DAUA_PSEAE
ID DAUA_PSEAE Reviewed; 375 AA.
AC Q9HXE3;
DT 27-MAY-2015, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2001, sequence version 1.
DT 03-AUG-2022, entry version 113.
DE RecName: Full=FAD-dependent catabolic D-arginine dehydrogenase DauA {ECO:0000303|PubMed:20809650};
DE EC=1.4.99.6 {ECO:0000269|PubMed:19139398, ECO:0000269|PubMed:19850617, ECO:0000269|PubMed:20809650, ECO:0000269|PubMed:3141581};
DE AltName: Full=D-arginine dehydrogenase {ECO:0000303|PubMed:19139398};
DE Short=DADH {ECO:0000303|PubMed:19139398};
DE AltName: Full=D-arginine utilization protein A {ECO:0000303|PubMed:19139398};
DE Short=Dau {ECO:0000303|PubMed:19139398};
GN Name=dauA {ECO:0000303|PubMed:19139398}; OrderedLocusNames=PA3863;
OS Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM
OS 14847 / LMG 12228 / 1C / PRS 101 / PAO1).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
OC Pseudomonadaceae; Pseudomonas.
OX NCBI_TaxID=208964;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C /
RC PRS 101 / PAO1;
RX PubMed=10984043; DOI=10.1038/35023079;
RA Stover C.K., Pham X.-Q.T., Erwin A.L., Mizoguchi S.D., Warrener P.,
RA Hickey M.J., Brinkman F.S.L., Hufnagle W.O., Kowalik D.J., Lagrou M.,
RA Garber R.L., Goltry L., Tolentino E., Westbrock-Wadman S., Yuan Y.,
RA Brody L.L., Coulter S.N., Folger K.R., Kas A., Larbig K., Lim R.M.,
RA Smith K.A., Spencer D.H., Wong G.K.-S., Wu Z., Paulsen I.T., Reizer J.,
RA Saier M.H. Jr., Hancock R.E.W., Lory S., Olson M.V.;
RT "Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic
RT pathogen.";
RL Nature 406:959-964(2000).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, INDUCTION, AND SUBSTRATE SPECIFICITY.
RC STRAIN=ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C /
RC PRS 101 / PAO1;
RX PubMed=3141581; DOI=10.1099/00221287-134-9-2633;
RA Jann A., Matsumoto H., Haas D.;
RT "The fourth arginine catabolic pathway of Pseudomonas aeruginosa.";
RL J. Gen. Microbiol. 134:1043-1053(1988).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, INDUCTION, DISRUPTION PHENOTYPE, AND SUBUNIT.
RC STRAIN=ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C /
RC PRS 101 / PAO1;
RX PubMed=19139398; DOI=10.1073/pnas.0808269106;
RA Li C., Lu C.D.;
RT "Arginine racemization by coupled catabolic and anabolic dehydrogenases.";
RL Proc. Natl. Acad. Sci. U.S.A. 106:906-911(2009).
RN [4]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, DISRUPTION
RP PHENOTYPE, ACTIVITY REGULATION, INDUCTION, AND SUBSTRATE SPECIFICITY.
RC STRAIN=ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C /
RC PRS 101 / PAO1;
RX PubMed=19850617; DOI=10.1099/mic.0.033282-0;
RA Li C., Yao X., Lu C.D.;
RT "Regulation of the dauBAR operon and characterization of D-amino acid
RT dehydrogenase DauA in arginine and lysine catabolism of Pseudomonas
RT aeruginosa PAO1.";
RL Microbiology 156:60-71(2010).
RN [5]
RP FUNCTION IN VIRULENCE.
RX PubMed=24011342; DOI=10.1139/cjm-2013-0289;
RA Oliver K.E., Silo-Suh L.;
RT "Impact of D-amino acid dehydrogenase on virulence factor production by a
RT Pseudomonas aeruginosa.";
RL Can. J. Microbiol. 59:598-603(2013).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (1.06 ANGSTROMS) OF 2-375 IN COMPLEX WITH FAD,
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, AND
RP SUBSTRATE SPECIFICITY.
