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This is an extracellular cadherin (EC) domain which can be found at the N-terminal region of Protocadherin 15 (Pcdh15). Pcdh15 features exceptionally long extracellular domains containing 11 ECs . These repeats are structurally similar, but not identical in sequence, often featuring linkers with conserved calcium-binding sites that confer mechanical strength to them .

Biological Magnetic Resonance Bank Entry 15166: Pac1-Rshort N-terminal EC domain Pacap(6-38) complex

SMOC-2, also termed SPARC-related modular calcium-binding protein 2, or smooth muscle-associated protein 2 (SMAP-2), is a ubiquitously expressed matricellular protein that enhances the response to angiogenic growth factors, mediate cell adhesion, keratinocyte migration, and metastasis. It is also associated with vitiligo and craniofacial and dental defects. Moreover, SMOC-2 acts as an Arf1 GTPase-activating protein (GAP) that interacts with clathrin heavy chain (CHC) and clathrin assembly protein CALM and functions in the retrograde, early endosome/trans-Golgi network (TGN) pathway in a clathrin- and AP-1-dependent manner. It also contributes to mitogenesis via activation of integrin-linked kinase (ILK). SMOC-2 contains a follistatin-like (FS) domain, two thyroglobulin-like (TY) domains, a novel domain, which is found only in the homologous SMOC-1, and an extracellular calcium-binding (EC) domain with two EF-hand calcium-binding motifs.

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Most mRNAs undergo a chemical modification called capping resulting in a capat the 5' end of the newly transcribed mRNA. The 5' cap 0 structure consistsof a guanine nucleotide methylated at position 7 connected to the mRNA'sinitiating nucleoside via an inverted 5'-5' triphosphate linkage. Afterformation of the 5' cap 0, the mRNA's first base usually goes through amethylation on the 2'-O position of its ribose resulting in the 5' cap 1structure. Further methylations can occur on the first and second nucleotidesleading to the 5' cap 2 structure .The 5' cap structure is essential as it protects mRNA by preventingdegradation by 5' exoribonucleases and it also promotes translation .Before capping, the precursor (pre-) mRNA has three phosphate groups linked tothe 5'carbon of its first nucleoside. Capping (here: formation of the 5' cap 0structure only) calls for three consecutive reactions on the nascent pre-mRNA:1. Removal by hydrolysis of the pre-mRNA's gamma-phosphate by RNA 5'triphosphatase (EC 3.1.3.33) [E1].2. Addition of GMP from GTP to the 5' diphosphate RNA by RNAguanylyltransferase (EC 2.7.7.50) [E2].3. Methylation of the 5' GpppN by a cap-specific RNA (guanine-N7)methyltransferase (EC 2.1.1.56) [E3]. The enzyme uses S-adenosylmethionine(AdoMet or SAM) as the methyl donor and leads to the formation of them7GpppRNA structure (the 5' cap) and S-adenosylhomocysteine (AdoHcy) .As the capping apparatus, formed by the protein(s) carrying out the threecapping reactions, is specifically targeted to RNA polymerase II transcripts,capping concerns most eukaryotic cellular and viral eukaryotic mRNAs. Althoughthe capping apparatus is functionally conserved in eukaryotes, it differsbetween organisms regarding subunit organization. In yeast, there is oneenzyme per each catalytic activity while in metazoans and plants thetriphosphatase and the guanylyltransferase are encoded by a single gene. Inall eukaryotic organisms, the methyltransferase is encoded by a gene that onlyencodes this activity .The 3D structure of the cap methyltransferase Ecm1 from the microsporidianparasite Encephalitozoon cuniculi has been determined bound to AdoMet, AdoHcyand the cap guanilate methyl acceptor. It is a smallmonomeric enzyme that contains virtually nothing more than the catalyticdomain. The protein contains 9 alpha helices and 11 beta strands andaltogether displays a rossmanoidal fold characteristic of Class I SAM-bindingmethyltransferases.It also exhibits structural features that appear unique to mRNA(guanine-N(7)-)-methyltransferases (mRNA-Cap0-MTs hereafter) such as aN-terminal region comprising about 40 amino acids that are disordered in thecrystals, among which amino acids 30 to 40, not visible in the crystalstructure, happen to be essential for Ecm1 activity .The structure of Ecm1 can be divided up into two segments in-between which alarge cleft with two ligand binding pockets results. This cleft containssolvent exposed amino acids that are conserved among other mRNA-Cap0-MTs. Thesecond segment contains the elements associated with AdoMet binding in otherClass I MTs and when AdoMet is bound to Ecm1, this segments forms a pocketthat AdoMet expectedly occupies. When co-crystallized with Ecm1, the capanalog m7GpppG is bound in a pocket adjacent to the one binding AdoMet.Catalysis seems not to be operated through direct involvement of specificamino acid side chains, since no residue is observed to be in direct contactwith the guanosine-N7 nucleophile, nor the the AdoMet methyl carbon nor theAdoHcy sulfur leaving group. Instead, Ecm1 manifestly ease methyl transfer tothe cap guanine-N7 by coordinating the different players in an environmentthat optimizes substrate proximity and orientation .Several eukaryotic DNA and RNA viruses encode some or all the cappingenzymatic activities, often on a single polypeptide. As such, the vacciniavirus, a poxvirus used in vaccination against smallpox, encodes for twopolypeptides responsible for mRNA capping: D1 and D12. D1 contains anN-terminal domain responsible for the triphosphatase and theguanylyltransferase activities and a C-terminal region containing themRNA-Cap0-MT domain. In order for the mRNA-Cap0-MT domain of D1 to be fullyactive, D1 needs to associate with D12, a stimulatory subunit .The crystal structure of the mRNA-Cap0-MT domain of the vaccinia virus D1bound to AdoHcy in complex with its stimulatory D12 subunit has also beendescribed. All in all, the vaccinia mRNA-Cap0-MT domain showsa conformation that is quite similar to the one of Ecm1, except for onedifference: the N-terminal extension of the vaccinia domain folds back overthe AdoHcy binding site, burying the ligand; this N-terminal section isinvolved catalytically as several amino acids in it bind AdoHcy .The profile we developed covers the entire mRNA-Cap0-MT domain.

