BAH_RHOER
ID BAH_RHOER Reviewed; 369 AA.
AC Q8RSQ2;
DT 13-APR-2004, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 03-AUG-2022, entry version 65.
DE RecName: Full=Barbiturase {ECO:0000255|HAMAP-Rule:MF_01989};
DE EC=3.5.2.1 {ECO:0000255|HAMAP-Rule:MF_01989, ECO:0000269|PubMed:11485332, ECO:0000269|PubMed:11748240};
DE AltName: Full=Barbituric acid hydrolase {ECO:0000255|HAMAP-Rule:MF_01989};
DE Short=BAH {ECO:0000255|HAMAP-Rule:MF_01989};
GN Name=bar;
OS Rhodococcus erythropolis (Arthrobacter picolinophilus).
OC Bacteria; Actinobacteria; Corynebacteriales; Nocardiaceae; Rhodococcus;
OC Rhodococcus erythropolis group.
OX NCBI_TaxID=1833;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-37; 68-101;
RP 108-136; 163-175; 262-295 AND 301-328, FUNCTION, CATALYTIC ACTIVITY,
RP SUBUNIT, BIOPHYSICOCHEMICAL PROPERTIES, AND ACTIVITY REGULATION.
RC STRAIN=ATCC 11048 / DSM 43060 / JCM 3132 / NBRC 13914 / NCIMB 8147 / NCTC
RC 8036 / NRRL B-1574;
RX PubMed=11748240; DOI=10.1074/jbc.m110784200;
RA Soong C.-L., Ogawa J., Sakuradani E., Shimizu S.;
RT "Barbiturase, a novel zinc-containing amidohydrolase involved in oxidative
RT pyrimidine metabolism.";
RL J. Biol. Chem. 277:7051-7058(2002).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, AND PATHWAY.
RC STRAIN=ATCC 11048 / DSM 43060 / JCM 3132 / NBRC 13914 / NCIMB 8147 / NCTC
RC 8036 / NRRL B-1574;
RX PubMed=11485332; DOI=10.1006/bbrc.2001.5356;
RA Soong C.-L., Ogawa J., Shimizu S.;
RT "Novel amidohydrolytic reactions in oxidative pyrimidine metabolism:
RT analysis of the barbiturase reaction and discovery of a novel enzyme,
RT ureidomalonase.";
RL Biochem. Biophys. Res. Commun. 286:222-226(2001).
RN [3] {ECO:0007744|PDB:5HWE, ECO:0007744|PDB:5HXU, ECO:0007744|PDB:5HXZ, ECO:0007744|PDB:5HY1}
RP X-RAY CRYSTALLOGRAPHY (1.71 ANGSTROMS), BIOPHYSICOCHEMICAL PROPERTIES, AND
RP SUBUNIT.
RX PubMed=28235873; DOI=10.1128/aem.03365-16;
RA Peat T.S., Balotra S., Wilding M., Hartley C.J., Newman J., Scott C.;
RT "High resolution X-ray structures of two functionally distinct members of
RT the cyclic amide hydrolase (CyAH) family of Toblerone fold enzymes.";
RL Appl. Environ. Microbiol. 0:0-0(2017).
CC -!- FUNCTION: Responsible for the hydrolysis of barbituric acid (2,4,6-
CC trihydroxy-1,3-pyrimidine), an intermediate in the oxidative catabolism
CC of pyrimidines. Catalyzes the hydrolytic opening of the pyrimidine ring
CC of barbituric acid to yield ureidomalonic acid. {ECO:0000255|HAMAP-
CC Rule:MF_01989, ECO:0000269|PubMed:11485332,
CC ECO:0000269|PubMed:11748240}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=barbiturate + H2O = 3-oxo-3-ureidopropanoate;
CC Xref=Rhea:RHEA:18653, ChEBI:CHEBI:15377, ChEBI:CHEBI:58775,
CC ChEBI:CHEBI:77938; EC=3.5.2.1; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_01989, ECO:0000269|PubMed:11485332,
CC ECO:0000269|PubMed:11748240};
CC -!- ACTIVITY REGULATION: Inhibited by cyanuric acid. {ECO:0000255|HAMAP-
CC Rule:MF_01989, ECO:0000269|PubMed:11748240}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1.0 mM for barbituric acid {ECO:0000269|PubMed:11748240};
CC KM=0.25 uM for barbituric acid {ECO:0000269|PubMed:28235873};
CC Vmax=2.5 umol/min/mg enzyme {ECO:0000269|PubMed:11748240};
CC Note=kcat is 115 sec(-1) with barbituric acid as substrate.
