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Neomycin C epimerase (EC 5.1.3.-) (Radical S-adenosyl-L-methionine epimerase NeoN) (Radical SAM epimerase NeoN)

 NEOEP_STRFR             Reviewed;         299 AA.
Q53U14;
07-JAN-2015, integrated into UniProtKB/Swiss-Prot.
24-MAY-2005, sequence version 1.
05-DEC-2018, entry version 58.
RecName: Full=Neomycin C epimerase {ECO:0000305|PubMed:25230155};
EC=5.1.3.- {ECO:0000269|PubMed:25230155};
AltName: Full=Radical S-adenosyl-L-methionine epimerase NeoN {ECO:0000303|PubMed:25230155};
Short=Radical SAM epimerase NeoN {ECO:0000303|PubMed:25230155};
Name=neoN {ECO:0000303|PubMed:25230155, ECO:0000312|EMBL:CAF33317.1};
Synonyms=neoH {ECO:0000312|EMBL:BAD95825.1};
Streptomyces fradiae (Streptomyces roseoflavus).
Bacteria; Actinobacteria; Streptomycetales; Streptomycetaceae;
Streptomyces.
NCBI_TaxID=1906;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=ATCC 10745 / CBS 498.68 / DSM 40063 / JCM 4133 / NBRC 12773 /
NCIMB 8233 / NRRL B-1195 / VKM Ac-150;
Aboshanab K.M., Schmidt-Beissner H., Wehmeier U.F., Piepersberg W.,
Welzel K., Vente A.;
"Analysis and comparison of biosynthetic gene clusters for the 2-
deoxy-inosamine containing aminoglycoside antibiotics ribostamycin,
neomycin, lividomycin, paromomycin and butirosin.";
Submitted (FEB-2004) to the EMBL/GenBank/DDBJ databases.
[2]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=ATCC 10745 / CBS 498.68 / DSM 40063 / JCM 4133 / NBRC 12773 /
NCIMB 8233 / NRRL B-1195 / VKM Ac-150;
Subba B., Kharel M.K., Sthapit B., Liou K., Lee H.C., Woo J.S.,
Sohng J.K.;
"Cloning and characterization of a neomycin biosynthetic gene cluster
from Streptomyces fradiae, ATCC 10745.";
Submitted (JUL-2004) to the EMBL/GenBank/DDBJ databases.
[3]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=ATCC 10745 / CBS 498.68 / DSM 40063 / JCM 4133 / NBRC 12773 /
NCIMB 8233 / NRRL B-1195 / VKM Ac-150;
PubMed=16506694; DOI=10.1038/ja.2005.104;
Kudo F., Yamamoto Y., Yokoyama K., Eguchi T., Kakinuma K.;
"Biosynthesis of 2-deoxystreptamine by three crucial enzymes in
Streptomyces fradiae NBRC 12773.";
J. Antibiot. 58:766-774(2005).
[4]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=ATCC 10745 / CBS 498.68 / DSM 40063 / JCM 4133 / NBRC 12773 /
NCIMB 8233 / NRRL B-1195 / VKM Ac-150;
PubMed=15827636; DOI=10.1039/b501199j;
Huang F., Haydock S.F., Mironenko T., Spiteller D., Li Y.,
Spencer J.B.;
"The neomycin biosynthetic gene cluster of Streptomyces fradiae NCIMB
8233: characterisation of an aminotransferase involved in the
formation of 2-deoxystreptamine.";
Org. Biomol. Chem. 3:1410-1418(2005).
[5]
FUNCTION, CATALYTIC ACTIVITY, COFACTOR, REACTION MECHANISM, ACTIVE
SITE, AND MUTAGENESIS OF 26-CYS--CYS-33 AND CYS-249.
STRAIN=ATCC 10745 / CBS 498.68 / DSM 40063 / JCM 4133 / NBRC 12773 /
NCIMB 8233 / NRRL B-1195 / VKM Ac-150;
PubMed=25230155; DOI=10.1021/ja507759f;
Kudo F., Hoshi S., Kawashima T., Kamachi T., Eguchi T.;
"Characterization of a radical S-adenosyl-L-methionine epimerase,
NeoN, in the last step of neomycin B biosynthesis.";
J. Am. Chem. Soc. 136:13909-13915(2014).
-!- FUNCTION: Catalyzes the last step of neomycin B biosynthesis, i.e.
the irreversible epimerization at C-5''' of neomycin C to give
neomycin B. To a lesser extent, is also able to convert neomycin
Y2 to neomycin Y1. {ECO:0000269|PubMed:25230155}.
