GCI_AGRFC
ID GCI_AGRFC Reviewed; 378 AA.
AC A9CEQ8;
DT 11-JUN-2014, integrated into UniProtKB/Swiss-Prot.
DT 15-JAN-2008, sequence version 1.
DT 03-AUG-2022, entry version 78.
DE RecName: Full=D-galactarolactone cycloisomerase;
DE EC=5.5.1.27 {ECO:0000269|PubMed:22493433, ECO:0000269|PubMed:24450804};
GN Name=gci; OrderedLocusNames=Atu3139;
OS Agrobacterium fabrum (strain C58 / ATCC 33970) (Agrobacterium tumefaciens
OS (strain C58)).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Rhizobiaceae; Rhizobium/Agrobacterium group; Agrobacterium;
OC Agrobacterium tumefaciens complex.
OX NCBI_TaxID=176299;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=C58 / ATCC 33970;
RX PubMed=11743193; DOI=10.1126/science.1066804;
RA Wood D.W., Setubal J.C., Kaul R., Monks D.E., Kitajima J.P., Okura V.K.,
RA Zhou Y., Chen L., Wood G.E., Almeida N.F. Jr., Woo L., Chen Y.,
RA Paulsen I.T., Eisen J.A., Karp P.D., Bovee D. Sr., Chapman P.,
RA Clendenning J., Deatherage G., Gillet W., Grant C., Kutyavin T., Levy R.,
RA Li M.-J., McClelland E., Palmieri A., Raymond C., Rouse G.,
RA Saenphimmachak C., Wu Z., Romero P., Gordon D., Zhang S., Yoo H., Tao Y.,
RA Biddle P., Jung M., Krespan W., Perry M., Gordon-Kamm B., Liao L., Kim S.,
RA Hendrick C., Zhao Z.-Y., Dolan M., Chumley F., Tingey S.V., Tomb J.-F.,
RA Gordon M.P., Olson M.V., Nester E.W.;
RT "The genome of the natural genetic engineer Agrobacterium tumefaciens
RT C58.";
RL Science 294:2317-2323(2001).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=C58 / ATCC 33970;
RX PubMed=11743194; DOI=10.1126/science.1066803;
RA Goodner B., Hinkle G., Gattung S., Miller N., Blanchard M., Qurollo B.,
RA Goldman B.S., Cao Y., Askenazi M., Halling C., Mullin L., Houmiel K.,
RA Gordon J., Vaudin M., Iartchouk O., Epp A., Liu F., Wollam C., Allinger M.,
RA Doughty D., Scott C., Lappas C., Markelz B., Flanagan C., Crowell C.,
RA Gurson J., Lomo C., Sear C., Strub G., Cielo C., Slater S.;
RT "Genome sequence of the plant pathogen and biotechnology agent
RT Agrobacterium tumefaciens C58.";
RL Science 294:2323-2328(2001).
RN [3]
RP IDENTIFICATION BY MASS SPECTROMETRY, FUNCTION, CATALYTIC ACTIVITY, GENE
RP NAME, SUBSTRATE SPECIFICITY, COFACTOR, PH DEPENDENCE, AND SUBUNIT.
RC STRAIN=C58 / ATCC 33970;
RX PubMed=22493433; DOI=10.1074/jbc.m111.335240;
RA Andberg M., Maaheimo H., Boer H., Penttila M., Koivula A., Richard P.;
RT "Characterization of a novel Agrobacterium tumefaciens galactarolactone
RT cycloisomerase enzyme for direct conversion of D-galactarolactone to 3-
RT deoxy-2-keto-L-threo-hexarate.";
RL J. Biol. Chem. 287:17662-17671(2012).
RN [4]
RP FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, AND PATHWAY.
RC STRAIN=C58 / ATCC 33970;
RX PubMed=24450804; DOI=10.1021/bi5000492;
RA Bouvier J.T., Groninger-Poe F.P., Vetting M., Almo S.C., Gerlt J.A.;
RT "Galactaro delta-lactone isomerase: lactone isomerization by a member of
RT the amidohydrolase superfamily.";
RL Biochemistry 53:614-616(2014).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) IN COMPLEX WITH CALCIUM.
RC STRAIN=C58 / ATCC 33970;
RG Enzyme Function Initiative (EFI);
RA Vetting M.W., Bouvier J.T., Morisco L.L., Wasserman S.R., Sojitra S.,
RA Imker H.J., Gerlt J.A., Almo S.C.;
RT "Crystal structures of a proposed galactarolactone cycloisomerase from
RT Agrobacterium tumefaciens, target EFI-500704, with bound Ca, ordered and
RT disordered loops.";
RL Submitted (OCT-2012) to the PDB data bank.