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Biological Magnetic Resonance Bank Entry 19443: 1H, 13C and 15N Backbone Assignment of the EC-1 Domain of Human E-Cadherin

For SVM, it reports the accuracy of a leave-one-domain-out cross-validation. Experiments were performed on Arabidopsis DCNs. “Known EC” indicates the number of known EC numbers occurrences in the radius one neighboring domains. “Target Number” indicates the number of target domains. The features used in SVM-based method are the GO and EC number occurrence-frequencies, with the linear kernel function.

Methyltransferases (MTs) (EC 2.1.1.-) constitute an important class of enzymespresent in every life form. They transfer a methyl group most frequently fromS-adenosyl L-methionine (SAM or AdoMet) to a nucleophilic acceptor such asnitrogen, oxygen, sulfur or carbon leading to S-adenosyl-L-homocysteine(AdoHcy) and a methylated molecule. The substrates that are methylated bythese enzymes cover virtually every kind of biomolecules ranging from smallmolecules, to lipids, proteins and nucleic acids. MTs are therefore involvedin many essential cellular processes including biosynthesis, signaltransduction, protein repair, chromatin regulation and gene silencing .More than 230 different enzymatic reactions of MTs have been described so far,of which more than 220 use SAM as the methyl donor [E1]. A review published in2003 divides all MTs into 5 classes based on the structure of theircatalytic domain (fold): - class I: Rossmann-like alpha/beta - class II: TIM beta/alpha-barrel alpha/beta - class III: tetrapyrrole methylase alpha/beta - class IV: SPOUT alpha/beta see {PDOC51604} - class V: SET domain all beta see {PDOC51565}A more recent paper based on a study of the Saccharomyces cerevisiaemethyltransferome argues for four more folds: - class VI: transmembrane all alpha see {PDOC51598} - class VII: DNA/RNA-binding 3-helical bundle all alpha - class VIII: SSo0622-like alpha+beta - class IX: thymidylate synthetase alpha+betaThe vast majority of MTs belong to the Rossmann-like fold (Class I) whichconsists in a seven-stranded beta sheet adjoined by alpha helices. The betasheet contains a central topological switch-point resulting in a deep cleft inwhich SAM binds. Class I MTs display two conserved positions, the first one isa GxGxG motif (or at least a GxG motif) at the end of the first beta strandwhich is characteristic of a nucleotide-binding site and is hence used to bindthe adenosyl part of SAM, the second conserved position is an acidic residueat the end of the second beta strand that forms one hydrogen bond to eachhydroxyl of the SAM ribose part. The core of these enzymes is composed byabout 150 amino acids that show very strong spatial conservation. Catechol O-MT (EC 2.1.1.6) is the canonical Class I MT considering that it consists inthe exact consensus structural core with no extra domain .Some enzymatic activities known to belong to the Class I superfamily:Profiles directed against domains: - C5-MTs: