GRDC_RHIS5
ID GRDC_RHIS5 Reviewed; 327 AA.
AC Q60GU1;
DT 23-FEB-2022, integrated into UniProtKB/Swiss-Prot.
DT 23-NOV-2004, sequence version 1.
DT 03-AUG-2022, entry version 65.
DE RecName: Full=Gamma-resorcylate decarboxylase {ECO:0000303|PubMed:15466039};
DE Short=GRDC {ECO:0000303|PubMed:16963440};
DE Short=Gamma-RDC {ECO:0000303|PubMed:15466039};
DE EC=4.1.1.103 {ECO:0000269|PubMed:15466039};
DE AltName: Full=2,6-dihydroxybenzoate decarboxylase {ECO:0000303|PubMed:16963440};
GN Name=graF {ECO:0000303|PubMed:17158677};
OS Rhizobium sp. (strain MTP-10005).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Rhizobiaceae; Rhizobium/Agrobacterium group; Rhizobium.
OX NCBI_TaxID=267998;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-23; 46-60 AND
RP 73-87, FUNCTION, CATALYTIC ACTIVITY, ACTIVITY REGULATION,
RP BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, AND INDUCTION.
RC STRAIN=MTP-10005;
RX PubMed=15466039; DOI=10.1128/jb.186.20.6855-6863.2004;
RA Yoshiada M., Fukuhara N., Oikawa T.;
RT "Thermophilic, reversible gamma-resorcylate decarboxylase from Rhizobium
RT sp. strain MTP-10005: purification, molecular characterization, and
RT expression.";
RL J. Bacteriol. 186:6855-6863(2004).
RN [2]
RP INDUCTION.
RC STRAIN=MTP-10005;
RX PubMed=17158677; DOI=10.1128/jb.01675-06;
RA Yoshida M., Oikawa T., Obata H., Abe K., Mihara H., Esaki N.;
RT "Biochemical and genetic analysis of the gamma-resorcylate (2,6-
RT dihydroxybenzoate) catabolic pathway in Rhizobium sp. strain MTP-10005:
RT identification and functional analysis of its gene cluster.";
RL J. Bacteriol. 189:1573-1581(2007).
RN [3] {ECO:0007744|PDB:2DVT, ECO:0007744|PDB:2DVU, ECO:0007744|PDB:2DVX}
RP X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) IN COMPLEXES WITH ZINC;
RP 2,6-DIHYDROXYBENZOATE AND 2,3-DIHYDROXYBENZALDEHYDE, COFACTOR, ACTIVITY
RP REGULATION, SUBUNIT, AND ACTIVE SITE.
RX PubMed=16963440; DOI=10.1074/jbc.m607270200;
RA Goto M., Hayashi H., Miyahara I., Hirotsu K., Yoshida M., Oikawa T.;
RT "Crystal structures of nonoxidative zinc-dependent 2,6-dihydroxybenzoate
RT (gamma-resorcylate) decarboxylase from Rhizobium sp. strain MTP-10005.";
RL J. Biol. Chem. 281:34365-34373(2006).
CC -!- FUNCTION: Involved in the gamma-resorcylate (2,6-dihydroxybenzoate)
CC catabolism (PubMed:15466039). Catalyzes the reversible decarboxylation
CC of gamma-resorcylate to resorcinol (PubMed:15466039). The reaction is
CC reversible, but equilibrium greatly favors the decarboxylation reaction
CC (PubMed:15466039). Also catalyzes the decarboxylation of 2,3-
CC dihydroxybenzoate to catechol, but does not act on 2,4-
CC dihydroxybenzoate, 2,5-dihydroxybenzoate, 3,4-dihydroxybenzoate, 3,5-
CC dihydroxybenzoate, 2-hydroxybenzoate, or 3-hydroxybenzoate. Only
CC resorcinol is carboxylated by the reverse reaction (PubMed:15466039).
CC {ECO:0000269|PubMed:15466039}.
