LIGU_NOVK1
ID LIGU_NOVK1 Reviewed; 357 AA.
AC Q0KJL4;
DT 13-FEB-2019, integrated into UniProtKB/Swiss-Prot.
DT 03-OCT-2006, sequence version 1.
DT 25-MAY-2022, entry version 48.
DE RecName: Full=(4E)-oxalomesaconate Delta-isomerase {ECO:0000305|PubMed:29658701};
DE Short=OMA isomerase {ECO:0000305|PubMed:29658701};
DE EC=5.3.3.- {ECO:0000269|PubMed:29658701};
DE AltName: Full=1,3-allylic isomerase LigU {ECO:0000303|PubMed:29658701};
GN Name=ligU {ECO:0000303|PubMed:29658701};
GN ORFNames=ORF100 {ECO:0000312|EMBL:BAF03328.1};
OS Novosphingobium sp. (strain KA1) (Sphingomonas sp. (strain KA1)).
OG Plasmid pCAR3 {ECO:0000312|EMBL:BAF03328.1}.
OC Bacteria; Proteobacteria; Alphaproteobacteria; Sphingomonadales;
OC Sphingomonadaceae; Novosphingobium; unclassified Novosphingobium.
OX NCBI_TaxID=164608;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=KA1 {ECO:0000312|EMBL:BAF03328.1};
RC PLASMID=pCAR3 {ECO:0000312|EMBL:BAF03328.1};
RX PubMed=17172338; DOI=10.1128/jb.01486-06;
RA Shintani M., Urata M., Inoue K., Eto K., Habe H., Omori T., Yamane H.,
RA Nojiri H.;
RT "The Sphingomonas plasmid pCAR3 is involved in complete mineralization of
RT carbazole.";
RL J. Bacteriol. 189:2007-2020(2007).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND PATHWAY.
RC STRAIN=KA1;
RX PubMed=29658701; DOI=10.1021/acs.biochem.8b00295;
RA Hogancamp T.N., Raushel F.M.;
RT "Functional annotation of LigU as a 1,3-allylic isomerase during the
RT degradation of lignin in the protocatechuate 4,5-cleavage pathway from the
RT soil bacterium Sphingobium sp. SYK-6.";
RL Biochemistry 57:2837-2845(2018).
CC -!- FUNCTION: Contributes to the degradation of lignin at the level of the
CC protocatechuate 4,5-cleavage pathway. Catalyzes the isomerization of
CC the double bond between C4 and C5 in (4E)-oxalomesaconate (OMA) to
CC (3Z)-2-keto-4-carboxy-3-hexenedioate (KCH), where the double bond has
CC migrated between C3 and C4 via a 1,3-allylic isomerization.
CC {ECO:0000269|PubMed:29658701}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(1E)-4-oxobut-1-ene-1,2,4-tricarboxylate = (3Z)-2-oxo-4-
CC carboxy-3-hexenedioate; Xref=Rhea:RHEA:58504, ChEBI:CHEBI:57471,
CC ChEBI:CHEBI:142690; Evidence={ECO:0000269|PubMed:29658701};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=170 uM for (4E)-oxalomesaconate (at pH 8.0)
CC {ECO:0000269|PubMed:29658701};
CC Note=kcat is 1300 sec(-1) (at pH 8.0). {ECO:0000269|PubMed:29658701};
CC -!- PATHWAY: Secondary metabolite metabolism; lignin degradation.
CC {ECO:0000305|PubMed:29658701}.
CC -!- SIMILARITY: Belongs to the PrpF family. {ECO:0000305}.
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DR EMBL; AB270530; BAF03328.1; -; Genomic_DNA.
DR RefSeq; WP_011607995.1; NC_008308.1.
DR RefSeq; YP_718040.1; NC_008308.1.
DR PDB; 6P3H; X-ray; 1.62 A; A/B/C/D=1-357.
DR PDB; 6P3J; X-ray; 2.02 A; A/B=1-357.
DR PDB; 6P3K; X-ray; 1.88 A; A/B=1-357.
DR PDBsum; 6P3H; -.
DR PDBsum; 6P3J; -.
DR PDBsum; 6P3K; -.
DR AlphaFoldDB; Q0KJL4; -.
DR SMR; Q0KJL4; -.
DR SABIO-RK; Q0KJL4; -.
DR UniPathway; UPA00892; -.
DR GO; GO:0016853; F:isomerase activity; IEA:UniProtKB-KW.