CC {ECO:0000269|PubMed:28235873};
CC -!- PATHWAY: Pyrimidine metabolism; uracil degradation via oxidative
CC pathway; malonate and urea from uracil: step 2/3. {ECO:0000255|HAMAP-
CC Rule:MF_01989, ECO:0000269|PubMed:11485332}.
CC -!- SUBUNIT: Homotetramer. {ECO:0000255|HAMAP-Rule:MF_01989,
CC ECO:0000269|PubMed:11748240, ECO:0000269|PubMed:28235873}.
CC -!- DOMAIN: The monomer structure is formed from three repeating units
CC (RUs) that share the same structure as one another. The monomer and the
CC active site possess nearly threefold rotational symmetry, to the extent
CC that the active site possesses three potential Ser-Lys catalytic dyads,
CC but one of the 3 active site surfaces varies in composition suggesting
CC it is involved in confering substrate specificity. {ECO:0000255|HAMAP-
CC Rule:MF_01989, ECO:0000305|PubMed:28235873}.
CC -!- SIMILARITY: Belongs to the cyclic amide hydrolase (CyAH) family.
CC {ECO:0000255|HAMAP-Rule:MF_01989, ECO:0000305}.
CC -!- CAUTION: PubMed:11748240 suggested that BAH was dependent upon Zn(2+),
CC but according to PubMed:28235873, there is no indication of zinc in the
CC structure: synchrotron X-ray fluorescence scans failed to detect a peak
CC corresponding to zinc, and there was no indication of an atom with
CC sufficient electron density in the resulting high-resolution structure.
CC The enzyme does contain a metal cation, but the electron density
CC identifies this cation as either Mg(2+) or Na(+) and not zinc.
CC {ECO:0000305|PubMed:11748240, ECO:0000305|PubMed:28235873}.
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DR EMBL; AJ320520; CAC86669.1; -; Genomic_DNA.
DR RefSeq; WP_019746095.1; NZ_UGVH01000001.1.
DR PDB; 5HWE; X-ray; 1.71 A; A=1-369.
DR PDB; 5HXU; X-ray; 1.83 A; A/B=1-369.
DR PDB; 5HXZ; X-ray; 2.36 A; A/B/C/D=1-369.
DR PDB; 5HY1; X-ray; 2.01 A; A=1-369.
DR PDBsum; 5HWE; -.
DR PDBsum; 5HXU; -.
DR PDBsum; 5HXZ; -.
DR PDBsum; 5HY1; -.
DR AlphaFoldDB; Q8RSQ2; -.
DR SMR; Q8RSQ2; -.
DR STRING; 1833.XU06_28640; -.
DR KEGG; ag:CAC86669; -.
DR BioCyc; MetaCyc:MON-15393; -.
DR BRENDA; 3.5.2.1; 5389.
DR UniPathway; UPA00582; UER00644.
DR GO; GO:0047694; F:barbiturase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0006212; P:uracil catabolic process; IEA:UniProtKB-UniRule.
DR Gene3D; 3.30.1330.160; -; 1.
DR Gene3D; 3.30.1330.170; -; 1.
DR Gene3D; 3.30.1330.180; -; 1.
DR HAMAP; MF_01989; Cyc_amidohydrol; 1.
DR InterPro; IPR014086; AtzD/Barbiturase.
DR InterPro; IPR043008; AtzD/Barbiturase_RUA.
DR InterPro; IPR043006; AtzD/Barbiturase_RUB.
DR InterPro; IPR043007; AtzD/Barbiturase_RUC.
DR Pfam; PF09663; Amido_AtzD_TrzD; 1.
