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Histidine N-alpha-methyltransferase (EC 2.1.1.44) (Histidine trimethyltransferase)

 EGTD_MYCS2              Reviewed;         321 AA.
A0R5M8; I7GAE1;
19-OCT-2011, integrated into UniProtKB/Swiss-Prot.
09-JAN-2007, sequence version 1.
10-OCT-2018, entry version 80.
RecName: Full=Histidine N-alpha-methyltransferase {ECO:0000305};
EC=2.1.1.44 {ECO:0000269|PubMed:20420449, ECO:0000269|PubMed:25404173};
AltName: Full=Histidine trimethyltransferase {ECO:0000303|PubMed:25251321};
Name=egtD {ECO:0000303|PubMed:20420449};
OrderedLocusNames=MSMEG_6247, MSMEI_6086;
Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155).
Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
Mycolicibacterium.
NCBI_TaxID=246196;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 700084 / mc(2)155;
Fleischmann R.D., Dodson R.J., Haft D.H., Merkel J.S., Nelson W.C.,
Fraser C.M.;
Submitted (OCT-2006) to the EMBL/GenBank/DDBJ databases.
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 700084 / mc(2)155;
PubMed=17295914; DOI=10.1186/gb-2007-8-2-r20;
Deshayes C., Perrodou E., Gallien S., Euphrasie D., Schaeffer C.,
Van-Dorsselaer A., Poch O., Lecompte O., Reyrat J.-M.;
"Interrupted coding sequences in Mycobacterium smegmatis: authentic
mutations or sequencing errors?";
Genome Biol. 8:R20.1-R20.9(2007).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 700084 / mc(2)155;
PubMed=18955433; DOI=10.1101/gr.081901.108;
Gallien S., Perrodou E., Carapito C., Deshayes C., Reyrat J.-M.,
Van Dorsselaer A., Poch O., Schaeffer C., Lecompte O.;
"Ortho-proteogenomics: multiple proteomes investigation through
orthology and a new MS-based protocol.";
Genome Res. 19:128-135(2009).
[4]
FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, GENE NAME, AND
PATHWAY.
STRAIN=ATCC 607 / DSM 43465 / JCM 20379 / NBRC 3207 / NRRL B-692;
PubMed=20420449; DOI=10.1021/ja101721e;
Seebeck F.P.;
"In vitro reconstitution of Mycobacterial ergothioneine
biosynthesis.";
J. Am. Chem. Soc. 132:6632-6633(2010).
[5]
DISRUPTION PHENOTYPE, AND PATHWAY.
STRAIN=ATCC 700084 / mc(2)155;
PubMed=23629716; DOI=10.1128/AAC.02572-12;
Sao Emani C., Williams M.J., Wiid I.J., Hiten N.F., Viljoen A.J.,
Pietersen R.D., van Helden P.D., Baker B.;
"Ergothioneine is a secreted antioxidant in Mycobacterium smegmatis.";
Antimicrob. Agents Chemother. 57:3202-3207(2013).
[6]
CRYSTALLIZATION, AND SUBUNIT.
STRAIN=ATCC 607 / DSM 43465 / JCM 20379 / NBRC 3207 / NRRL B-692;
PubMed=24817736; DOI=10.1107/S2053230X1400805X;
Vit A., Misson L., Blankenfeldt W., Seebeck F.P.;
"Crystallization and preliminary X-ray analysis of the ergothioneine-
biosynthetic methyltransferase EgtD.";
Acta Crystallogr. F 70:676-680(2014).
[7]
X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) OF APOENYZME AND COMPLEXES WITH
L-HISTIDINE AND S-ADENOSYL-L-HOMOCYSTEINE, DOMAIN, SUBUNIT, AND
REACTION MECHANISM.
PubMed=25251321; DOI=10.1016/j.bbrc.2014.09.058;
Jeong J.H., Cha H.J., Ha S.C., Rojviriya C., Kim Y.G.;
"Structural insights into the histidine trimethylation activity of
EgtD from Mycobacterium smegmatis.";
Biochem. Biophys. Res. Commun. 452:1098-1103(2014).