DNA (cytosine-5-)-MT (EC 2.1.1.37) and tRNA (cytosine(38)-C(5))-MT (EC 2.1.1.204). - Domains rearranged MTs (DRMs) (EC=2.1.1.37). - Dot 1 MT (EC 2.1.1.43). - Eukaryotic and dsDNA viruses mRNA cap 0 MT (EC 2.1.1.56). - Flavivirus mRNA cap 0 and cap 1 MT (EC 2.1.1.56 and EC 2.1.1.57) . - Mononegavirus L protein 2'-O-ribose MT domain, involved in the capping of viral mRNAs (cap 1 structure) . - Protein arginine N-MTs (PRMTs) including histone-arginine N-MT (EC 2.1.1.125) and [Myelin basic protein]-arginine N-MT (EC 2.1.1.126). - RMT2 MTs: arginine N-MT 2 (EC 2.1.1.-) and guanidinoacetate N-MT (EC 2.1.1.2) . - TRM1 tRNA (guanine(26)-N(2))-diMT (EC 2.1.1.216). - TRM5/TYW2 tRNA (guanine(37)-N(1))-MT (EC 2.1.1.228). - ERG6/SMT MTs: methylate sterol and triterpene. - RsmB/NOP MTs: RNA (cytosine-5-)-MTs. - RNA 5-methyluridine (m(5)U) MTs (EC 2.1.1.35, EC 2.1.1.189 and EC 2.1.1.190). - RrmJ mRNA (nucleoside-2'-O-)-MT (EC 2.1.1.57). - Adrift ribose 2'-O-MT (EC 2.1.1.-). - TrmB tRNA (guanine(46)-N(7))-MT (EC 2.1.1.33).Profiles directed against whole-length proteins: - Glycine and glycine/sarcosine N-methyltransferase (EC 2.1.1.20 and EC 2.1.1.156). - mRNA (2'-O-methyladenosine-N(6)-)-MT (EC 2.1.1.62) and other MT-A70-like MTs. - Phosphoethanolamine N-MT (PEAMT) (EC 2.1.1.103). - dsRNA viruses mRNA cap 0 MT (EC 2.1.1.56). - Poxvirus/kinetoplastid cap ribose 2'-O-MT. - NNT1 nicotinamide N-MT (EC 2.1.1.1). - NNMT/PNMT/TEMT MTs: nicotinamide N-MT (EC 2.1.1.1), phenylethanolamine N-MT (EC 2.1.1.28) and amine N-MT (EC 2.1.1.49). - HNMT histamine N-MT (EC 2.1.1.8). - Putrescine N-MT (EC 2.1.1.53). - CLNMT calmodulin-lysine N-MT (EC 2.1.1.60). - TRM61 tRNA (adenine(57)-N(1)/adenine(58)-N(1) or adenine(58)-N(1))-MT (EC 2.1.1.219 or EC 2.1.1.220). - UbiE 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase (EC 2.1.1.201). - Tocopherol O-MT (EC 2.1.1.95). The Synechocystis homologue has not a tocopherol MT but a MPBQ/MSBQ activity (EC 2.1.1.295) (see below) . - 2-methyl-6-phytyl-1,4-benzoquinone/2-methyl-6-solanyl-1,4-benzoquinone MT (MPBQ/MSBQ MT) (EC 2.1.1.295) . - Cation-dependent O-MT includes caffeoyl-CoA O-MT (CCoAOMT) (EC 2.1.1.104) that is involved in plant defense, catechol O-MT (COMT) (EC 2.1.1.6) that plays an important role in the central nervous system in the mammalian organism, and a family of bacterial OMTs that may be involved in antibiotic production. - Cation-independent O-MT includes caffeic acid OMTs that are able to methylate the monolignol precursors caffeic acid (EC 2.1.1.68), caffeyl aldehyde, or caffeyl alcohol, acetylserotonin OMT (EC 2.1.1.4) and acetylserotonin OMT-like (EC 2.1.1.-). - Magnesium protoporphyrin IX MT (EC 2.1.1.11). - rRNA adenine N(6)-MT and adenine N(6), N(6)-diMT. - TRM11 MTs: tRNA (guanine(10)-N2)-MT (EC 2.1.1.214) and homologs (EC 2.1.1.-). - Methionine S-MT (EC 2.1.1.12). - TPMT MTs: thiopurine S-MT (EC 2.1.1.67), thiol S-MT (EC 2.1.1.9) and thiocyanate MT (EC 2.1.1.n4).The profiles we developed cover the entire domains or families.

