NOVW_STRNV
ID NOVW_STRNV Reviewed; 207 AA.
AC Q9L9E5;
DT 16-OCT-2013, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 69.
DE RecName: Full=dTDP-4-dehydrorhamnose 3-epimerase {ECO:0000305};
DE EC=5.1.3.-;
DE AltName: Full=Novobiocin biosynthesis protein W {ECO:0000303|PubMed:10770754};
DE AltName: Full=dTDP-6-deoxy-D-xylo-4-hexulose 3-epimerase {ECO:0000303|PubMed:16514445};
GN Name=novW {ECO:0000303|PubMed:10770754};
OS Streptomyces niveus (Streptomyces spheroides).
OC Bacteria; Actinobacteria; Streptomycetales; Streptomycetaceae;
OC Streptomyces.
OX NCBI_TaxID=193462;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 23965 / DSM 40292 / JCM 4252 / NBRC 12917 / NCIMB 11891 / NRRL
RC 2449;
RX PubMed=10770754; DOI=10.1128/aac.44.5.1214-1222.2000;
RA Steffensky M., Muhlenweg A., Wang Z.X., Li S.M., Heide L.;
RT "Identification of the novobiocin biosynthetic gene cluster of Streptomyces
RT spheroides NCIB 11891.";
RL Antimicrob. Agents Chemother. 44:1214-1222(2000).
RN [2]
RP FUNCTION, AND PATHWAY.
RC STRAIN=ATCC 23965 / DSM 40292 / JCM 4252 / NBRC 12917 / NCIMB 11891 / NRRL
RC 2449;
RX PubMed=15752721; DOI=10.1016/j.abb.2005.01.012;
RA Thuy T.T., Lee H.C., Kim C.G., Heide L., Sohng J.K.;
RT "Functional characterizations of novWUS involved in novobiocin biosynthesis
RT from Streptomyces spheroides.";
RL Arch. Biochem. Biophys. 436:161-167(2005).
RN [3]
RP FUNCTION.
RC STRAIN=ATCC 23965 / DSM 40292 / JCM 4252 / NBRC 12917 / NCIMB 11891 / NRRL
RC 2449;
RX PubMed=16514445; DOI=10.1039/b515763c;
RA Tello M., Jakimowicz P., Errey J.C., Freel Meyers C.L., Walsh C.T.,
RA Buttner M.J., Lawson D.M., Field R.A.;
RT "Characterisation of Streptomyces spheroides NovW and revision of its
RT functional assignment to a dTDP-6-deoxy-D-xylo-4-hexulose 3-epimerase.";
RL Chem. Commun. (Camb.) 2006:1079-1081(2006).
RN [4]
RP CRYSTALLIZATION.
RC STRAIN=ATCC 23965 / DSM 40292 / JCM 4252 / NBRC 12917 / NCIMB 11891 / NRRL
RC 2449;
RX PubMed=12876368; DOI=10.1107/s0907444903012848;
RA Jakimowicz P., Freel Meyers C.L., Walsh C.T., Buttner M.J., Lawson D.M.;
RT "Crystallization and preliminary X-ray studies on the putative dTDP sugar
RT epimerase NovW from the novobiocin biosynthetic cluster of Streptomyces
RT spheroides.";
RL Acta Crystallogr. D 59:1507-1509(2003).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS).
RC STRAIN=ATCC 23965 / DSM 40292 / JCM 4252 / NBRC 12917 / NCIMB 11891 / NRRL
RC 2449;
RX PubMed=16411240; DOI=10.1002/prot.20818;
RA Jakimowicz P., Tello M., Meyers C.L., Walsh C.T., Buttner M.J., Field R.A.,
RA Lawson D.M.;
RT "The 1.6-A resolution crystal structure of NovW: a 4-keto-6-deoxy sugar
RT epimerase from the novobiocin biosynthetic gene cluster of Streptomyces
RT spheroides.";
RL Proteins 63:261-265(2006).
CC -!- FUNCTION: dTDP-6-deoxy-D-xylo-4-hexulose 3-epimerase that acts together
CC with NovU to catalyze the formation of dTDP-4-keto-6-deoxy-5-C-methyl-
CC L-lyxo-hexose from dTDP-4-keto-6-deoxy-D-glucose in the novobiocin
CC biosynthesis pathway, an aminocoumarin family antibiotic that targets
CC bacterial DNA gyrases. {ECO:0000269|PubMed:15752721,
CC ECO:0000269|PubMed:16514445}.
CC -!- PATHWAY: Antibiotic biosynthesis; novobiocin biosynthesis.
CC {ECO:0000269|PubMed:15752721}.
CC -!- MISCELLANEOUS: It is unclear whether NovW acts before or after C-
CC methyltransferase NovU in the novobiocin biosynthesis pathway.
CC {ECO:0000305|PubMed:16514445}.
CC -!- SIMILARITY: Belongs to the dTDP-4-dehydrorhamnose 3,5-epimerase family.
CC {ECO:0000305}.
CC -!- CAUTION: Was initially characterized as a 3,5-epimerase in vitro
CC (PubMed:15752721). However, it was later shown that it acts as a dTDP-
CC 6-deoxy-D-xylo-4-hexulose 3-epimerase in vivo (PubMed:16514445).
