PDA_AGRRK
ID PDA_AGRRK Reviewed; 437 AA.
AC B9J8S0;
DT 04-FEB-2015, integrated into UniProtKB/Swiss-Prot.
DT 24-MAR-2009, sequence version 1.
DT 03-AUG-2022, entry version 67.
DE RecName: Full=Pterin deaminase {ECO:0000303|PubMed:23256477};
DE Short=PDA {ECO:0000303|PubMed:23256477};
DE EC=3.5.4.11 {ECO:0000269|PubMed:23256477};
GN Name=codAch2 {ECO:0000312|EMBL:ACM27458.1};
GN OrderedLocusNames=Arad_3529 {ECO:0000312|EMBL:ACM27458.1};
OS Agrobacterium radiobacter (strain K84 / ATCC BAA-868).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Rhizobiaceae; Rhizobium/Agrobacterium group; Agrobacterium;
OC Agrobacterium tumefaciens complex.
OX NCBI_TaxID=311403;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K84 / ATCC BAA-868;
RX PubMed=19251847; DOI=10.1128/jb.01779-08;
RA Slater S.C., Goldman B.S., Goodner B., Setubal J.C., Farrand S.K.,
RA Nester E.W., Burr T.J., Banta L., Dickerman A.W., Paulsen I., Otten L.,
RA Suen G., Welch R., Almeida N.F., Arnold F., Burton O.T., Du Z., Ewing A.,
RA Godsy E., Heisel S., Houmiel K.L., Jhaveri J., Lu J., Miller N.M.,
RA Norton S., Chen Q., Phoolcharoen W., Ohlin V., Ondrusek D., Pride N.,
RA Stricklin S.L., Sun J., Wheeler C., Wilson L., Zhu H., Wood D.W.;
RT "Genome sequences of three Agrobacterium biovars help elucidate the
RT evolution of multichromosome genomes in bacteria.";
RL J. Bacteriol. 191:2501-2511(2009).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, BIOPHYSICOCHEMICAL
RP PROPERTIES, HOMOLOGY MODELING, AND MOLECULAR DOCKING.
RC STRAIN=K84 / ATCC BAA-868;
RX PubMed=23256477; DOI=10.1021/ja309680b;
RA Fan H., Hitchcock D.S., Seidel R.D. II, Hillerich B., Lin H., Almo S.C.,
RA Sali A., Shoichet B.K., Raushel F.M.;
RT "Assignment of pterin deaminase activity to an enzyme of unknown function
RT guided by homology modeling and docking.";
RL J. Am. Chem. Soc. 135:795-803(2013).
CC -!- FUNCTION: Catalyzes the deamination of many pterin metabolites, such as
CC formylpterin, pterin-6-carboxylate, pterin-7-carboxylate, pterin,
CC hydroxymethylpterin, biopterin, D-(+)-neopterin, isoxanthopterin,
CC sepiapterin, folate, xanthopterin, and 7,8-dihydrohydroxymethylpterin.
CC May be involved in a degradative pathway for catabolizing pterin rings.
CC {ECO:0000269|PubMed:23256477}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 2-amino-4-hydroxypteridine + H(+) + H2O = a 2,4-
CC dihydroxypteridine + NH4(+); Xref=Rhea:RHEA:36055, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:28938, ChEBI:CHEBI:73184,
CC ChEBI:CHEBI:73186; EC=3.5.4.11;
CC Evidence={ECO:0000269|PubMed:23256477};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H(+) + H2O + sepiapterin = NH4(+) + xanthopterin-B2;
CC Xref=Rhea:RHEA:14025, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:16095, ChEBI:CHEBI:17953, ChEBI:CHEBI:28938;
CC Evidence={ECO:0000269|PubMed:23256477};
CC -!- COFACTOR:
CC Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
CC Evidence={ECO:0000250|UniProtKB:P25524};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=12 uM for formylpterin {ECO:0000269|PubMed:23256477};
CC KM=27 uM for pterin-6-carboxylate {ECO:0000269|PubMed:23256477};
CC KM=13 uM for pterin-7-carboxylate {ECO:0000269|PubMed:23256477};
CC KM=39 uM for pterin {ECO:0000269|PubMed:23256477};
CC KM=23 uM for hydroxymethylpterin {ECO:0000269|PubMed:23256477};
CC KM=47 uM for biopterin {ECO:0000269|PubMed:23256477};
CC KM=61 uM for D-(+)-neopterin {ECO:0000269|PubMed:23256477};
CC KM=5.7 uM for isoxanthopterin {ECO:0000269|PubMed:23256477};
CC KM=22 uM for sepiapterin {ECO:0000269|PubMed:23256477};