DR TIGRFAMs; TIGR02714; amido_AtzD_TrzD; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Hydrolase; Magnesium;
KW Metal-binding.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:11748240"
FT CHAIN 2..369
FT /note="Barbiturase"
FT /id="PRO_0000064828"
FT REGION 2..104
FT /note="RU A"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01989"
FT REGION 112..247
FT /note="RU B"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01989"
FT REGION 253..369
FT /note="RU C"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01989"
FT ACT_SITE 162
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01989"
FT ACT_SITE 230
FT /note="Nucleophile"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01989"
FT BINDING 53
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01989,
FT ECO:0000269|PubMed:28235873"
FT BINDING 83..84
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01989,
FT ECO:0000269|PubMed:28235873"
FT BINDING 194
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01989,
FT ECO:0000269|PubMed:28235873"
FT BINDING 230..231
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01989,
FT ECO:0000269|PubMed:28235873"
FT BINDING 301
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01989,
FT ECO:0000269|PubMed:28235873"
FT BINDING 328
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01989,
FT ECO:0000269|PubMed:28235873"
FT BINDING 347..348
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01989,
FT ECO:0000269|PubMed:28235873"
FT BINDING 350
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01989,
FT ECO:0000269|PubMed:28235873"
FT BINDING 353
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01989,
FT ECO:0000269|PubMed:28235873"
FT BINDING 354
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01989,
FT ECO:0000269|PubMed:28235873"
FT BINDING 355
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01989,
FT ECO:0000269|PubMed:28235873"
FT BINDING 358
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01989,
FT ECO:0000269|PubMed:28235873"
FT SITE 324
FT /note="Important for substrate specificity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01989"
FT STRAND 5..11
FT /evidence="ECO:0007829|PDB:5HWE"
FT HELIX 19..26
FT /evidence="ECO:0007829|PDB:5HWE"
FT HELIX 32..34
FT /evidence="ECO:0007829|PDB:5HWE"
FT STRAND 35..44
FT /evidence="ECO:0007829|PDB:5HWE"
FT STRAND 46..49
FT /evidence="ECO:0007829|PDB:5HWE"
FT HELIX 52..66
FT /evidence="ECO:0007829|PDB:5HWE"
FT STRAND 67..70
FT /evidence="ECO:0007829|PDB:5HWE"
FT HELIX 72..76
FT /evidence="ECO:0007829|PDB:5HWE"
FT STRAND 80..84
FT /evidence="ECO:0007829|PDB:5HWE"
FT STRAND 93..99
FT /evidence="ECO:0007829|PDB:5HWE"
FT HELIX 102..104
FT /evidence="ECO:0007829|PDB:5HWE"
FT STRAND 112..119
FT /evidence="ECO:0007829|PDB:5HWE"
FT HELIX 125..127
FT /evidence="ECO:0007829|PDB:5HWE"
FT HELIX 131..147
FT /evidence="ECO:0007829|PDB:5HWE"
FT HELIX 153..155
FT /evidence="ECO:0007829|PDB:5HWE"
FT STRAND 156..163
FT /evidence="ECO:0007829|PDB:5HWE"
FT HELIX 168..176
FT /evidence="ECO:0007829|PDB:5HWE"
FT HELIX 186..204
FT /evidence="ECO:0007829|PDB:5HWE"
FT HELIX 213..215
FT /evidence="ECO:0007829|PDB:5HWE"
FT TURN 216..218
FT /evidence="ECO:0007829|PDB:5HWE"
FT STRAND 224..231
FT /evidence="ECO:0007829|PDB:5HWE"
FT STRAND 239..249
FT /evidence="ECO:0007829|PDB:5HWE"
FT STRAND 252..262
FT /evidence="ECO:0007829|PDB:5HWE"
FT HELIX 266..275
FT /evidence="ECO:0007829|PDB:5HWE"
FT HELIX 286..288
FT /evidence="ECO:0007829|PDB:5HWE"
FT STRAND 293..300
FT /evidence="ECO:0007829|PDB:5HWE"
FT STRAND 306..308
FT /evidence="ECO:0007829|PDB:5HXU"
FT HELIX 315..317
FT /evidence="ECO:0007829|PDB:5HWE"
FT STRAND 319..321
FT /evidence="ECO:0007829|PDB:5HWE"
FT HELIX 323..339
FT /evidence="ECO:0007829|PDB:5HWE"
FT STRAND 345..348
FT /evidence="ECO:0007829|PDB:5HWE"
FT STRAND 353..355
FT /evidence="ECO:0007829|PDB:5HWE"
FT STRAND 359..366
FT /evidence="ECO:0007829|PDB:5HWE"
SQ SEQUENCE 369 AA; 38998 MW; E8C6419B71EFF38E CRC64;
MPEAIEVRKV PLHSVSDASE LAKLIDDGVL EADRVIAVIG KTEGNGGVND YTRIIADRAF
REVLSAKGNR SPEEVAEVPI VWSGGTDGVI SPHATIFATV PADKVTKTDE PRLTVGVAMS
EQLLPEDIGR TAMITKVAAA VKDAMADAGI TDPADVHYVQ TKTPLLTIHT IRDAKSRGKT
VWTEQTHESM DLSNGGTALG IAVALGEIDM PTDEDVMHSR ELFSSVASCS SGVELDRAQI
VVVGNARGVG GRYRIGHSVM KDPLDQDGIW AAIRDAGLEL PERPHSNDLD GQLVNVFLKC
EASQDGTVRG RRNAMLDDSD VHWHRQIKSC VGGVTAAVTG DPAVFVSVSA AHQGPEGGGP
VAAIVDLGQ