CC -!- FUNCTION: Catalyzes the ring opening of D-galactaro-1,4-lactone to
CC yield 5-keto-4-deoxy-D-glucarate (KDG) via a beta-elimination reaction.
CC This is a step in the oxidative degradation pathway of D-galacturonate,
CC which allows A.tumefaciens to utilize D-galacturonate as a sole carbon
CC source. To a lesser extent, can also use D-glucaro-1,4-lactone as
CC substrate to produce KDG, but cannot use D-galactaro-1,5-lactone, D-
CC glucaro-6,3-lactone and linear D-glucarate.
CC {ECO:0000269|PubMed:22493433, ECO:0000269|PubMed:24450804}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-glucaro-1,4-lactone = 5-dehydro-4-deoxy-D-glucarate + H(+);
CC Xref=Rhea:RHEA:45604, ChEBI:CHEBI:15378, ChEBI:CHEBI:42819,
CC ChEBI:CHEBI:85336; EC=5.5.1.27;
CC Evidence={ECO:0000269|PubMed:22493433, ECO:0000269|PubMed:24450804};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-galactaro-1,4-lactone = 5-dehydro-4-deoxy-D-glucarate +
CC H(+); Xref=Rhea:RHEA:45600, ChEBI:CHEBI:15378, ChEBI:CHEBI:42819,
CC ChEBI:CHEBI:85317; EC=5.5.1.27;
CC Evidence={ECO:0000269|PubMed:22493433, ECO:0000269|PubMed:24450804};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:22493433};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is 8.5. {ECO:0000269|PubMed:22493433};
CC -!- PATHWAY: Carbohydrate acid metabolism; D-galacturonate degradation via
CC prokaryotic oxidative pathway. {ECO:0000269|PubMed:24450804}.
CC -!- SUBUNIT: Homooctamer. {ECO:0000269|PubMed:22493433, ECO:0000269|Ref.5}.
CC -!- SIMILARITY: Belongs to the mandelate racemase/muconate lactonizing
CC enzyme family. {ECO:0000305}.
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DR EMBL; AE007870; AAK90247.1; -; Genomic_DNA.
DR PIR; AE2942; AE2942.
DR PIR; E98340; E98340.
DR RefSeq; NP_357462.1; NC_003063.2.
DR RefSeq; WP_010972789.1; NC_003063.2.
DR PDB; 4GGB; X-ray; 2.00 A; A=1-378.
DR PDB; 4HPN; X-ray; 1.60 A; A=1-378.
DR PDBsum; 4GGB; -.
DR PDBsum; 4HPN; -.
DR AlphaFoldDB; A9CEQ8; -.
DR SMR; A9CEQ8; -.
DR STRING; 176299.Atu3139; -.
DR DNASU; 1134941; -.
DR EnsemblBacteria; AAK90247; AAK90247; Atu3139.
DR GeneID; 66223457; -.
DR KEGG; atu:Atu3139; -.
DR PATRIC; fig|176299.10.peg.2984; -.
DR eggNOG; COG4948; Bacteria.
DR HOGENOM; CLU_030273_3_0_5; -.
DR OMA; FAPHLWA; -.
DR PhylomeDB; A9CEQ8; -.
DR BioCyc; AGRO:ATU3139-MON; -.
DR BioCyc; MetaCyc:MON-18901; -.
DR BRENDA; 5.5.1.27; 200.
DR UniPathway; UPA01050; -.
DR Proteomes; UP000000813; Chromosome linear.
DR GO; GO:0016853; F:isomerase activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0009063; P:cellular amino acid catabolic process; IEA:InterPro.
DR Gene3D; 3.20.20.120; -; 1.
DR Gene3D; 3.30.390.10; -; 1.
DR InterPro; IPR036849; Enolase-like_C_sf.
DR InterPro; IPR029017; Enolase-like_N.
DR InterPro; IPR029065; Enolase_C-like.
DR InterPro; IPR034618; GLI.
DR InterPro; IPR018110; Mandel_Rmase/mucon_lact_enz_CS.
DR InterPro; IPR013342; Mandelate_racemase_C.
DR InterPro; IPR013341; Mandelate_racemase_N_dom.
DR Pfam; PF13378; MR_MLE_C; 1.
DR Pfam; PF02746; MR_MLE_N; 1.
DR SFLD; SFLDF00553; galactarolactone_cycloisomeras; 1.
DR SMART; SM00922; MR_MLE; 1.