[8]
X-RAY CRYSTALLOGRAPHY (1.51 ANGSTROMS) OF APOENYZME; WILD-TYPE IN
COMPLEXES WITH N,N-DIMETHYL-L-HISTIDINE AND S-ADENOSYL-L-HOMOCYSTEINE
(SAH) AND MUTANT VAL-252/ALA-282 IN COMPLEX WITH TRYPTOPHAN AND SAH,
FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND
MUTAGENESIS OF MET-252 AND GLU-282.
STRAIN=ATCC 607 / DSM 43465 / JCM 20379 / NBRC 3207 / NRRL B-692;
PubMed=25404173; DOI=10.1002/cbic.201402522;
Vit A., Misson L., Blankenfeldt W., Seebeck F.P.;
"Ergothioneine biosynthetic methyltransferase EgtD reveals the
structural basis of aromatic amino acid betaine biosynthesis.";
ChemBioChem 16:119-125(2015).
-!- FUNCTION: Catalyzes the SAM-dependent triple methylation of the
alpha-amino group of histidine to form hercynine, a step in the
biosynthesis pathway of ergothioneine. Among all the proteinogenic
amino acids, only L-histidine is a substrate.
{ECO:0000269|PubMed:20420449, ECO:0000269|PubMed:25404173}.
-!- CATALYTIC ACTIVITY: 3 S-adenosyl-L-methionine + L-histidine = 3 S-
adenosyl-L-homocysteine + hercynine. {ECO:0000269|PubMed:20420449,
ECO:0000269|PubMed:25404173}.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=109 uM for L-histidine {ECO:0000269|PubMed:25404173};
KM=17.7 uM for N-alpha-methyl-L-histidine
{ECO:0000269|PubMed:25404173};
KM=25.3 uM for N-alpha,N-alpha-dimethyl-L-histidine
{ECO:0000269|PubMed:25404173};
Note=kcat is 0.58 sec(-1) for the methylation of L-histidine.
kcat is 0.23 sec(-1) for the methylation of N-alpha-methyl-L-
histidine. kcat is 0.23 sec(-1) for the methylation of N-
alpha,N-alpha-dimethyl-L-histidine.
{ECO:0000269|PubMed:25404173};
-!- PATHWAY: Amino-acid biosynthesis; ergothioneine biosynthesis.
{ECO:0000269|PubMed:23629716, ECO:0000305|PubMed:20420449}.
-!- SUBUNIT: Monomer. {ECO:0000269|PubMed:24817736,
ECO:0000269|PubMed:25251321}.
-!- DOMAIN: Consists of two distinct domains: a typical
methyltransferase domain and a unique substrate binding domain.
{ECO:0000305|PubMed:25251321}.
-!- DISRUPTION PHENOTYPE: Cells lacking this gene are unable to
synthesize ergothioneine (ERG), but do not show growth defect.
Deletion of egtD from wild-type M.smegmatis and a mycothiol (MSH)-
deficient mutant does not affect their susceptibility to tested
antibiotics. The ERG- and MSH-deficient double mutant is
significantly more sensitive to peroxide than either of the single
mutants lacking either ERG or MSH, suggesting that both thiols
play a role in protecting M.smegmatis against oxidative stress and
that ERG is able to partly compensate for the loss of MSH.
{ECO:0000269|PubMed:23629716}.
-!- SIMILARITY: Belongs to the methyltransferase superfamily. EgtD
family. {ECO:0000305}.
-----------------------------------------------------------------------
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-----------------------------------------------------------------------
EMBL; CP000480; ABK75457.1; -; Genomic_DNA.
EMBL; CP001663; AFP42517.1; -; Genomic_DNA.
RefSeq; WP_011731156.1; NZ_CP009494.1.
RefSeq; YP_890466.1; NC_008596.1.
PDB; 4PIM; X-ray; 1.75 A; A/B=1-321.
PDB; 4PIN; X-ray; 1.90 A; A/B=1-321.
PDB; 4PIO; X-ray; 1.51 A; A/B=1-321.
PDB; 4PIP; X-ray; 1.80 A; A/B/C/D=1-321.
PDB; 4UY5; X-ray; 2.00 A; A=1-321.
