NEOEP_STRFR
ID NEOEP_STRFR Reviewed; 299 AA.
AC Q53U14;
DT 07-JAN-2015, integrated into UniProtKB/Swiss-Prot.
DT 24-MAY-2005, sequence version 1.
DT 03-AUG-2022, entry version 65.
DE RecName: Full=Neomycin C epimerase {ECO:0000305|PubMed:25230155};
DE EC=5.1.3.- {ECO:0000269|PubMed:25230155};
DE AltName: Full=Radical S-adenosyl-L-methionine epimerase NeoN {ECO:0000303|PubMed:25230155};
DE Short=Radical SAM epimerase NeoN {ECO:0000303|PubMed:25230155};
GN Name=neoN {ECO:0000303|PubMed:25230155, ECO:0000312|EMBL:CAF33317.1};
GN Synonyms=neoH {ECO:0000312|EMBL:BAD95825.1};
OS Streptomyces fradiae (Streptomyces roseoflavus).
OC Bacteria; Actinobacteria; Streptomycetales; Streptomycetaceae;
OC Streptomyces.
OX NCBI_TaxID=1906;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 10745 / CBS 498.68 / DSM 40063 / JCM 4133 / NBRC 12773 / NCIMB
RC 8233 / NRRL B-1195 / VKM Ac-150;
RA Aboshanab K.M., Schmidt-Beissner H., Wehmeier U.F., Piepersberg W.,
RA Welzel K., Vente A.;
RT "Analysis and comparison of biosynthetic gene clusters for the 2-deoxy-
RT inosamine containing aminoglycoside antibiotics ribostamycin, neomycin,
RT lividomycin, paromomycin and butirosin.";
RL Submitted (FEB-2004) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 10745 / CBS 498.68 / DSM 40063 / JCM 4133 / NBRC 12773 / NCIMB
RC 8233 / NRRL B-1195 / VKM Ac-150;
RA Subba B., Kharel M.K., Sthapit B., Liou K., Lee H.C., Woo J.S., Sohng J.K.;
RT "Cloning and characterization of a neomycin biosynthetic gene cluster from
RT Streptomyces fradiae, ATCC 10745.";
RL Submitted (JUL-2004) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 10745 / CBS 498.68 / DSM 40063 / JCM 4133 / NBRC 12773 / NCIMB
RC 8233 / NRRL B-1195 / VKM Ac-150;
RX PubMed=16506694; DOI=10.1038/ja.2005.104;
RA Kudo F., Yamamoto Y., Yokoyama K., Eguchi T., Kakinuma K.;
RT "Biosynthesis of 2-deoxystreptamine by three crucial enzymes in
RT Streptomyces fradiae NBRC 12773.";
RL J. Antibiot. 58:766-774(2005).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 10745 / CBS 498.68 / DSM 40063 / JCM 4133 / NBRC 12773 / NCIMB
RC 8233 / NRRL B-1195 / VKM Ac-150;
RX PubMed=15827636; DOI=10.1039/b501199j;
RA Huang F., Haydock S.F., Mironenko T., Spiteller D., Li Y., Spencer J.B.;
RT "The neomycin biosynthetic gene cluster of Streptomyces fradiae NCIMB 8233:
RT characterisation of an aminotransferase involved in the formation of 2-
RT deoxystreptamine.";
RL Org. Biomol. Chem. 3:1410-1418(2005).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, REACTION MECHANISM, ACTIVE SITE,
RP AND MUTAGENESIS OF 26-CYS--CYS-33 AND CYS-249.
RC STRAIN=ATCC 10745 / CBS 498.68 / DSM 40063 / JCM 4133 / NBRC 12773 / NCIMB
RC 8233 / NRRL B-1195 / VKM Ac-150;
RX PubMed=25230155; DOI=10.1021/ja507759f;
RA Kudo F., Hoshi S., Kawashima T., Kamachi T., Eguchi T.;
RT "Characterization of a radical S-adenosyl-L-methionine epimerase, NeoN, in
RT the last step of neomycin B biosynthesis.";
RL J. Am. Chem. Soc. 136:13909-13915(2014).
CC -!- FUNCTION: Catalyzes the last step of neomycin B biosynthesis, i.e. the
CC irreversible epimerization at C-5''' of neomycin C to give neomycin B.
CC To a lesser extent, is also able to convert neomycin Y2 to neomycin Y1.