RX PubMed=20809650; DOI=10.1021/bi1005865;
RA Fu G., Yuan H., Li C., Lu C.D., Gadda G., Weber I.T.;
RT "Conformational changes and substrate recognition in Pseudomonas aeruginosa
RT D-arginine dehydrogenase.";
RL Biochemistry 49:8535-8545(2010).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (1.07 ANGSTROMS) OF 2-375 IN COMPLEX WITH FAD ANALOG,
RP AND COFACTOR.
RX PubMed=21707047; DOI=10.1021/bi200831a;
RA Fu G., Yuan H., Wang S., Gadda G., Weber I.T.;
RT "Atomic-resolution structure of an N5 flavin adduct in D-arginine
RT dehydrogenase.";
RL Biochemistry 50:6292-6294(2011).
CC -!- FUNCTION: DauA is highly expressed within the cystic fibrosis (CF)
CC lung, and it is required for virulence via the optimal production of
CC hydrogen cyanide, pyocyanine, pyoverdine, rhamnolipid and alginate
CC during biofilm formation (PubMed:24011342). Involved in the catabolism
CC of D-lysine and D-arginine. Under aerobic conditions, the arginine
CC succinyltransferase (AST) and arginine transaminase (ATA) pathways are
CC 2 major routes for L-arginine utilization as the sole source of carbon
CC and nitrogen. The D-to-L racemization of arginine by DauA and DauB is
CC necessary, before to be channeled into the AST and/or ATA pathways.
CC DauA catalyzes the flavin-dependent oxidative deamination of D-arginine
CC into 2-ketoarginine (2-KA) and ammonia (PubMed:3141581,
CC PubMed:19139398, PubMed:19850617, PubMed:20809650). It has also
CC dehydrogenase activity towards D-lysine, D-tyrosine, D-methionine, D-
CC phenylalanine, D-ornithine, D-histidine and D-leucine as substrates
CC (PubMed:19850617, PubMed:20809650). {ECO:0000269|PubMed:19139398,
CC ECO:0000269|PubMed:19850617, ECO:0000269|PubMed:20809650,
CC ECO:0000269|PubMed:24011342, ECO:0000269|PubMed:3141581}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=A + D-arginine + H2O = 5-guanidino-2-oxopentanoate + AH2 +
CC NH4(+); Xref=Rhea:RHEA:43572, ChEBI:CHEBI:13193, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:17499, ChEBI:CHEBI:28938, ChEBI:CHEBI:32689,
CC ChEBI:CHEBI:58489; EC=1.4.99.6;
CC Evidence={ECO:0000269|PubMed:19139398, ECO:0000269|PubMed:19850617,
CC ECO:0000269|PubMed:20809650, ECO:0000269|PubMed:3141581};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=A + a D-alpha-amino acid + H2O = a 2-oxocarboxylate + AH2 +
CC NH4(+); Xref=Rhea:RHEA:18125, ChEBI:CHEBI:13193, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:17499, ChEBI:CHEBI:28938, ChEBI:CHEBI:35179,
CC ChEBI:CHEBI:59871; Evidence={ECO:0000269|PubMed:19850617,
CC ECO:0000269|PubMed:20809650};
CC -!- COFACTOR:
CC Name=FAD; Xref=ChEBI:CHEBI:57692;
CC Evidence={ECO:0000269|PubMed:20809650, ECO:0000269|PubMed:21707047};
CC -!- ACTIVITY REGULATION: Inhibited by D-arginine and D-lysine at high
CC concentration. {ECO:0000269|PubMed:19850617}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.06 mM for D-arginine (at pH 8.7 and 25 degrees Celsius)
CC {ECO:0000269|PubMed:20809650};
CC KM=0.08 mM for D-arginine (at pH 8.7 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:19850617};
CC KM=0.19 mM for D-lysine (at pH 8.7 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:19850617};
CC KM=0.26 mM for D-lysine (at pH 8.7 and 25 degrees Celsius)
CC {ECO:0000269|PubMed:20809650};
CC KM=0.4 mM for D-tyrosine (at pH 8.7 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:19850617};
CC KM=0.8 mM for D-tyrosine (at pH 8.7 and 25 degrees Celsius)
CC {ECO:0000269|PubMed:20809650};