CC KM=50 uM for folate {ECO:0000269|PubMed:23256477};
CC KM=40 uM for xanthopterin {ECO:0000269|PubMed:23256477};
CC KM=37 uM for 7,8-dihydro-hydroxymethylpterin
CC {ECO:0000269|PubMed:23256477};
CC KM=200 uM for 7,8-dihydroneopterin {ECO:0000269|PubMed:23256477};
CC KM=93 uM for 7,8-dihydrobiopterin {ECO:0000269|PubMed:23256477};
CC Note=kcat is 64 sec(-1) with formylpterin as substrate. kcat is 110
CC sec(-1) with pterin-6-carboxylate as substrate. kcat is 48 sec(-1)
CC with pterin-7-carboxylate as substrate. kcat is 131 sec(-1) with
CC pterin as substrate. kcat is 28 sec(-1) with hydroxymethylpterin as
CC substrate. kcat is 46 sec(-1) with biopterin as substrate. kcat is 19
CC sec(-1) with D-(+)-neopterin as substrate. kcat is 1.6 sec(-1) with
CC isoxanthopterin as substrate. kcat is 2.9 sec(-1) with sepiapterin as
CC substrate. kcat is 6.4 sec(-1) with folate as substrate. kcat is 0.46
CC sec(-1) with xanthopterin as substrate. kcat is 1.2 sec(-1) with 7,8-
CC dihydro-hydroxymethylpterin as substrate. kcat is 0.036 sec(-1) with
CC 7,8-dihydroneopterin as substrate. kcat is 0.090 sec(-1) with 7,8-
CC dihydrobiopterin as substrate. {ECO:0000269|PubMed:23256477};
CC -!- SIMILARITY: Belongs to the metallo-dependent hydrolases superfamily.
CC Pterin deaminase family. {ECO:0000305}.
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DR EMBL; CP000628; ACM27458.1; -; Genomic_DNA.
DR RefSeq; WP_012652141.1; NC_011985.1.
DR AlphaFoldDB; B9J8S0; -.
DR SMR; B9J8S0; -.
DR STRING; 311403.Arad_3529; -.
DR EnsemblBacteria; ACM27458; ACM27458; Arad_3529.
DR KEGG; ara:Arad_3529; -.
DR eggNOG; COG0402; Bacteria.
DR HOGENOM; CLU_031758_5_1_5; -.
DR OMA; SDNTRDP; -.
DR OrthoDB; 1456605at2; -.
DR SABIO-RK; B9J8S0; -.
DR Proteomes; UP000001600; Chromosome 1.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0050228; F:pterin deaminase activity; IDA:UniProtKB.
DR GO; GO:0050279; F:sepiapterin deaminase activity; IDA:CACAO.
DR Gene3D; 2.30.40.10; -; 1.
DR InterPro; IPR013108; Amidohydro_3.
DR InterPro; IPR011059; Metal-dep_hydrolase_composite.
DR InterPro; IPR032466; Metal_Hydrolase.
DR Pfam; PF07969; Amidohydro_3; 1.
DR SUPFAM; SSF51338; SSF51338; 1.
DR SUPFAM; SSF51556; SSF51556; 1.
PE 1: Evidence at protein level;
KW Hydrolase; Metal-binding; Reference proteome.
FT CHAIN 1..437
FT /note="Pterin deaminase"
FT /id="PRO_0000431902"
FT ACT_SITE 234
FT /note="Proton donor"
FT /evidence="ECO:0000305|PubMed:23256477"
FT BINDING 80
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:P25524"
FT BINDING 82
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:P25524"
FT BINDING 85
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:23256477"
FT BINDING 231
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:P25524"
FT BINDING 331..332
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:23256477"
FT BINDING 331
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:P25524"
FT SITE 263
FT /note="Activates the nucleophilic water"
FT /evidence="ECO:0000250|UniProtKB:P25524"
SQ SEQUENCE 437 AA; 47425 MW; BC7CA943AEDABB86 CRC64;
MSYSFMSPPN AARFVLSNAT VPAVTVVGFT GPSSEGLMKA DIVVADGLIK DILPAGTAPA
ELAKADMRDG MVWPTFADMH THLDKGHIWE RRANPDGSFM GALDAVRSDR EANWSAADVR
KRMEFSLRAA YAHGTSLIRT HLDSLAPQHR ISFEVFSEVR EAWKDKIALQ AVALFPLDFM
VDDAFFADLT TVVREAGGLL GGVTQMNPDI DAQLDKLIRA AAANGLDIDL HVDETEDREV
LTLKAIAAAV LRNGFTGKVT AGHCCSLARQ DENVAAATID LVAKAGISIV ALPMCNMYLQ
DRHPGRTPRW RGVTLLHELA AAGVPTAVAS DNTRDPFYAY GDLDPVEVFR EAVRILHLDH
PLDTAARVVT TSPASILGRP DIGRIAVGGP ADLVLFSARR WSEFLSRPQS DRVVLRKGKV
IDRSLPDYRE LDTVIGA