Convection-permitting simulation for the Med-CORDEX domain (0.03° resolution) with ICON-CLM (Version 2.6.5). The simulation is driven by 1st realization (r1i1p1f1) of the EC-Earth3-Veg/SSP1-2.6 Scenario. The dataset covers the period 2041-2055 in hourly and daily temporal resolutions, with vertical coverage extending from the surface to 50 hPa. Surface/Single-level Variables in: out01 (hourly), out03 (daily), and out04 (daily). Pressure levels (50 hPa to 1000 hPa) variables in: out02 (hourly).

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The mechanisms of allosteric action within pentameric ligand-gated ion channels (pLGICs) remain to be determined. Using crystallography, site-directed mutagenesis, and two-electrode voltage clamp measurements, we identified two functionally relevant sites in the extracellular (EC) domain of the bacterial pLGIC from Gloeobacter violaceus (GLIC). One site is at the C-loop region, where the NQN mutation (D91N, E177Q, and D178N) eliminated inter-subunit salt bridges in the open-channel GLIC structure and thereby shifted the channel activation to a higher agonist concentration. The other site is below the C-loop, where binding of the anesthetic ketamine inhibited GLIC currents in a concentration dependent manner. To understand how a perturbation signal in the EC domain, either resulting from the NQN mutation or ketamine binding, is transduced to the channel gate, we have used the Perturbation-based Markovian Transmission (PMT) model to determine dynamic responses of the GLIC channel and signaling pathways upon initial perturbations in the EC domain of GLIC. Despite the existence of many possible routes for the initial perturbation signal to reach the channel gate, the PMT model in combination with Yen's algorithm revealed that perturbation signals with the highest probability flow travel either via the β1–β2 loop or through pre-TM1. The β1–β2 loop occurs in either intra- or inter-subunit pathways, while pre-TM1 occurs exclusively in inter-subunit pathways. Residues involved in both types of pathways are well supported by previous experimental data on nAChR. The direct coupling between pre-TM1 and TM2 of the adjacent subunit adds new insight into the allosteric signaling mechanism in pLGICs.

Human pro-EGF peptide sequences obtained from MS-MS sequencing (ITSI Biosciences) of human SMOC-1 (R&D Systems).

Biological Magnetic Resonance Bank Entry 17295: Protein and metal cluster structure of the wheat metallothionein domain g-Ec-1. The second part of the puzzle.

Contains the following files: S1 Fig. The relation between percentage of full length fusion protein and ability to inhibit MGC formation. Fig S1A is a graphical representation of the level of protein present in the major 35–36 kDa tetraspanin band on SDS-PAGE plotted against the percentage inhibition of MGC fusion at 500 nM total protein concentration. Fig. S1B is a representative SDS-PAGE experiment, showing the full-length GST fusion protein indicated by the arrow on the right and with the percentage of each chimera at full length, measured by densitometry, shown in each lane. S1 Table. Details of chimeras. (DOCX)