CC KM=1.13 mM for D-phenylalanine (at pH 8.7 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:19850617};
CC KM=1.43 mM for D-methionine (at pH 8.7 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:19850617};
CC KM=1.48 mM for D-ornithine (at pH 8.7 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:19850617};
CC KM=3.52 mM for D-histidine (at pH 8.7 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:19850617};
CC KM=10 mM for D-methionine (at pH 8.7 and 25 degrees Celsius)
CC {ECO:0000269|PubMed:20809650};
CC KM=11 mM for D-phenylalanine (at pH 8.7 and 25 degrees Celsius)
CC {ECO:0000269|PubMed:20809650};
CC KM=11 mM for D-histidine (at pH 8.7 and 25 degrees Celsius)
CC {ECO:0000269|PubMed:20809650};
CC KM=12 mM for D-leucine (at pH 8.7 and 25 degrees Celsius)
CC {ECO:0000269|PubMed:20809650};
CC Note=kcat is 204 sec(-1) for dehydrogenase activity with D-arginine
CC as substrate (at pH 8.7 and 25 degrees Celsius). kcat is 154 sec(-1)
CC for dehydrogenase activity with D-methionine as substrate (at pH 8.7
CC and 25 degrees Celsius). kcat is 141 sec(-1) for dehydrogenase
CC activity with D-lysine as substrate (at pH 8.7 and 25 degrees
CC Celsius). kcat is 75 sec(-1) for dehydrogenase activity with D-
CC phenylalanine as substrate (at pH 8.7 and 25 degrees Celsius). kcat
CC is 35 sec(-1) for dehydrogenase activity with D-histidine as
CC substrate (at pH 8.7 and 25 degrees Celsius). kcat is 23 sec(-1) for
CC dehydrogenase activity with D-tyrosine as substrate (at pH 8.7 and 25
CC degrees Celsius). kcat is 11.1 sec(-1) for dehydrogenase activity
CC with D-arginine as substrate (at pH 8.7 and 37 degrees Celsius). kcat
CC is 9.2 sec(-1) for dehydrogenase activity with D-lysine as substrate
CC (at pH 8.7 and 37 degrees Celsius). kcat is 6.8 sec(-1) for
CC dehydrogenase activity with D-methionine as substrate (at pH 8.7 and
CC 37 degrees Celsius). kcat is 6.4 sec(-1) for dehydrogenase activity
CC with D-leucine as substrate (at pH 8.7 and 25 degrees Celsius). kcat
CC is 6.2 sec(-1) for dehydrogenase activity with D-ornithine as
CC substrate (at pH 8.7 and 37 degrees Celsius). kcat is 5.3 sec(-1) for
CC dehydrogenase activity with D-phenylalanine as substrate (at pH 8.7
CC and 37 degrees Celsius). kcat is 3.6 sec(-1) for dehydrogenase
CC activity with D-histidine and D-tyrosine as substrates (at pH 8.7 and
CC 37 degrees Celsius). {ECO:0000269|PubMed:19850617,
CC ECO:0000269|PubMed:20809650};
CC pH dependence:
CC Optimum pH is 8.7. {ECO:0000269|PubMed:19850617};
CC Temperature dependence:
CC Optimum temperature is 37 degrees Celsius.
CC {ECO:0000269|PubMed:19850617};
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:19139398}.
CC -!- INDUCTION: Induced by growth on D-arginine, D-lysine and 2-ketoarginine
CC (2-KA), but not on L-arginine (PubMed:3141581, PubMed:19139398).
CC Repressed by DauR. ArgR could be a transcriptional activator of the
CC dauBAR operon in response to the presence of L-Arg (PubMed:19850617).
CC {ECO:0000269|PubMed:19139398, ECO:0000269|PubMed:19850617,
CC ECO:0000269|PubMed:3141581}.
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene are unable to grow on D-
CC arginine or D-lysine as sole nitrogen source.
CC {ECO:0000269|PubMed:19139398, ECO:0000269|PubMed:19850617}.
CC -!- MISCELLANEOUS: In vitro, it is essential to include phenazine
CC methosulfate (PMS) or iodonitrotetrazolium chloride (INT) as the
CC artificial electron acceptor in the reaction to ensure DauA remains
CC active with FAD. {ECO:0000269|PubMed:19139398,
CC ECO:0000269|PubMed:3141581}.