CC {ECO:0000269|PubMed:25230155}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=AH2 + neomycin C + S-adenosyl-L-methionine = 5'-deoxyadenosine
CC + A + H(+) + L-methionine + neomycin B; Xref=Rhea:RHEA:47692,
CC ChEBI:CHEBI:13193, ChEBI:CHEBI:15378, ChEBI:CHEBI:17319,
CC ChEBI:CHEBI:17499, ChEBI:CHEBI:57844, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:65077, ChEBI:CHEBI:87835;
CC Evidence={ECO:0000269|PubMed:25230155};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000269|PubMed:25230155};
CC Note=Binds 2 [4Fe-4S] clusters. One cluster is coordinated with 3
CC cysteines and an exchangeable S-adenosyl-L-methionine. The second
CC cluster is proposed to be involved in the electron-transfer mechanism
CC for the catalytic cycle. {ECO:0000269|PubMed:25230155};
CC -!- PATHWAY: Antibiotic biosynthesis; neomycin biosynthesis.
CC {ECO:0000303|PubMed:25230155}.
CC -!- SIMILARITY: Belongs to the radical SAM superfamily. {ECO:0000305}.
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DR EMBL; AB211959; BAD95825.1; -; Genomic_DNA.
DR EMBL; AJ629247; CAF33317.1; -; Genomic_DNA.
DR EMBL; AJ786317; CAH05096.1; -; Genomic_DNA.
DR EMBL; AJ843080; CAH58695.1; -; Genomic_DNA.
DR RefSeq; WP_031132490.1; NZ_MUNC01000172.1.
DR AlphaFoldDB; Q53U14; -.
DR SMR; Q53U14; -.
DR KEGG; ag:BAD95825; -.
DR UniPathway; UPA00969; -.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0016853; F:isomerase activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0017000; P:antibiotic biosynthetic process; IEA:UniProtKB-KW.
DR Gene3D; 3.20.20.70; -; 1.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR000385; MoaA_NifB_PqqE_Fe-S-bd_CS.
DR InterPro; IPR007197; rSAM.
DR Pfam; PF04055; Radical_SAM; 1.
DR SFLD; SFLDS00029; Radical_SAM; 1.
DR PROSITE; PS01305; MOAA_NIFB_PQQE; 1.
DR PROSITE; PS51918; RADICAL_SAM; 1.
PE 1: Evidence at protein level;
KW 4Fe-4S; Antibiotic biosynthesis; Iron; Iron-sulfur; Isomerase;
KW Metal-binding; S-adenosyl-L-methionine.
FT CHAIN 1..299
FT /note="Neomycin C epimerase"
FT /id="PRO_0000431421"
FT DOMAIN 10..222
FT /note="Radical SAM core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT ACT_SITE 249
FT /note="Proton donor"
FT /evidence="ECO:0000303|PubMed:25230155"
FT BINDING 26
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000303|PubMed:25230155, ECO:0000305"
FT BINDING 30
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000303|PubMed:25230155, ECO:0000305"
FT BINDING 33
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000303|PubMed:25230155, ECO:0000305"
FT BINDING 226
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000303|PubMed:25230155"
FT BINDING 247
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000303|PubMed:25230155"
FT BINDING 271
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000303|PubMed:25230155"
FT BINDING 274
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000303|PubMed:25230155"
FT MUTAGEN 26..33
FT /note="CNIRCTYC->ANIRATYA: Loss of enzymatic activity."
FT /evidence="ECO:0000269|PubMed:25230155"
FT MUTAGEN 249
FT /note="C->A: Reacts with neomycin C, but generates a new
FT enzymatic product and not neomycin B."
FT /evidence="ECO:0000269|PubMed:25230155"
SQ SEQUENCE 299 AA; 34363 MW; A1F806B2BE28A2ED CRC64;
MTTDIVWPPP VRQVRAYRNI VVDGACNIRC TYCEVKKTKV DQPATIRSLD RIFAEYEPDA
VLFRVESDGE ITLYPKIVDH LQKRAAEGYR VEVLSNGTKL PRALEGRPDL LWVFSVDGHT
EAMNAKRGLK QPQIDRILDA AVELGAELQT VYWGQPVEEV NAYIDLLESR GYRGLLHFMP
LLAFKGRPLT VNLRYQDLHP ADFLAPPEYF RRWNHIFETG RRDAVCDQIT NGYNYQVSGD
EIRMVKCDCY SVPKHLVHGF GPIREFDDWP CGTCIANQEF NNSRERMRVP QGRIPLPLV