FRP-1, also termed follistatin-like protein 1 (fstl-1), TGF-beta-stimulated clone 36 (TSC-36/Flik), or TGF-beta inducible protein, is a secreted glycoprotein that is overexpressed in certain inflammatory diseases and has been implicated in many autoimmune diseases. FRP-1 functions as an important proinflammatory factor in the pathogenesis of osteoarthritis (OA) by activating the canonical NF-kappaB-mediated inflammatory cytokines, including tumor necrosis factor alpha (TNF-alpha), interleukin-1beta (IL-1beta) and interleukin-6 (IL-6), and enhancing fibroblast like synoviocytes proliferation. It also acts as a critical mediator of collagen-induced arthritis (CIA), juvenile rheumatoid arthritis (JRA), as well as Lyme arthritis observed after Borrelia burgdorferi infection. Meanwhile, it enhances nod-like receptor family, pyrin domain containing 3 (NLRP3) inflammasome-mediated IL-1beta secretion from monocytes and macrophages. Moreover, FRP-1 shows critical functions in the nervous system. It differentially regulates transforming growth factor beta (TGF-beta) and bone morphogenetic protein (BMP) signaling, leading to epithelial injury and fibroblast activation. Furthermore, FRP-1 functions as a cardiokine with cardioprotective properties. It may play a potential role in ischemic stroke through decreasing neuronal apoptosis and improving neurological deficits via disco-interacting protein 2 homolog A (DIP2A)/Akt pathway after middle cerebral artery occlusion (MCAO). Plasma FRP-1 is elevated in Kawasaki disease (KD) and thus may play a possible role in the formation of coronary artery aneurysm (CAA). FRP-1 contains a follistatin-like (FS) domain, an extracellular calcium-binding (EC) domain including a pair of EF hands, and a von Willebrand factor type C (VWC) domain. The EC domain does not undergo characteristic structural changes upon calcium addition or depletion and therefore is not a functional calcium binding domain.

