GRDC_POLSJ
ID GRDC_POLSJ Reviewed; 326 AA.
AC Q12BV1;
DT 23-FEB-2022, integrated into UniProtKB/Swiss-Prot.
DT 22-AUG-2006, sequence version 1.
DT 03-AUG-2022, entry version 90.
DE RecName: Full=Gamma-resorcylate decarboxylase {ECO:0000303|PubMed:29283551};
DE Short=Gamma-RSD {ECO:0000303|PubMed:29283551};
DE EC=4.1.1.103 {ECO:0000269|PubMed:29283551};
DE AltName: Full=2,6-dihydroxybenzoate decarboxylase {ECO:0000303|PubMed:29283551};
DE Short=2,6-DHBD {ECO:0000303|PubMed:29283551};
GN OrderedLocusNames=Bpro_2061 {ECO:0000312|EMBL:ABE43991.1};
OS Polaromonas sp. (strain JS666 / ATCC BAA-500).
OC Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;
OC Comamonadaceae; Polaromonas; unclassified Polaromonas.
OX NCBI_TaxID=296591;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=JS666 / ATCC BAA-500;
RX PubMed=18723656; DOI=10.1128/aem.00197-08;
RA Mattes T.E., Alexander A.K., Richardson P.M., Munk A.C., Han C.S.,
RA Stothard P., Coleman N.V.;
RT "The genome of Polaromonas sp. strain JS666: insights into the evolution of
RT a hydrocarbon- and xenobiotic-degrading bacterium, and features of
RT relevance to biotechnology.";
RL Appl. Environ. Microbiol. 74:6405-6416(2008).
RN [2] {ECO:0007744|PDB:3S4T}
RP X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS).
RC STRAIN=JS666 / ATCC BAA-500;
RA Ramagopal U.A., Toro R., Girlt J.A., Almo S.C.;
RT "Crystal structure of putative amidohydrolase-2 (EFI-target 500288) from
RT Polaromonas sp. JS666.";
RL Submitted (MAY-2011) to the PDB data bank.
RN [3] {ECO:0007744|PDB:4QRO}
RP X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS) IN COMPLEX WITH MANGANESE AND THE
RP INHIBITOR 2-NITRORESORCINOL, FUNCTION, CATALYTIC ACTIVITY, REACTION
RP MECHANISM, COFACTOR, ACTIVITY REGULATION, BIOPHYSICOCHEMICAL PROPERTIES,
RP SUBUNIT, AND ACTIVE SITE.
RC STRAIN=JS666 / ATCC BAA-500;
RX PubMed=29283551; DOI=10.1021/acs.biochem.7b01213;
RA Sheng X., Patskovsky Y., Vladimirova A., Bonanno J.B., Almo S.C., Himo F.,
RA Raushel F.M.;
RT "Mechanism and structure of gamma-resorcylate decarboxylase.";
RL Biochemistry 57:3167-3175(2018).
CC -!- FUNCTION: Involved in the gamma-resorcylate (2,6-dihydroxybenzoate)
CC catabolism (Probable). Catalyzes the reversible decarboxylation of
CC gamma-resorcylate to resorcinol (PubMed:29283551). Also catalyzes the
CC decarboxylation of 2,3-dihydroxybenzoate to catechol, 2,4,6-
CC trihydroxybenzoate to benzene-1,3,5-triol, and 2,6-dihydroxy-4-
CC methylbenzoate to 5-methylbenzene-1,3-diol (PubMed:29283551).
CC {ECO:0000269|PubMed:29283551, ECO:0000305}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2,6-dihydroxybenzoate + H(+) = CO2 + resorcinol;
CC Xref=Rhea:RHEA:49464, ChEBI:CHEBI:15378, ChEBI:CHEBI:16526,
CC ChEBI:CHEBI:27810, ChEBI:CHEBI:131450; EC=4.1.1.103;
CC Evidence={ECO:0000269|PubMed:29283551};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2,3-dihydroxybenzoate + H(+) = catechol + CO2;
CC Xref=Rhea:RHEA:21492, ChEBI:CHEBI:15378, ChEBI:CHEBI:16526,
CC ChEBI:CHEBI:18135, ChEBI:CHEBI:36654;
CC Evidence={ECO:0000269|PubMed:29283551};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:29283551};
CC Note=Binds 1 Mn(2+) ion per subunit. {ECO:0000269|PubMed:29283551};
CC -!- ACTIVITY REGULATION: Activity is inhibited by 2-nitroresorcinol (2-NR).