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:15466039};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:49465;
CC Evidence={ECO:0000269|PubMed:15466039};
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:15466039};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000269|PubMed:16963440};
CC Note=Binds 1 Zn(2+) ion per subunit. {ECO:0000269|PubMed:16963440};
CC -!- ACTIVITY REGULATION: Inhibited by CuCl(2), monoiodoacetate and
CC diethylpyrocarbonate (PubMed:15466039). Inhibited by 2,3-
CC dihydroxybenzaldehyde, which is an analog of the substrate 2,3-
CC dihydroxybenzoate (PubMed:16963440). {ECO:0000269|PubMed:15466039,
CC ECO:0000269|PubMed:16963440}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=70.7 uM for gamma-resorcylate (for decarboxylation)
CC {ECO:0000269|PubMed:15466039};
CC KM=123 uM for 2,3-dihydroxybenzoate (for decarboxylation)
CC {ECO:0000269|PubMed:15466039};
CC KM=45.7 mM for resorcinol (for carboxylation)
CC {ECO:0000269|PubMed:15466039};
CC KM=22.2 mM for NaHCO(3) (for carboxylation)
CC {ECO:0000269|PubMed:15466039};
CC Vmax=0.377 umol/min/mg enzyme with gamma-resorcylate as substrate
CC (for decarboxylation) {ECO:0000269|PubMed:15466039};
CC Vmax=1.06 umol/min/mg enzyme with 2,3-dihydroxybenzoate as substrate
CC (for decarboxylation) {ECO:0000269|PubMed:15466039};
CC Vmax=1.78 umol/min/mg enzyme with resorcinol as substrate (for
CC carboxylation) {ECO:0000269|PubMed:15466039};
CC Vmax=1.75 umol/min/mg enzyme with NaHCO(3) as substrate (for
CC carboxylation) {ECO:0000269|PubMed:15466039};
CC pH dependence:
CC Optimum pH is 8.0 for decarboxylation. Optimum pH is 7.0 for
CC carboxylation. {ECO:0000269|PubMed:15466039};
CC Temperature dependence:
CC Optimum temperature is 70 degrees Celsius.
CC {ECO:0000269|PubMed:15466039};
CC -!- PATHWAY: Aromatic compound metabolism. {ECO:0000305}.
CC -!- SUBUNIT: Homotetramer (PubMed:15466039, PubMed:16963440). Dimer of
CC dimers (PubMed:16963440). {ECO:0000269|PubMed:15466039,
CC ECO:0000269|PubMed:16963440}.
CC -!- INDUCTION: Induced in the presence of gamma-resorcylate.
CC {ECO:0000269|PubMed:15466039, ECO:0000269|PubMed:17158677}.
CC -!- SIMILARITY: Belongs to the metallo-dependent hydrolases superfamily.
CC ACMSD family. {ECO:0000305}.
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DR EMBL; AB170010; BAD54753.1; -; Genomic_DNA.
DR PDB; 2DVT; X-ray; 1.70 A; A/B/C/D=1-327.
DR PDB; 2DVU; X-ray; 1.90 A; A/B/C/D=1-327.
DR PDB; 2DVX; X-ray; 1.70 A; A/B/C/D=1-327.
DR PDBsum; 2DVT; -.
DR PDBsum; 2DVU; -.
DR PDBsum; 2DVX; -.
DR SMR; Q60GU1; -.
DR KEGG; ag:BAD54753; -.
DR BioCyc; MetaCyc:MON-19787; -.
DR BRENDA; 4.1.1.103; 5351.
DR EvolutionaryTrace; Q60GU1; -.
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; Direct protein sequencing; Lyase;
KW Metal-binding; Zinc.
FT CHAIN 1..327
FT /note="Gamma-resorcylate decarboxylase"
FT /id="PRO_0000454504"
FT ACT_SITE 287
FT /evidence="ECO:0000305|PubMed:16963440"
FT BINDING 8
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:16963440,
FT ECO:0007744|PDB:2DVT, ECO:0007744|PDB:2DVU,
FT ECO:0007744|PDB:2DVX"
FT BINDING 10
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:16963440,
FT ECO:0007744|PDB:2DVT, ECO:0007744|PDB:2DVU,