DR GO; GO:0046274; P:lignin catabolic process; IEA:UniProtKB-UniPathway.
DR InterPro; IPR007400; PrpF_protein.
DR PANTHER; PTHR43709; PTHR43709; 1.
DR Pfam; PF04303; PrpF; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Aromatic hydrocarbons catabolism; Isomerase; Plasmid.
FT CHAIN 1..357
FT /note="(4E)-oxalomesaconate Delta-isomerase"
FT /id="PRO_0000446300"
FT STRAND 10..18
FT /evidence="ECO:0007829|PDB:6P3H"
FT STRAND 21..27
FT /evidence="ECO:0007829|PDB:6P3H"
FT HELIX 28..30
FT /evidence="ECO:0007829|PDB:6P3H"
FT HELIX 35..46
FT /evidence="ECO:0007829|PDB:6P3H"
FT HELIX 62..64
FT /evidence="ECO:0007829|PDB:6P3H"
FT STRAND 65..72
FT /evidence="ECO:0007829|PDB:6P3H"
FT STRAND 80..87
FT /evidence="ECO:0007829|PDB:6P3H"
FT STRAND 89..92
FT /evidence="ECO:0007829|PDB:6P3H"
FT HELIX 101..113
FT /evidence="ECO:0007829|PDB:6P3H"
FT STRAND 121..130
FT /evidence="ECO:0007829|PDB:6P3H"
FT TURN 131..133
FT /evidence="ECO:0007829|PDB:6P3H"
FT STRAND 136..142
FT /evidence="ECO:0007829|PDB:6P3H"
FT HELIX 144..146
FT /evidence="ECO:0007829|PDB:6P3H"
FT STRAND 152..154
FT /evidence="ECO:0007829|PDB:6P3H"
FT STRAND 166..172
FT /evidence="ECO:0007829|PDB:6P3H"
FT TURN 175..178
FT /evidence="ECO:0007829|PDB:6P3H"
FT STRAND 179..182
FT /evidence="ECO:0007829|PDB:6P3H"
FT STRAND 185..187
FT /evidence="ECO:0007829|PDB:6P3K"
FT STRAND 189..191
FT /evidence="ECO:0007829|PDB:6P3H"
FT STRAND 194..209
FT /evidence="ECO:0007829|PDB:6P3H"
FT HELIX 210..213
FT /evidence="ECO:0007829|PDB:6P3H"
FT HELIX 221..225
FT /evidence="ECO:0007829|PDB:6P3H"
FT HELIX 228..241
FT /evidence="ECO:0007829|PDB:6P3H"
FT TURN 242..246
FT /evidence="ECO:0007829|PDB:6P3H"
FT STRAND 256..262
FT /evidence="ECO:0007829|PDB:6P3H"
FT STRAND 265..280
FT /evidence="ECO:0007829|PDB:6P3H"
FT HELIX 286..295
FT /evidence="ECO:0007829|PDB:6P3H"
FT HELIX 302..306
FT /evidence="ECO:0007829|PDB:6P3H"
FT STRAND 312..321
FT /evidence="ECO:0007829|PDB:6P3H"
FT STRAND 324..332
FT /evidence="ECO:0007829|PDB:6P3H"
FT STRAND 334..336
FT /evidence="ECO:0007829|PDB:6P3J"
FT STRAND 338..345
FT /evidence="ECO:0007829|PDB:6P3H"
FT STRAND 347..356
FT /evidence="ECO:0007829|PDB:6P3H"
SQ SEQUENCE 357 AA; 36855 MW; AFDF27DD10A5D6A6 CRC64;
MPRRDRNMDS APCMWMRGGT SKGGYFLRAD LPADTAARDA FLLAVMGSPD PRQIDGMGGA
DPLTSKVAVV SKSERPGIDV DYLFLQVFVD QAIVTDAQNC GNILAGVGPF AIERGLVAAS
GDETRVAIFM ENTGQVAVAT VRTPGGSVTY AGDAAIDGVP GTHAPIPTEF RDTAGSSCGA
LLPSGNAVDV VNGLPVTLID NGMPCVVMKA ADVGITGYED RDSLDANAEL KAKIEAIRLA
VGELMNLGDV TEKSVPKMML VAPPRDGGAV CVRSFIPHRA HATIGVLGAV SVATACLIPG
SPAAEVAVVP EGARKTLSIE HPTGEMSCVL EVDDAGNVVS AALLRTARKL MDGVVFV
