EzCatDB: D00076

DB codeD00076
RLCP classification3.747.29000.21
CATH domainDomain 13.40.50.150Catalytic domain
Domain 21.10.8.100
E.C.2.1.1.184
CSA1qam

CATH domainRelated DB codes (homologues)
3.40.50.150S00637,S00639,S00262,S00261,S00291,S00412,D00075,D00079,D00080,D00082,D00083,D00823

Enzyme Name
Swiss-protKEGG

P13956P21236
Protein namerRNA adenine N-6-methyltransferaserRNA adenine N-6-methyltransferase23S rRNA (adenine2085-N6)-dimethyltransferase
ErmC' methyltransferase
ermC methylase
ermC 23S rRNA methyltransferase
rRNA:m6A methyltransferase ErmC'
ErmC'
rRNA methyltransferase ErmC'
SynonymsEC 2.1.1.48
Macrolide-lincosamide-streptogramin B resistance protein
Erythromycin resistance protein
EC 2.1.1.48
ErmAM
Macrolide-lincosamide-streptogramin B resistance protein


Swiss-prot:Accession NumberP13956P21236
Entry nameERM_BACSUERM_STRPN
Activity2 S-adenosyl-L-methionine + adenine(2085) in 23S rRNA = 2 S-adenosyl-L-homocysteine + N(6)-dimethyladenine(2085) in 23S rRNA.2 S-adenosyl-L-methionine + adenine(2085) in 23S rRNA = 2 S-adenosyl-L-homocysteine + N(6)-dimethyladenine(2085) in 23S rRNA.
Subunit

Subcellular location

Cofactor



SubstratesProducts
KEGG-idC00019L00096C00021L00097
CompoundS-Adenosyl-L-methionineadenine2085 in 23S rRNAS-Adenosyl-L-homocysteineN6-dimethyladenine2085 in 23S rRNA
Typeamino acids,amine group,nucleoside,sulfonium ionamine group,nucleic acidsamino acids,amine group,nucleoside,sulfide groupamine group,nucleic acids
1qamA01UnboundUnboundUnboundUnbound
1qanA01UnboundUnboundBound:SAHUnbound
1qaoA01Bound:SAMUnboundUnboundUnbound
1qaqA01Analogue:SFGUnboundUnboundUnbound
2ercA01UnboundUnboundUnboundUnbound
2ercB01UnboundUnboundUnboundUnbound
1yubA01UnboundUnboundUnboundUnbound
1qamA02UnboundUnboundUnboundUnbound
1qanA02UnboundUnboundUnboundUnbound
1qaoA02UnboundUnboundUnboundUnbound
1qaqA02UnboundUnboundUnboundUnbound
2ercA02UnboundUnboundUnboundUnbound
2ercB02UnboundUnboundUnboundUnbound
1yubA02UnboundUnboundUnboundUnbound

Active-site residues
resource
literature [5] & [9]
pdbCatalytic residuesMain-chain involved in catalysiscomment
1qamA01ASN 101;TYR 104;PHE 163
ILE 102

1qanA01ASN 101;TYR 104;PHE 163
ILE 102

1qaoA01ASN 101;TYR 104;PHE 163
ILE 102

1qaqA01ASN 101;TYR 104;PHE 163
ILE 102

2ercA01ASN 101;TYR 104;PHE 163
ILE 102

2ercB01ASN 101;TYR 104;PHE 163
ILE 102

1yubA01ASN 100;TYR 103;PHE 162
ILE 101
mutant I75T, S100N, H118R
1qamA02                               


1qanA02                               


1qaoA02                               


1qaqA02                               


2ercA02                               


2ercB02                               


1yubA02                               



References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[5]p.287
[9]Fig.4, p.102-106

