rab family of small GTPases and functions enzymatically as Rab-specific guanine nucleotide exchange factors.  Human MTMR5 and MTMR13 have GEF activity toward Rab28, a poorly characterized and distant member of the Rab superfamily <cite>yashimura10</cite>. Fruit fly Sbf regulates Rab21, which specifies an endosomal pathway and cortical control.
+The DENN domain interacts directly with members of the Rab family of 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 distant member of the Rab superfamily <cite>yashimura10</cite>. Drosophila Sbf regulates Rab21, which specifies an endosomal pathway and cortical control.
-Coiled-coil domain mediates the interactions of MTMR5 and MTMR13 with MTMR2, which results in the increase of enzymatic activity of MTMR2 <cite>kim03, robinson05</cite>.
+A coiled-coil domain mediates the interactions of MTMR5 and MTMR13 with MTMR2, which results in the increase of enzymatic activity of MTMR2 <cite>kim03, robinson05</cite>.
 ===Catalytic activity and functions===
-MTMR5 subfamily is conservatively inactive in metazoan.
+All MTMR5 members are predicted to be catalytically inactive [[pseudophosphatase]]s. Human MTMR5 interacts with MTMR2 (see [[Phosphatase_Subfamily_MTMR1|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 <cite>kim03</cite>. This is a good example of inactive phosphatase functions as regulator of active phosphatase.
-−
 Human MTMR5 interacts with MTMR2 (see [[Phosphatase_Subfamily_MTMR1|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 <cite>kim03</cite>. This is a good example of inactive phosphatase functions as regulator of active phosphatase.
 The interaction between MTMR5 subfamily and MTMR1 subfamily is also observed in fruit fly, which indicates the conservation of the this regulatory mechanism. 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 <cite>jean12</cite>,.

@@ Line 39: / Line 39: @@
 === Technical notes ===
 ===== C1 domain lost in vertebrates =====
-We noticed sea urchin, Drosophila melanogaster, C. elegans, and sponge has 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:
+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:
-# We searched the presence of C1 domain in MTMR5 orthologs in [http://resdev.gene.com/gOrtholog/view/cluster/MC0003324/sequence/fasta 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 two ciona genomes do not C1 domain. Nematostella does not have C1 domain, either.
+# We searched the presence of C1 domain in MTMR5 orthologs in [http://resdev.gene.com/gOrtholog/view/cluster/MC0003324/sequence/fasta 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 does not have C1 domain, either.
 # 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<sup>-5</sup>. We then searched against chordates NR dataset, and did not find MTMR5 and MTMR13, either.
 # 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.

@@ Line 40: / Line 40: @@
 === Technical notes ===
-===== C1 domain lost in chordates =====
+===== C1 domain lost in vertebrates =====
 We noticed sea urchin, Drosophila melanogaster, C. elegans, and sponge has 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:
-# We first searched the C1 domain against protein NR dataset of human and chordates. 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<sup>-5</sup>. We then searched against chordates NR dataset, and did not find MTMR5 and MTMR13, either.
+# We first 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<sup>-5</sup>. We then searched against chordates NR dataset, and did not find MTMR5 and MTMR13, either.
-# We then searched the full sequence of C1-containing MTMR5, the Drosophila melanogaster Sbf against protein NR dataset against chordates, 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.
+# 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