FT ECO:0007744|PDB:2DVX"
FT BINDING 23
FT /ligand="2,6-dihydroxybenzoate"
FT /ligand_id="ChEBI:CHEBI:131450"
FT /evidence="ECO:0000269|PubMed:16963440,
FT ECO:0007744|PDB:2DVU"
FT BINDING 164
FT /ligand="2,6-dihydroxybenzoate"
FT /ligand_id="ChEBI:CHEBI:131450"
FT /evidence="ECO:0000269|PubMed:16963440,
FT ECO:0007744|PDB:2DVU"
FT BINDING 164
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:16963440,
FT ECO:0007744|PDB:2DVT, ECO:0007744|PDB:2DVU,
FT ECO:0007744|PDB:2DVX"
FT BINDING 287
FT /ligand="2,6-dihydroxybenzoate"
FT /ligand_id="ChEBI:CHEBI:131450"
FT /evidence="ECO:0000269|PubMed:16963440,
FT ECO:0007744|PDB:2DVU"
FT BINDING 287
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:16963440,
FT ECO:0007744|PDB:2DVT, ECO:0007744|PDB:2DVU,
FT ECO:0007744|PDB:2DVX"
FT STRAND 3..11
FT /evidence="ECO:0007829|PDB:2DVT"
FT HELIX 14..17
FT /evidence="ECO:0007829|PDB:2DVT"
FT HELIX 18..20
FT /evidence="ECO:0007829|PDB:2DVT"
FT HELIX 28..37
FT /evidence="ECO:0007829|PDB:2DVT"
FT STRAND 39..41
FT /evidence="ECO:0007829|PDB:2DVT"
FT HELIX 42..49
FT /evidence="ECO:0007829|PDB:2DVT"
FT STRAND 52..59
FT /evidence="ECO:0007829|PDB:2DVT"
FT HELIX 63..66
FT /evidence="ECO:0007829|PDB:2DVT"
FT HELIX 70..90
FT /evidence="ECO:0007829|PDB:2DVT"
FT TURN 92..94
FT /evidence="ECO:0007829|PDB:2DVT"
FT STRAND 95..99
FT /evidence="ECO:0007829|PDB:2DVT"
FT HELIX 106..118
FT /evidence="ECO:0007829|PDB:2DVT"
FT STRAND 124..131
FT /evidence="ECO:0007829|PDB:2DVT"
FT HELIX 145..147
FT /evidence="ECO:0007829|PDB:2DVT"
FT HELIX 148..157
FT /evidence="ECO:0007829|PDB:2DVT"
FT STRAND 161..164
FT /evidence="ECO:0007829|PDB:2DVT"
FT HELIX 170..172
FT /evidence="ECO:0007829|PDB:2DVT"
FT HELIX 174..176
FT /evidence="ECO:0007829|PDB:2DVT"
FT HELIX 180..182
FT /evidence="ECO:0007829|PDB:2DVT"
FT HELIX 184..186
FT /evidence="ECO:0007829|PDB:2DVT"
FT HELIX 188..202
FT /evidence="ECO:0007829|PDB:2DVT"
FT HELIX 205..208
FT /evidence="ECO:0007829|PDB:2DVT"
FT STRAND 214..217
FT /evidence="ECO:0007829|PDB:2DVT"
FT HELIX 218..220
FT /evidence="ECO:0007829|PDB:2DVT"
FT HELIX 223..232
FT /evidence="ECO:0007829|PDB:2DVT"
FT TURN 233..236
FT /evidence="ECO:0007829|PDB:2DVT"
FT STRAND 242..244
FT /evidence="ECO:0007829|PDB:2DVT"
FT HELIX 249..256
FT /evidence="ECO:0007829|PDB:2DVT"
FT STRAND 257..260
FT /evidence="ECO:0007829|PDB:2DVT"
FT HELIX 267..274
FT /evidence="ECO:0007829|PDB:2DVT"
FT TURN 275..277
FT /evidence="ECO:0007829|PDB:2DVT"
FT HELIX 279..281
FT /evidence="ECO:0007829|PDB:2DVT"
FT TURN 288..290
FT /evidence="ECO:0007829|PDB:2DVT"
FT HELIX 293..302
FT /evidence="ECO:0007829|PDB:2DVT"
FT STRAND 303..305
FT /evidence="ECO:0007829|PDB:2DVT"
FT HELIX 307..314
FT /evidence="ECO:0007829|PDB:2DVT"
FT HELIX 316..321
FT /evidence="ECO:0007829|PDB:2DVT"
SQ SEQUENCE 327 AA; 37423 MW; 05B1A427BF2E5E42 CRC64;
MQGKVALEEH FAIPETLQDS AGFVPGDYWK ELQHRLLDIQ DTRLKLMDAH GIETMILSLN
APAVQAIPDR RKAIEIARRA NDVLAEECAK RPDRFLAFAA LPLQDPDAAT EELQRCVNDL
GFVGALVNGF SQEGDGQTPL YYDLPQYRPF WGEVEKLDVP FYLHPRNPLP QDSRIYDGHP
WLLGPTWAFA QETAVHALRL MASGLFDEHP RLNIILGHMG EGLPYMMWRI DHRNAWVKLP
PRYPAKRRFM DYFNENFHIT TSGNFRTQTL IDAILEIGAD RILFSTDWPF ENIDHASDWF
NATSIAEADR VKIGRTNARR LFKLDGA