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Methyltransferases (MTs) (EC 2.1.1.-) constitute an important class of enzymespresent in every life form. They transfer a methyl group most frequently fromS-adenosyl L-methionine (SAM or AdoMet) to a nucleophilic acceptor such asnitrogen, oxygen, sulfur or carbon leading to S-adenosyl-L-homocysteine(AdoHcy) and a methylated molecule. The substrates that are methylated bythese enzymes cover virtually every kind of biomolecules ranging from smallmolecules, to lipids, proteins and nucleic acids. MTs are therefore involvedin many essential cellular processes including biosynthesis, signaltransduction, protein repair, chromatin regulation and gene silencing .More than 230 different enzymatic reactions of MTs have been described so far,of which more than 220 use SAM as the methyl donor [E1]. A review published in2003 divides all MTs into 5 classes based on the structure of theircatalytic domain (fold): - class I: Rossmann-like alpha/beta - class II: TIM beta/alpha-barrel alpha/beta - class III: tetrapyrrole methylase alpha/beta - class IV: SPOUT alpha/beta see {PDOC51604} - class V: SET domain all beta see {PDOC51565}A more recent paper based on a study of the Saccharomyces cerevisiaemethyltransferome argues for four more folds: - class VI: transmembrane all alpha see {PDOC51598} - class VII: DNA/RNA-binding 3-helical bundle all alpha - class VIII: SSo0622-like alpha+beta - class IX: thymidylate synthetase alpha+betaThe vast majority of MTs belong to the Rossmann-like fold (Class I) whichconsists in a seven-stranded beta sheet adjoined by alpha helices. The betasheet contains a central topological switch-point resulting in a deep cleft inwhich SAM binds. Class I MTs display two conserved positions, the first one isa GxGxG motif (or at least a GxG motif) at the end of the first beta strandwhich is characteristic of a nucleotide-binding site and is hence used to bindthe adenosyl part of SAM, the second conserved position is an acidic residueat the end of the second beta strand that forms one hydrogen bond to eachhydroxyl of the SAM ribose part. The core of these enzymes is composed byabout 150 amino acids that show very strong spatial conservation. Catechol O-MT (EC 2.1.1.6) is the canonical Class I MT considering that it consists inthe exact consensus structural core with no extra domain .Some enzymatic activities known to belong to the Class I superfamily:Profiles directed against domains: - C5-MTs: DNA (cytosine-5-)-MT (EC 2.1.1.37) and tRNA (cytosine(38)-C(5))-MT (EC 2.1.1.204). - Domains rearranged MTs (DRMs) (EC=2.1.1.37). - Dot 1 MT (EC 2.1.1.43). - Eukaryotic and dsDNA viruses mRNA cap 0 MT (EC 2.1.1.56). - Flavivirus mRNA cap 0 and cap 1 MT (EC 2.1.1.56 and EC 2.1.1.57) . - Mononegavirus L protein 2'-O-ribose MT domain, involved in the capping of viral mRNAs (cap 1 structure) . - Protein arginine N-MTs (PRMTs) including histone-arginine N-MT (EC 2.1.1.125) and [Myelin basic protein]-arginine N-MT (EC 2.1.1.126). - RMT2 MTs: arginine N-MT 2 (EC 2.1.1.-) and guanidinoacetate N-MT (EC 2.1.1.2) . - TRM1 tRNA (guanine(26)-N(2))-diMT (EC 2.1.1.216). - TRM5/TYW2 tRNA (guanine(37)-N(1))-MT (EC 2.1.1.228). - ERG6/SMT MTs: methylate sterol and triterpene. - RsmB/NOP MTs: RNA (cytosine-5-)-MTs. - RNA 5-methyluridine (m(5)U) MTs (EC 2.1.1.35, EC 2.1.1.189 and EC 2.1.1.190). - RrmJ mRNA (nucleoside-2'-O-)-MT (EC 2.1.1.57). - Adrift ribose 2'-O-MT (EC 2.1.1.-). - TrmB tRNA (guanine(46)-N(7))-MT (EC 2.1.1.33).Profiles directed against whole-length proteins: - Glycine and glycine/sarcosine N-methyltransferase (EC 2.1.1.20 and EC 2.1.1.156). - mRNA (2'-O-methyladenosine-N(6)-)-MT (EC 2.1.1.62) and other MT-A70-like MTs. - Phosphoethanolamine N-MT (PEAMT) (EC 2.1.1.103). - dsRNA viruses mRNA cap 0 MT (EC 2.1.1.56). - Poxvirus/kinetoplastid cap ribose 2'-O-MT. - NNT1 nicotinamide N-MT (EC 2.1.1.1). - NNMT/PNMT/TEMT MTs: nicotinamide N-MT (EC 2.1.1.1), phenylethanolamine N-MT (EC 2.1.1.28) and amine N-MT (EC 2.1.1.49). - HNMT histamine N-MT (EC 2.1.1.8). - Putrescine N-MT (EC 2.1.1.53). - CLNMT calmodulin-lysine N-MT (EC 2.1.1.60). - TRM61 tRNA (adenine(57)-N(1)/adenine(58)-N(1) or adenine(58)-N(1))-MT (EC 2.1.1.219 or EC 2.1.1.220). - UbiE 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase (EC 2.1.1.201). - Tocopherol O-MT (EC 2.1.1.95). The Synechocystis homologue has not a tocopherol MT but a MPBQ/MSBQ activity (EC 2.1.1.295) (see below) . - 2-methyl-6-phytyl-1,4-benzoquinone/2-methyl-6-solanyl-1,4-benzoquinone MT (MPBQ/MSBQ MT) (EC 2.1.1.295) . - Cation-dependent O-MT includes caffeoyl-CoA O-MT (CCoAOMT) (EC 2.1.1.104) that is involved in plant defense, catechol O-MT (COMT) (EC 2.1.1.6) that plays an important role in the central nervous system in the mammalian organism, and a family of bacterial OMTs that may be involved in antibiotic production. - Cation-independent O-MT includes caffeic acid OMTs that are able to methylate the monolignol precursors caffeic acid (EC 2.1.1.68), caffeyl aldehyde, or caffeyl alcohol, acetylserotonin OMT (EC 2.1.1.4) and acetylserotonin OMT-like (EC 2.1.1.-). - Magnesium protoporphyrin IX MT (EC 2.1.1.11). - rRNA adenine N(6)-MT and adenine N(6), N(6)-diMT. - TRM11 MTs: tRNA (guanine(10)-N2)-MT (EC 2.1.1.214) and homologs (EC 2.1.1.-). - Methionine S-MT (EC 2.1.1.12). - TPMT MTs: thiopurine S-MT (EC 2.1.1.67), thiol S-MT (EC 2.1.1.9) and thiocyanate MT (EC 2.1.1.n4).The profiles we developed cover the entire domains or families.