PDB; 4UY6; X-ray; 2.04 A; A=2-321.
PDB; 4UY7; X-ray; 2.31 A; A/B=2-321.
PDBsum; 4PIM; -.
PDBsum; 4PIN; -.
PDBsum; 4PIO; -.
PDBsum; 4PIP; -.
PDBsum; 4UY5; -.
PDBsum; 4UY6; -.
PDBsum; 4UY7; -.
SMR; A0R5M8; -.
STRING; 246196.MSMEG_6247; -.
EnsemblBacteria; ABK75457; ABK75457; MSMEG_6247.
EnsemblBacteria; AFP42517; AFP42517; MSMEI_6086.
GeneID; 4537704; -.
KEGG; msb:LJ00_30890; -.
KEGG; msg:MSMEI_6086; -.
KEGG; msm:MSMEG_6247; -.
PATRIC; fig|246196.19.peg.6086; -.
eggNOG; ENOG41067HS; Bacteria.
eggNOG; COG4301; LUCA.
HOGENOM; HOG000253490; -.
KO; K18911; -.
OMA; RVEMHLV; -.
OrthoDB; POG091H0987; -.
BioCyc; MetaCyc:MONOMER-17984; -.
BioCyc; MSME246196:G1H7P-6216-MONOMER; -.
UniPathway; UPA01014; -.
Proteomes; UP000000757; Chromosome.
Proteomes; UP000006158; Chromosome.
GO; GO:0030745; F:dimethylhistidine N-methyltransferase activity; IEA:UniProtKB-UniRule.
GO; GO:0008276; F:protein methyltransferase activity; IDA:UniProtKB.
GO; GO:0052704; P:ergothioneine biosynthesis from histidine via N-alpha,N-alpha,N-alpha-trimethyl-L-histidine; IDA:UniProtKB.
GO; GO:0052707; P:N-alpha,N-alpha,N-alpha-trimethyl-L-histidine biosynthesis from histidine; IDA:UniProtKB.
HAMAP; MF_02037; EgtD; 1.
InterPro; IPR035094; EgtD.
InterPro; IPR032888; EgtD_Actinobacteria.
InterPro; IPR019257; MeTrfase_dom.
InterPro; IPR017804; MeTrfase_EgtD-like.
InterPro; IPR029063; SAM-dependent_MTases.
Pfam; PF10017; Methyltransf_33; 1.
PIRSF; PIRSF018005; UCP018005; 1.
SUPFAM; SSF53335; SSF53335; 2.
TIGRFAMs; TIGR03438; egtD_ergothio; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; Methyltransferase;
Reference proteome; S-adenosyl-L-methionine; Transferase.
CHAIN 1 321 Histidine N-alpha-methyltransferase.
/FTId=PRO_0000413651.
REGION 141 142 S-adenosyl-L-methionine binding.
{ECO:0000244|PDB:4PIO,
ECO:0000244|PDB:4PIP,
ECO:0000244|PDB:4UY6,
ECO:0000305|PubMed:25251321,
ECO:0000305|PubMed:25404173}.
REGION 282 284 L-histidine binding.
{ECO:0000244|PDB:4UY6,
ECO:0000244|PDB:4UY7,
ECO:0000269|PubMed:25251321,
ECO:0000305|PubMed:25404173}.
BINDING 56 56 L-histidine. {ECO:0000244|PDB:4UY6,
ECO:0000244|PDB:4UY7,
ECO:0000269|PubMed:25251321,
ECO:0000305|PubMed:25404173}.
BINDING 86 86 S-adenosyl-L-methionine; via carbonyl
oxygen. {ECO:0000305|PubMed:25251321,
ECO:0000305|PubMed:25404173}.
BINDING 92 92 S-adenosyl-L-methionine.
{ECO:0000305|PubMed:25251321,
ECO:0000305|PubMed:25404173}.
BINDING 113 113 S-adenosyl-L-methionine.
{ECO:0000305|PubMed:25251321,
ECO:0000305|PubMed:25404173}.
BINDING 166 166 L-histidine. {ECO:0000244|PDB:4UY6,
ECO:0000244|PDB:4UY7,
ECO:0000269|PubMed:25251321,
ECO:0000305|PubMed:25404173}.
