DESII_STRVZ
ID DESII_STRVZ Reviewed; 485 AA.
AC Q9ZGH1;
DT 29-OCT-2014, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-1999, sequence version 1.
DT 03-AUG-2022, entry version 58.
DE RecName: Full=dTDP-4-amino-4,6-dideoxy-D-glucose ammonia-lyase {ECO:0000303|PubMed:19746907};
DE EC=4.3.1.30 {ECO:0000269|PubMed:16187386, ECO:0000269|PubMed:19746907, ECO:0000269|PubMed:20121093};
DE AltName: Full=dTDP-D-quinovose dehydrogenase {ECO:0000305};
DE AltName: Full=dTDP-D-quinovose:S-adenosyl-L-methionine 1-oxidoreductase {ECO:0000305};
DE EC=1.1.99.- {ECO:0000269|PubMed:20121093};
GN Name=desII {ECO:0000303|PubMed:9770448};
OS Streptomyces venezuelae.
OC Bacteria; Actinobacteria; Streptomycetales; Streptomycetaceae;
OC Streptomyces.
OX NCBI_TaxID=54571;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 15439 / DSM 41110 / IMRU3627 / M-2140;
RX PubMed=9770448; DOI=10.1073/pnas.95.21.12111;
RA Xue Y., Zhao L., Liu H.W., Sherman D.H.;
RT "A gene cluster for macrolide antibiotic biosynthesis in Streptomyces
RT venezuelae: architecture of metabolic diversity.";
RL Proc. Natl. Acad. Sci. U.S.A. 95:12111-12116(1998).
RN [2]
RP PROTEIN SEQUENCE OF 2-11, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL
RP PROPERTIES, COFACTOR, SUBSTRATE SPECIFICITY, AND SUBUNIT.
RX PubMed=19746907; DOI=10.1021/ja903354k;
RA Szu P.H., Ruszczycky M.W., Choi S.H., Yan F., Liu H.W.;
RT "Characterization and mechanistic studies of DesII: a radical S-adenosyl-L-
RT methionine enzyme involved in the biosynthesis of TDP-D-desosamine.";
RL J. Am. Chem. Soc. 131:14030-14042(2009).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, AND SUBUNIT.
RX PubMed=16187386; DOI=10.1002/anie.200501998;
RA Szu P.H., He X., Zhao L., Liu H.W.;
RT "Biosynthesis of TDP-D-desosamine: identification of a strategy for C4
RT deoxygenation.";
RL Angew. Chem. Int. Ed. Engl. 44:6742-6746(2005).
RN [4]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, AND REACTION MECHANISM.
RX PubMed=20121093; DOI=10.1021/ja909451a;
RA Ruszczycky M.W., Choi S.H., Liu H.W.;
RT "Stoichiometry of the redox neutral deamination and oxidative
RT dehydrogenation reactions catalyzed by the radical SAM enzyme DesII.";
RL J. Am. Chem. Soc. 132:2359-2369(2010).
RN [5]
RP FUNCTION, COFACTOR, AND REACTION MECHANISM.
RX PubMed=21513273; DOI=10.1021/ja201212f;
RA Ruszczycky M.W., Choi S.H., Mansoorabadi S.O., Liu H.W.;
RT "Mechanistic studies of the radical S-adenosyl-L-methionine enzyme DesII:
RT EPR characterization of a radical intermediate generated during its
RT catalyzed dehydrogenation of TDP-D-quinovose.";
RL J. Am. Chem. Soc. 133:7292-7295(2011).
CC -!- FUNCTION: Involved in the biosynthesis of dTDP-alpha-D-desosamine, a
CC sugar found in several bacterial macrolide antibiotics. Catalyzes the
CC SAM-dependent deamination of dTDP-4-amino-4,6-deoxyglucose (dTDP-
CC viosamine) to yield dTDP-3-keto-4,6-deoxyglucose. It can also catalyze
CC the oxidative dehydrogenation of the non-physiological substrate dTDP-
CC D-quinovose to dTDP-3-keto-6-deoxy-d-glucose. It can also deaminate
CC dTDP-3-amino-3,6-deoxyglucose. {ECO:0000269|PubMed:16187386,
CC ECO:0000269|PubMed:19746907, ECO:0000269|PubMed:20121093,
CC ECO:0000269|PubMed:21513273}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=AH2 + dTDP-4-amino-4,6-dideoxy-alpha-D-glucose + S-adenosyl-L-
CC methionine = 5'-deoxyadenosine + A + dTDP-3-dehydro-4,6-dideoxy-
CC alpha-D-glucose + H(+) + L-methionine + NH4(+); Xref=Rhea:RHEA:39647,
CC ChEBI:CHEBI:13193, ChEBI:CHEBI:15378, ChEBI:CHEBI:17319,
CC ChEBI:CHEBI:17499, ChEBI:CHEBI:28938, ChEBI:CHEBI:57844,
CC ChEBI:CHEBI:59789, ChEBI:CHEBI:68501, ChEBI:CHEBI:76280; EC=4.3.1.30;
CC Evidence={ECO:0000269|PubMed:16187386, ECO:0000269|PubMed:19746907,
CC ECO:0000269|PubMed:20121093};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000269|PubMed:16187386, ECO:0000269|PubMed:19746907,
CC ECO:0000269|PubMed:20121093, ECO:0000269|PubMed:21513273};
CC Note=Binds 1 [4Fe-4S] cluster. {ECO:0000269|PubMed:16187386,
CC ECO:0000269|PubMed:19746907, ECO:0000269|PubMed:20121093,
CC ECO:0000269|PubMed:21513273};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=50 uM for dTDP-viosamine (at pH 8 and 25 degrees Celsius)
CC {ECO:0000269|PubMed:19746907};
CC Note=kcat is 0.017 sec(-1) for ammonia-lyase activity with dTDP-
CC viosamine as substrate (at pH 8 and 25 degrees Celsius).