CC {ECO:0000269|PubMed:29283551}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=32 uM for gamma-resorcylate {ECO:0000269|PubMed:29283551};
CC KM=111 uM for 2,3-dihydroxybenzoate {ECO:0000269|PubMed:29283551};
CC KM=48 uM for 2,4,6-trihydroxybenzoate {ECO:0000269|PubMed:29283551};
CC KM=79 uM for 2,6-dihydroxy-4-methylbenzoate
CC {ECO:0000269|PubMed:29283551};
CC Note=kcat is 0.44 sec(-1) with gamma-resorcylate as substrate. kcat
CC is 0.47 sec(-1) with 2,3-dihydroxybenzoate as substrate. kcat is 0.18
CC sec(-1) with 2,4,6-trihydroxybenzoate as substrate. kcat is 0.38
CC sec(-1) with 2,6-dihydroxy-4-methylbenzoate as substrate.
CC {ECO:0000269|PubMed:29283551};
CC -!- PATHWAY: Aromatic compound metabolism. {ECO:0000305}.
CC -!- SUBUNIT: Homotetramer. {ECO:0000269|PubMed:29283551}.
CC -!- SIMILARITY: Belongs to the metallo-dependent hydrolases superfamily.
CC ACMSD family. {ECO:0000305}.
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DR EMBL; CP000316; ABE43991.1; -; Genomic_DNA.
DR RefSeq; WP_011482990.1; NC_007948.1.
DR PDB; 3S4T; X-ray; 1.90 A; A/B/C/D/E/F/G/H=1-326.
DR PDB; 4QRO; X-ray; 1.65 A; A/B/C/D/E/F/G/H=1-326.
DR PDBsum; 3S4T; -.
DR PDBsum; 4QRO; -.
DR SMR; Q12BV1; -.
DR STRING; 296591.Bpro_2061; -.
DR EnsemblBacteria; ABE43991; ABE43991; Bpro_2061.
DR KEGG; pol:Bpro_2061; -.
DR eggNOG; COG2159; Bacteria.
DR HOGENOM; CLU_039329_5_0_4; -.
DR OMA; FAQNIWI; -.
DR OrthoDB; 1832218at2; -.
DR BRENDA; 4.1.1.103; 15846.
DR Proteomes; UP000001983; Chromosome.
DR GO; GO:0016831; F:carboxy-lyase activity; IEA:UniProtKB-KW.
DR GO; GO:0016787; F:hydrolase activity; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR InterPro; IPR032465; ACMSD.
DR InterPro; IPR006680; Amidohydro-rel.
DR InterPro; IPR032466; Metal_Hydrolase.
DR PANTHER; PTHR21240; PTHR21240; 1.
DR Pfam; PF04909; Amidohydro_2; 1.
DR SUPFAM; SSF51556; SSF51556; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Decarboxylase; Lyase; Manganese; Metal-binding;
KW Reference proteome.