CC -!- SIMILARITY: Belongs to the FAD-dependent glycerol-3-phosphate
CC dehydrogenase family. {ECO:0000305}.
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DR EMBL; AE004091; AAG07250.1; -; Genomic_DNA.
DR PIR; E83163; E83163.
DR RefSeq; NP_252552.1; NC_002516.2.
DR RefSeq; WP_003113780.1; NZ_QZGE01000001.1.
DR PDB; 3NYC; X-ray; 1.06 A; A=2-375.
DR PDB; 3NYE; X-ray; 1.30 A; A=2-375.
DR PDB; 3NYF; X-ray; 1.30 A; A=2-375.
DR PDB; 3SM8; X-ray; 1.07 A; A=2-375.
DR PDB; 6P9D; X-ray; 1.33 A; A=1-375.
DR PDB; 6PLD; X-ray; 1.55 A; A=1-375.
DR PDB; 7RDF; X-ray; 1.29 A; A=1-375.
DR PDBsum; 3NYC; -.
DR PDBsum; 3NYE; -.
DR PDBsum; 3NYF; -.
DR PDBsum; 3SM8; -.
DR PDBsum; 6P9D; -.
DR PDBsum; 6PLD; -.
DR PDBsum; 7RDF; -.
DR AlphaFoldDB; Q9HXE3; -.
DR SMR; Q9HXE3; -.
DR STRING; 287.DR97_4003; -.
DR PaxDb; Q9HXE3; -.
DR PRIDE; Q9HXE3; -.
DR DNASU; 879806; -.
DR EnsemblBacteria; AAG07250; AAG07250; PA3863.
DR GeneID; 879806; -.
DR KEGG; pae:PA3863; -.
DR PATRIC; fig|208964.12.peg.4045; -.
DR PseudoCAP; PA3863; -.
DR HOGENOM; CLU_007884_4_2_6; -.
DR InParanoid; Q9HXE3; -.
DR OMA; FMESYGT; -.
DR PhylomeDB; Q9HXE3; -.
DR BioCyc; MetaCyc:MON-11563; -.
DR BioCyc; PAER208964:G1FZ6-3934-MON; -.
DR BRENDA; 1.4.99.6; 5087.
DR EvolutionaryTrace; Q9HXE3; -.
DR Proteomes; UP000002438; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0008718; F:D-amino-acid dehydrogenase activity; IDA:UniProtKB.
DR GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
DR GO; GO:0016491; F:oxidoreductase activity; IBA:GO_Central.
DR GO; GO:0006527; P:arginine catabolic process; IDA:UniProtKB.
DR GO; GO:0006525; P:arginine metabolic process; IDA:UniProtKB.
DR Gene3D; 3.50.50.60; -; 1.
DR InterPro; IPR006076; FAD-dep_OxRdtase.
DR InterPro; IPR036188; FAD/NAD-bd_sf.
DR Pfam; PF01266; DAO; 1.
DR SUPFAM; SSF51905; SSF51905; 1.
PE 1: Evidence at protein level;
KW 3D-structure; FAD; Flavoprotein; Nucleotide-binding; Oxidoreductase;
KW Reference proteome; Virulence.