references
[1]
PubMed ID7543473
JournalJ Bacteriol
Year1995
Volume177
Pages4327-32
AuthorsZhong P, Pratt SD, Edalji RP, Walter KA, Holzman TF, Shivakumar AG, Katz L
TitleSubstrate requirements for ErmC' methyltransferase activity.
[2]
CommentsSTRUCTURE BY NMR
Medline ID97331325
PubMed ID9187657
JournalNat Struct Biol
Year1997
Volume4
Pages483-9
AuthorsYu L, Petros AM, Schnuchel A, Zhong P, Severin JM, Walter K, Holzman TF, Fesik SW
TitleSolution structure of an rRNA methyltransferase (ErmAM) that confers macrolide-lincosamide-streptogramin antibiotic resistance.
Related PDB1yub
Related Swiss-protP21236
[3]
CommentsX-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 10-244
Medline ID98254494
PubMed ID9585521
JournalBiochemistry
Year1998
Volume37
Pages7103-12
AuthorsBussiere DE, Muchmore SW, Dealwis CG, Schluckebier G, Nienaber VL, Edalji RP, Walter KA, Ladror US, Holzman TF, Abad-Zapatero C
TitleCrystal structure of ErmC', an rRNA methyltransferase which mediates antibiotic resistance in bacteria.
Related PDB2erc
Related Swiss-protP13956
[4]
PubMed ID10508434
JournalJ Med Chem
Year1999
Volume42
Pages3852-9
AuthorsHajduk PJ, Dinges J, Schkeryantz JM, Janowick D, Kaminski M, Tufano M, Augeri DJ, Petros A, Nienaber V, Zhong P, Hammond R, Coen M, Beutel B, Katz L, Fesik SW
TitleNovel inhibitors of Erm methyltransferases from NMR and parallel synthesis.
[5]
CommentsX-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS)
Medline ID99296629
PubMed ID10366505
JournalJ Mol Biol
Year1999
Volume289
Pages277-91
AuthorsSchluckebier G, Zhong P, Stewart KD, Kavanaugh TJ, Abad-Zapatero C
TitleThe 2.2 A structure of the rRNA methyltransferase ErmC' and its complexes with cofactor and cofactor analogs: implications for the reaction mechanism.
Related PDB1qam,1qan,1qao,1qaq
Related Swiss-protP13956
[6]
PubMed ID11567089
JournalProtein Sci
Year2001
Volume10
Pages1980-8
AuthorsSchubot FD, Chen CJ, Rose JP, Dailey TA, Dailey HA, Wang BC
TitleCrystal structure of the transcription factor sc-mtTFB offers insights into mitochondrial transcription.
[7]
PubMed ID11959553
JournalAntimicrob Agents Chemother
Year2002
Volume46
Pages1253-61
AuthorsFarrow KA, Lyras D, Polekhina G, Koutsis K, Parker MW, Rood JI
TitleIdentification of essential residues in the Erm(B) rRNA methyltransferase of Clostridium perfringens.
[8]
PubMed ID11763974
JournalJ Mol Microbiol Biotechnol
Year2002
Volume4
Pages93-9
AuthorsBujnicki JM, Blumenthal RM, Rychlewski L
TitleSequence analysis and structure prediction of 23S rRNA:m1G methyltransferases reveals a conserved core augmented with a putative Zn-binding domain in the N-terminus and family-specific elaborations in the C-terminus.
[9]
PubMed ID12946350
JournalJ Mol Biol
Year2003
Volume332
Pages99-109
AuthorsMaravic G, Feder M, Pongor S, Flogel M, Bujnicki JM
TitleMutational analysis defines the roles of conserved amino acid residues in the predicted catalytic pocket of the rRNA:m6A methyltransferase ErmC'.
[10]
PubMed ID15114858
JournalFolia Microbiol (Praha)
Year2004
Volume49
Pages3-7
AuthorsMaravic G, Bujnicki JM, Flogel M
TitleMutational analysis of basic residues in the N-terminus of the rRNA:m6A methyltransferase ErmC'.
[11]
PubMed ID15136037
JournalJ Mol Biol
Year2004
Volume339
Pages337-53
AuthorsO'Farrell HC, Scarsdale JN, Rife JP
TitleCrystal structure of KsgA, a universally conserved rRNA adenine dimethyltransferase in Escherichia coli.
[12]
PubMed ID15929997
JournalProtein Sci
Year2005
Volume14
Pages1472-84
AuthorsConstantine KL, Krystek SR, Healy MD, Doyle ML, Siemers NO, Thanassi J, Yan N, Xie D, Goldfarb V, Yanchunas J, Tao L, Dougherty BA, Farmer BT 2nd
TitleStructural and functional characterization of CFE88: evidence that a conserved and essential bacterial protein is a methyltransferase.

comments
According to the literature [9], the catalytic residues of this enzyme is nearly the same as that of Modification methylase TaqI (D00080 in EzCatDB), suggesting that it has a similar mechanism to that.

createdupdated
2004-05-062012-10-03
Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

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