FT CHAIN 1..326
FT /note="Gamma-resorcylate decarboxylase"
FT /id="PRO_0000454502"
FT ACT_SITE 287
FT /evidence="ECO:0000303|PubMed:29283551"
FT BINDING 8
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000269|PubMed:29283551,
FT ECO:0007744|PDB:4QRO"
FT BINDING 10
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000269|PubMed:29283551,
FT ECO:0007744|PDB:4QRO"
FT BINDING 164
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000269|PubMed:29283551,
FT ECO:0007744|PDB:4QRO"
FT BINDING 287
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000269|PubMed:29283551,
FT ECO:0007744|PDB:4QRO"
FT STRAND 3..11
FT /evidence="ECO:0007829|PDB:4QRO"
FT HELIX 14..17
FT /evidence="ECO:0007829|PDB:4QRO"
FT HELIX 18..20
FT /evidence="ECO:0007829|PDB:4QRO"
FT HELIX 26..28
FT /evidence="ECO:0007829|PDB:4QRO"
FT HELIX 29..37
FT /evidence="ECO:0007829|PDB:4QRO"
FT STRAND 39..41
FT /evidence="ECO:0007829|PDB:4QRO"
FT HELIX 42..49
FT /evidence="ECO:0007829|PDB:4QRO"
FT STRAND 52..59
FT /evidence="ECO:0007829|PDB:4QRO"
FT HELIX 63..66
FT /evidence="ECO:0007829|PDB:4QRO"
FT HELIX 70..90
FT /evidence="ECO:0007829|PDB:4QRO"
FT TURN 92..94
FT /evidence="ECO:0007829|PDB:4QRO"
FT STRAND 95..97
FT /evidence="ECO:0007829|PDB:4QRO"
FT HELIX 106..118
FT /evidence="ECO:0007829|PDB:4QRO"
FT STRAND 125..131
FT /evidence="ECO:0007829|PDB:4QRO"
FT HELIX 145..147
FT /evidence="ECO:0007829|PDB:4QRO"
FT HELIX 148..157
FT /evidence="ECO:0007829|PDB:4QRO"
FT STRAND 161..164
FT /evidence="ECO:0007829|PDB:4QRO"
FT HELIX 170..172
FT /evidence="ECO:0007829|PDB:4QRO"
FT HELIX 174..176
FT /evidence="ECO:0007829|PDB:4QRO"
FT HELIX 180..182
FT /evidence="ECO:0007829|PDB:4QRO"
FT HELIX 184..186
FT /evidence="ECO:0007829|PDB:4QRO"
FT HELIX 188..202
FT /evidence="ECO:0007829|PDB:4QRO"
FT HELIX 205..208
FT /evidence="ECO:0007829|PDB:4QRO"
FT STRAND 214..217
FT /evidence="ECO:0007829|PDB:4QRO"
FT HELIX 218..220
FT /evidence="ECO:0007829|PDB:4QRO"
FT HELIX 223..232
FT /evidence="ECO:0007829|PDB:4QRO"
FT TURN 233..236
FT /evidence="ECO:0007829|PDB:4QRO"
FT STRAND 242..244
FT /evidence="ECO:0007829|PDB:4QRO"
FT HELIX 249..256
FT /evidence="ECO:0007829|PDB:4QRO"
FT STRAND 257..260
FT /evidence="ECO:0007829|PDB:4QRO"
FT HELIX 267..276
FT /evidence="ECO:0007829|PDB:4QRO"
FT HELIX 279..281
FT /evidence="ECO:0007829|PDB:4QRO"
FT TURN 288..290
FT /evidence="ECO:0007829|PDB:4QRO"
FT HELIX 293..302
FT /evidence="ECO:0007829|PDB:4QRO"
FT STRAND 303..305
FT /evidence="ECO:0007829|PDB:4QRO"
FT HELIX 307..314
FT /evidence="ECO:0007829|PDB:4QRO"
FT HELIX 316..321
FT /evidence="ECO:0007829|PDB:4QRO"
FT TURN 322..325
FT /evidence="ECO:0007829|PDB:4QRO"
SQ SEQUENCE 326 AA; 37341 MW; A127605F23AE82C6 CRC64;
MNGKIALEEH FATEETLMDS AGFVPDKDWP ELRSRLLDIQ DRRVRLMDEH GIETMILSLN
APAVQAIADS TRANETARRA NDFLAEQVAK QPTRFRGFAA LPMQDPELAA RELERCVKEL
GFVGALVNGF SQDNRSAVPL YYDMAQYWPF WETVQALDVP FYLHPRNPLP SDARIYDGHA
WLLGPTWAFG QETAVHALRL MGSGLFDKYP ALKIILGHMG EGLPYSMWRI DHRNAWIKTT
PKYPAKRKIV DYFNENFYLT TSGNFRTQTL IDAILEIGAD RILFSTDWPF ENIDHAADWF
ENTSISEADR KKIGWGNAQN LFKLNR