CC {ECO:0000305|PubMed:15752721, ECO:0000305|PubMed:16514445}.
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DR EMBL; AF170880; AAF67516.1; -; Genomic_DNA.
DR RefSeq; WP_069626151.1; NZ_MDCR01000039.1.
DR PDB; 2C0Z; X-ray; 1.60 A; A=1-207.
DR PDBsum; 2C0Z; -.
DR AlphaFoldDB; Q9L9E5; -.
DR SMR; Q9L9E5; -.
DR KEGG; ag:AAF67516; -.
DR BioCyc; MetaCyc:MON-18088; -.
DR UniPathway; UPA01035; -.
DR EvolutionaryTrace; Q9L9E5; -.
DR GO; GO:0008830; F:dTDP-4-dehydrorhamnose 3,5-epimerase activity; IEA:InterPro.
DR GO; GO:0016853; F:isomerase activity; IDA:UniProtKB.
DR GO; GO:0043642; P:novobiocin biosynthetic process; IDA:UniProtKB.
DR Gene3D; 2.60.120.10; -; 1.
DR InterPro; IPR000888; dTDP_sugar_isom.
DR InterPro; IPR014710; RmlC-like_jellyroll.
DR InterPro; IPR011051; RmlC_Cupin_sf.
DR PANTHER; PTHR21047; PTHR21047; 1.
DR Pfam; PF00908; dTDP_sugar_isom; 1.
DR SUPFAM; SSF51182; SSF51182; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Antibiotic biosynthesis; Isomerase.
FT CHAIN 1..207
FT /note="dTDP-4-dehydrorhamnose 3-epimerase"
FT /id="PRO_0000424010"
FT ACT_SITE 62
FT /note="Proton acceptor"
FT /evidence="ECO:0000250|UniProtKB:Q9HU21"
FT ACT_SITE 132
FT /note="Proton donor"
FT /evidence="ECO:0000250|UniProtKB:Q9HU21"
FT BINDING 23
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q9HU21"
FT BINDING 28
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q9HU21"
FT BINDING 47..49
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q9HU21"
FT BINDING 59
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q9HU21"
FT BINDING 72
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q9HU21"
FT BINDING 119
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q9HU21"
FT BINDING 143
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q9HU21"
FT BINDING 167
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q9HU21"
FT SITE 138
FT /note="Participates in a stacking interaction with the
FT thymidine ring of dTDP-4-oxo-6-deoxyglucose"
FT /evidence="ECO:0000250|UniProtKB:Q5SFD1"
FT STRAND 2..5
FT /evidence="ECO:0007829|PDB:2C0Z"
FT STRAND 11..15
FT /evidence="ECO:0007829|PDB:2C0Z"
FT STRAND 17..21
FT /evidence="ECO:0007829|PDB:2C0Z"
FT STRAND 24..28
FT /evidence="ECO:0007829|PDB:2C0Z"
FT HELIX 32..39
FT /evidence="ECO:0007829|PDB:2C0Z"
FT STRAND 47..54
FT /evidence="ECO:0007829|PDB:2C0Z"
FT STRAND 57..64
FT /evidence="ECO:0007829|PDB:2C0Z"
FT TURN 66..68
FT /evidence="ECO:0007829|PDB:2C0Z"
FT STRAND 72..87
FT /evidence="ECO:0007829|PDB:2C0Z"
FT TURN 93..96
FT /evidence="ECO:0007829|PDB:2C0Z"
FT STRAND 98..104
FT /evidence="ECO:0007829|PDB:2C0Z"
FT TURN 105..107
FT /evidence="ECO:0007829|PDB:2C0Z"
FT STRAND 110..113
FT /evidence="ECO:0007829|PDB:2C0Z"
FT STRAND 117..123
FT /evidence="ECO:0007829|PDB:2C0Z"
FT STRAND 125..136
FT /evidence="ECO:0007829|PDB:2C0Z"
FT TURN 140..142
FT /evidence="ECO:0007829|PDB:2C0Z"
FT STRAND 143..146
FT /evidence="ECO:0007829|PDB:2C0Z"
FT TURN 151..153
FT /evidence="ECO:0007829|PDB:2C0Z"
FT HELIX 166..169
FT /evidence="ECO:0007829|PDB:2C0Z"
FT HELIX 174..179
FT /evidence="ECO:0007829|PDB:2C0Z"
FT HELIX 186..189
FT /evidence="ECO:0007829|PDB:2C0Z"
SQ SEQUENCE 207 AA; 22289 MW; D3BEFC0B91F75867 CRC64;
MRLRPLGIEG VWEITPEQRA DPRGVFLDWY HVDRFAEAIG RPLRLAQANL SVSVRGVVRG
IHFVDVPPGQ AKYVTCVRGA VFDVVVDLRV GSPTYGCWEG TRLDDVSRRA VYLSEGIGHG
FCAISDEATL CYLSSGTYDP ATEHGVHPLD PELAIDWPTG TPLLSPRDQD ALLLAEARDA
GLLPTYATCQ AVTVPSPAPG SVGDPGP