BINDING 206 206 L-histidine. {ECO:0000244|PDB:4UY6,
ECO:0000244|PDB:4UY7,
ECO:0000269|PubMed:25251321,
ECO:0000305|PubMed:25404173}.
MUTAGEN 252 252 M->V: Dramatic change in substrate
specificity since the tryptophan-specific
activity is increased more than 2000-fold
and the histidine-specific activity is
reduced 3000-fold; when associated with
A-282. {ECO:0000269|PubMed:25404173}.
MUTAGEN 282 282 E->A: 130-fold reduction in catalytic
efficiency. Dramatic change in substrate
specificity since the tryptophan-specific
activity is increased more than 2000-fold
and the histidine-specific activity is
reduced 3000-fold; when associated with
V-252. {ECO:0000269|PubMed:25404173}.
STRAND 5 10 {ECO:0000244|PDB:4PIO}.
HELIX 11 14 {ECO:0000244|PDB:4PIO}.
HELIX 16 27 {ECO:0000244|PDB:4PIO}.
STRAND 28 30 {ECO:0000244|PDB:4PIO}.
HELIX 35 38 {ECO:0000244|PDB:4PIO}.
HELIX 41 50 {ECO:0000244|PDB:4PIO}.
STRAND 53 55 {ECO:0000244|PDB:4UY5}.
HELIX 58 77 {ECO:0000244|PDB:4PIO}.
STRAND 80 85 {ECO:0000244|PDB:4PIO}.
HELIX 93 102 {ECO:0000244|PDB:4PIO}.
STRAND 108 114 {ECO:0000244|PDB:4PIO}.
HELIX 116 129 {ECO:0000244|PDB:4PIO}.
STRAND 138 140 {ECO:0000244|PDB:4PIO}.
TURN 142 144 {ECO:0000244|PDB:4PIO}.
HELIX 146 148 {ECO:0000244|PDB:4PIO}.
STRAND 153 159 {ECO:0000244|PDB:4PIO}.
HELIX 163 166 {ECO:0000244|PDB:4PIO}.
HELIX 169 180 {ECO:0000244|PDB:4PIO}.
STRAND 188 195 {ECO:0000244|PDB:4PIO}.
HELIX 199 205 {ECO:0000244|PDB:4PIO}.
HELIX 212 228 {ECO:0000244|PDB:4PIO}.
HELIX 234 236 {ECO:0000244|PDB:4PIO}.
STRAND 237 244 {ECO:0000244|PDB:4PIO}.
TURN 245 248 {ECO:0000244|PDB:4PIO}.
STRAND 249 258 {ECO:0000244|PDB:4PIO}.
STRAND 260 264 {ECO:0000244|PDB:4PIO}.
HELIX 265 267 {ECO:0000244|PDB:4PIO}.
STRAND 269 273 {ECO:0000244|PDB:4PIO}.
STRAND 278 285 {ECO:0000244|PDB:4PIO}.
HELIX 289 298 {ECO:0000244|PDB:4PIO}.
STRAND 302 308 {ECO:0000244|PDB:4PIO}.
STRAND 314 320 {ECO:0000244|PDB:4PIO}.
SEQUENCE 321 AA; 35003 MW; 43FE091F6B4A48D6 CRC64;
MTLSLANYLA ADSAAEALRR DVRAGLTAAP KSLPPKWFYD AVGSDLFDQI TRLPEYYPTR
TEAQILRTRS AEIIAAAGAD TLVELGSGTS EKTRMLLDAM RDAELLRRFI PFDVDAGVLR
SAGAAIGAEY PGIEIDAVCG DFEEHLGKIP HVGRRLVVFL GSTIGNLTPA PRAEFLSTLA
DTLQPGDSLL LGTDLVKDTG RLVRAYDDAA GVTAAFNRNV LAVVNRELSA DFDLDAFEHV
AKWNSDEERI EMWLRARTAQ HVRVAALDLE VDFAAGEEML TEVSCKFRPE NVVAELAEAG
LRQTHWWTDP AGDFGLSLAV R


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