-!- CATALYTIC ACTIVITY:
Reaction=AH2 + neomycin C + S-adenosyl-L-methionine = 5'-
deoxyadenosine + A + H(+) + L-methionine + neomycin B;
Xref=Rhea:RHEA:47692, ChEBI:CHEBI:13193, ChEBI:CHEBI:15378,
ChEBI:CHEBI:17319, ChEBI:CHEBI:17499, ChEBI:CHEBI:57844,
ChEBI:CHEBI:59789, ChEBI:CHEBI:65077, ChEBI:CHEBI:87835;
Evidence={ECO:0000269|PubMed:25230155};
-!- COFACTOR:
Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
Evidence={ECO:0000269|PubMed:25230155};
Note=Binds 2 [4Fe-4S] clusters. One cluster is coordinated with 3
cysteines and an exchangeable S-adenosyl-L-methionine. The second
cluster is proposed to be involved in the electron-transfer
mechanism for the catalytic cycle. {ECO:0000269|PubMed:25230155};
-!- PATHWAY: Antibiotic biosynthesis; neomycin biosynthesis.
{ECO:0000303|PubMed:25230155}.
-!- SIMILARITY: Belongs to the radical SAM superfamily. {ECO:0000305}.
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EMBL; AB211959; BAD95825.1; -; Genomic_DNA.
EMBL; AJ629247; CAF33317.1; -; Genomic_DNA.
EMBL; AJ786317; CAH05096.1; -; Genomic_DNA.
EMBL; AJ843080; CAH58695.1; -; Genomic_DNA.
RefSeq; WP_031132490.1; NZ_MUNC01000172.1.
ProteinModelPortal; Q53U14; -.
KEGG; ag:BAD95825; -.
KO; K13557; -.
UniPathway; UPA00969; -.
GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
GO; GO:0016853; F:isomerase activity; IEA:UniProtKB-KW.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0017000; P:antibiotic biosynthetic process; IEA:UniProtKB-KW.
Gene3D; 3.20.20.70; -; 1.
InterPro; IPR013785; Aldolase_TIM.
InterPro; IPR000385; MoaA_NifB_PqqE_Fe-S-bd_CS.
InterPro; IPR007197; rSAM.
Pfam; PF04055; Radical_SAM; 1.
SFLD; SFLDS00029; Radical_SAM; 1.
PROSITE; PS01305; MOAA_NIFB_PQQE; 1.
1: Evidence at protein level;
4Fe-4S; Antibiotic biosynthesis; Iron; Iron-sulfur; Isomerase;
Metal-binding; S-adenosyl-L-methionine.
CHAIN 1 299 Neomycin C epimerase.
/FTId=PRO_0000431421.
ACT_SITE 249 249 Proton donor.
{ECO:0000303|PubMed:25230155}.
METAL 26 26 Iron-sulfur 1 (4Fe-4S-S-AdoMet).
{ECO:0000303|PubMed:25230155,
ECO:0000305}.
METAL 30 30 Iron-sulfur 1 (4Fe-4S-S-AdoMet).
{ECO:0000303|PubMed:25230155,
ECO:0000305}.
METAL 33 33 Iron-sulfur 1 (4Fe-4S-S-AdoMet).
{ECO:0000303|PubMed:25230155,
ECO:0000305}.
METAL 226 226 Iron-sulfur 2 (4Fe-4S).
{ECO:0000303|PubMed:25230155}.
METAL 247 247 Iron-sulfur 2 (4Fe-4S).
{ECO:0000303|PubMed:25230155}.
METAL 271 271 Iron-sulfur 2 (4Fe-4S).
{ECO:0000303|PubMed:25230155}.
METAL 274 274 Iron-sulfur 2 (4Fe-4S).
{ECO:0000303|PubMed:25230155}.
MUTAGEN 26 33 CNIRCTYC->ANIRATYA: Loss of enzymatic
activity. {ECO:0000269|PubMed:25230155}.
MUTAGEN 249 249 C->A: Reacts with neomycin C, but
generates a new enzymatic product and not
neomycin B.
{ECO:0000269|PubMed:25230155}.
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


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