CC {ECO:0000269|PubMed:19746907};
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:16187386,
CC ECO:0000269|PubMed:19746907}.
CC -!- MISCELLANEOUS: The reaction starts by the transfer of an electron from
CC the [4Fe-4S] cluster to S-adenosyl-L-methionine, spliting it into
CC methionine and the radical 5-deoxyadenosin-5'-yl, which attacks the
CC sugar substrate. {ECO:0000269|PubMed:20121093}.
CC -!- SIMILARITY: Belongs to the radical SAM superfamily. DesII family.
CC {ECO:0000305}.
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DR EMBL; AF079762; AAC68683.1; -; Genomic_DNA.
DR RefSeq; WP_055641636.1; NZ_CP013129.1.
DR AlphaFoldDB; Q9ZGH1; -.
DR SMR; Q9ZGH1; -.
DR KEGG; ag:AAC68683; -.
DR OrthoDB; 440726at2; -.
DR BioCyc; MetaCyc:MON-16951; -.
DR BRENDA; 4.3.1.30; 6106.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IDA:UniProtKB.
DR GO; GO:0016841; F:ammonia-lyase activity; IDA:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0016491; F:oxidoreductase activity; IEA:UniProtKB-KW.
DR GO; GO:0033068; P:macrolide biosynthetic process; IDA:UniProtKB.
DR Gene3D; 3.20.20.70; -; 1.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR016863; DesII.
DR InterPro; IPR007197; rSAM.
DR PIRSF; PIRSF027982; Reductase_EryCV_prd; 1.
DR SFLD; SFLDF00425; dTDP-4-amino-4_6-dideoxy-D-glu; 1.
DR SFLD; SFLDS00029; Radical_SAM; 1.
DR TIGRFAMs; TIGR04426; rSAM_desII; 1.
PE 1: Evidence at protein level;
KW 4Fe-4S; Antibiotic biosynthesis; Direct protein sequencing; Iron;
KW Iron-sulfur; Lyase; Metal-binding; Oxidoreductase; S-adenosyl-L-methionine.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:19746907"
FT CHAIN 2..485
FT /note="dTDP-4-amino-4,6-dideoxy-D-glucose ammonia-lyase"
FT /id="PRO_0000430850"
FT BINDING 141
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000250"
FT BINDING 145
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000250"
FT BINDING 148
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000250"
SQ SEQUENCE 485 AA; 53201 MW; E0EAC0C48025F1A1 CRC64;
MTAPALSATA PAERCAHPGA DLGAAVHAVG QTLAAGGLVP PDEAGTTARH LVRLAVRYGN
SPFTPLEEAR HDLGVDRDAF RRLLALFGQV PELRTAVETG PAGAYWKNTL LPLEQRGVFD
AALARKPVFP YSVGLYPGPT CMFRCHFCVR VTGARYDPSA LDAGNAMFRS VIDEIPAGNP
SAMYFSGGLE PLTNPGLGSL AAHATDHGLR PTVYTNSFAL TERTLERQPG LWGLHAIRTS
LYGLNDEEYE QTTGKKAAFR RVRENLRRFQ QLRAERESPI NLGFAYIVLP GRASRLLDLV
DFIADLNDAG QGRTIDFVNI REDYSGRDDG KLPQEERAEL QEALNAFEER VRERTPGLHI
DYGYALNSLR TGADAELLRI KPATMRPTAH PQVAVQVDLL GDVYLYREAG FPDLDGATRY
IAGRVTPDTS LTEVVRDFVE RGGEVAAVDG DEYFMDGFDQ VVTARLNQLE RDAADGWEEA
RGFLR