FT CHAIN 1..375
FT /note="FAD-dependent catabolic D-arginine dehydrogenase
FT DauA"
FT /id="PRO_0000433131"
FT BINDING 14
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:20809650,
FT ECO:0000269|PubMed:21707047"
FT BINDING 32..33
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:20809650,
FT ECO:0000269|PubMed:21707047"
FT BINDING 41..48
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:20809650,
FT ECO:0000269|PubMed:21707047"
FT BINDING 171
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:20809650,
FT ECO:0000269|PubMed:21707047"
FT BINDING 331..336
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:20809650,
FT ECO:0000269|PubMed:21707047"
FT SITE 87
FT /note="Important for specificity toward positively charged
FT susbtrates"
FT /evidence="ECO:0000269|PubMed:20809650"
FT STRAND 5..9
FT /evidence="ECO:0007829|PDB:3NYC"
FT HELIX 13..22
FT /evidence="ECO:0007829|PDB:3NYC"
FT TURN 23..25
FT /evidence="ECO:0007829|PDB:3NYC"
FT STRAND 28..31
FT /evidence="ECO:0007829|PDB:3NYC"
FT STRAND 33..36
FT /evidence="ECO:0007829|PDB:3NYC"
FT HELIX 41..43
FT /evidence="ECO:0007829|PDB:3NYC"
FT STRAND 51..54
FT /evidence="ECO:0007829|PDB:3NYC"
FT HELIX 56..70
FT /evidence="ECO:0007829|PDB:3NYC"
FT STRAND 81..84
FT /evidence="ECO:0007829|PDB:3NYC"
FT STRAND 87..90
FT /evidence="ECO:0007829|PDB:3NYC"
FT HELIX 96..109
FT /evidence="ECO:0007829|PDB:3NYC"
FT STRAND 114..116
FT /evidence="ECO:0007829|PDB:3NYC"
FT HELIX 118..124
FT /evidence="ECO:0007829|PDB:3NYC"
FT HELIX 130..132
FT /evidence="ECO:0007829|PDB:3NYC"
FT STRAND 136..139
FT /evidence="ECO:0007829|PDB:3NYC"
FT STRAND 143..145
FT /evidence="ECO:0007829|PDB:3NYC"
FT HELIX 147..160
FT /evidence="ECO:0007829|PDB:3NYC"
FT STRAND 164..168
FT /evidence="ECO:0007829|PDB:3NYC"
FT STRAND 173..177
FT /evidence="ECO:0007829|PDB:3NYC"
FT STRAND 180..184
FT /evidence="ECO:0007829|PDB:3NYC"
FT STRAND 186..197
FT /evidence="ECO:0007829|PDB:3NYC"
FT HELIX 200..202
FT /evidence="ECO:0007829|PDB:3NYC"
FT HELIX 203..210
FT /evidence="ECO:0007829|PDB:3NYC"
FT STRAND 218..227
FT /evidence="ECO:0007829|PDB:3NYC"
FT STRAND 240..243
FT /evidence="ECO:0007829|PDB:3NYC"
FT STRAND 249..253
FT /evidence="ECO:0007829|PDB:3NYC"
FT STRAND 256..260
FT /evidence="ECO:0007829|PDB:3NYC"
FT HELIX 276..289
FT /evidence="ECO:0007829|PDB:3NYC"
FT STRAND 298..307
FT /evidence="ECO:0007829|PDB:3NYC"
FT STRAND 314..317
FT /evidence="ECO:0007829|PDB:3NYC"
FT STRAND 324..328
FT /evidence="ECO:0007829|PDB:3NYC"
FT TURN 334..337
FT /evidence="ECO:0007829|PDB:3NYC"
FT HELIX 338..349
FT /evidence="ECO:0007829|PDB:3NYC"
FT HELIX 356..359
FT /evidence="ECO:0007829|PDB:3NYC"
FT TURN 360..362
FT /evidence="ECO:0007829|PDB:3NYC"
FT HELIX 365..368
FT /evidence="ECO:0007829|PDB:3NYC"
FT HELIX 370..373
FT /evidence="ECO:0007829|PDB:3NYC"
SQ SEQUENCE 375 AA; 40567 MW; 655001CB24FF13DE CRC64;
MIEADYLVIG AGIAGASTGY WLSAHGRVVV LEREAQPGYH STGRSAAHYT VAYGTPQVRA
LTAASRAFFD NPPAGFCEHP LLSPRPEMVV DFSDDPEELR RQYESGKALV PQMRLLDAEQ
ACSIVPVLRR DKVFGATYDP TGADIDTDAL HQGYLRGIRR NQGQVLCNHE ALEIRRVDGA
WEVRCDAGSY RAAVLVNAAG AWCDAIAGLA GVRPLGLQPK RRSAFIFAPP PGIDCHDWPM
LVSLDESFYL KPDAGMLLGS PANADPVEAH DVQPEQLDIA TGMYLIEEAT TLTIRRPEHT
WAGLRSFVAD GDLVAGYAAN AEGFFWVAAQ GGYGIQTSAA MGEASAALIR HQPLPAHLRE
HGLDEAMLSP RRLSP