DR SUPFAM; SSF51604; SSF51604; 1.
DR SUPFAM; SSF54826; SSF54826; 1.
DR PROSITE; PS00908; MR_MLE_1; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Isomerase; Magnesium; Metal-binding; Reference proteome.
FT CHAIN 1..378
FT /note="D-galactarolactone cycloisomerase"
FT /id="PRO_0000429433"
FT ACT_SITE 296
FT /note="Proton acceptor"
FT /evidence="ECO:0000250"
FT BINDING 194
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT BINDING 220
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT BINDING 246
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT SITE 269
FT /note="Increases basicity of active site His"
FT /evidence="ECO:0000250"
FT STRAND 3..20
FT /evidence="ECO:0007829|PDB:4HPN"
FT STRAND 25..38
FT /evidence="ECO:0007829|PDB:4HPN"
FT STRAND 43..48
FT /evidence="ECO:0007829|PDB:4HPN"
FT HELIX 52..63
FT /evidence="ECO:0007829|PDB:4HPN"
FT TURN 64..68
FT /evidence="ECO:0007829|PDB:4HPN"
FT HELIX 74..84
FT /evidence="ECO:0007829|PDB:4HPN"
FT HELIX 85..88
FT /evidence="ECO:0007829|PDB:4GGB"
FT HELIX 93..113
FT /evidence="ECO:0007829|PDB:4HPN"
FT HELIX 117..120
FT /evidence="ECO:0007829|PDB:4HPN"
FT STRAND 127..134
FT /evidence="ECO:0007829|PDB:4HPN"
FT HELIX 144..157
FT /evidence="ECO:0007829|PDB:4HPN"
FT STRAND 161..166
FT /evidence="ECO:0007829|PDB:4HPN"
FT HELIX 171..185
FT /evidence="ECO:0007829|PDB:4HPN"
FT TURN 186..188
FT /evidence="ECO:0007829|PDB:4HPN"
FT STRAND 189..194
FT /evidence="ECO:0007829|PDB:4HPN"
FT HELIX 201..211
FT /evidence="ECO:0007829|PDB:4HPN"
FT HELIX 212..214
FT /evidence="ECO:0007829|PDB:4HPN"
FT STRAND 217..220
FT /evidence="ECO:0007829|PDB:4GGB"
FT HELIX 228..237
FT /evidence="ECO:0007829|PDB:4HPN"
FT STRAND 238..240
FT /evidence="ECO:0007829|PDB:4HPN"
FT STRAND 242..244
FT /evidence="ECO:0007829|PDB:4HPN"
FT HELIX 250..259
FT /evidence="ECO:0007829|PDB:4HPN"
FT STRAND 264..266
FT /evidence="ECO:0007829|PDB:4HPN"
FT TURN 270..274
FT /evidence="ECO:0007829|PDB:4HPN"
FT HELIX 275..289
FT /evidence="ECO:0007829|PDB:4HPN"
FT HELIX 301..313
FT /evidence="ECO:0007829|PDB:4HPN"
FT STRAND 328..331
FT /evidence="ECO:0007829|PDB:4HPN"
FT HELIX 337..340
FT /evidence="ECO:0007829|PDB:4HPN"
FT STRAND 342..344
FT /evidence="ECO:0007829|PDB:4HPN"
FT STRAND 352..354
FT /evidence="ECO:0007829|PDB:4HPN"
FT STRAND 358..360
FT /evidence="ECO:0007829|PDB:4HPN"
FT HELIX 367..372
FT /evidence="ECO:0007829|PDB:4HPN"
SQ SEQUENCE 378 AA; 41456 MW; 3B4EC2C7877DDCD6 CRC64;
MKITAVRTHL LEHRLDTPFE SASMRFDRRA HVLVEIECDD GTVGWGECLG PARPNAAVVQ
AYSGWLIGQD PRQTEKIWAV LYNALRDQGQ RGLSLTALSG IDIALWDIKG KHYGASISML
LGGRWRESVR AYATGSFKRD NVDRVSDNAS EMAERRAEGF HACKIKIGFG VEEDLRVIAA
VREAIGPDMR LMIDANHGYT VTEAITLGDR AAGFGIDWFE EPVVPEQLDA YARVRAGQPI
PVAGGETWHG RYGMWQALSA GAVDILQPDL CGCGGFSEIQ KIATLATLHG VRIVPHVWGT
GVQIAAALQF MAAMTPDPVR VNPIEPIMEF DRTHNPFRQA VLREPLEAVN GVVTIPDGPG
LGIEINRDAL TEFRMPDP
