ID ALR2_PSEAE Reviewed; 357 AA.
AC Q9HTQ2; Q9S419;
DT 05-MAR-2002, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2001, sequence version 1.
DT 27-MAR-2024, entry version 143.
DE RecName: Full=Alanine racemase, catabolic {ECO:0000305|PubMed:10977898};
DE EC=5.1.1.1 {ECO:0000269|PubMed:10977898};
GN Name=dadX {ECO:0000303|PubMed:10977898, ECO:0000312|EMBL:AAG08687.1};
GN OrderedLocusNames=PA5302;
OS Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM
OS 14847 / LMG 12228 / 1C / PRS 101 / PAO1).
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Pseudomonadales;
OC Pseudomonadaceae; Pseudomonas.
OX NCBI_TaxID=208964;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, CATALYTIC ACTIVITY, AND
RP BIOPHYSICOCHEMICAL PROPERTIES.
RC STRAIN=ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C /
RC PRS 101 / PAO1;
RX PubMed=10977898; DOI=10.1007/s002840010136;
RA Strych U., Huang H.-C., Krause K.L., Benedik M.J.;
RT "Characterization of the alanine racemases from Pseudomonas aeruginosa
RT PAO1.";
RL Curr. Microbiol. 41:290-294(2000).
RN [2]
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 [3]
RP X-RAY CRYSTALLOGRAPHY (1.45 ANGSTROMS) IN COMPLEX WITH PYRIDOXAL PHOSPHATE
RP AND LYSINE, COFACTOR, SUBUNIT, PYRIDOXAL PHOSPHATE AT LYS-33, AND
RP CARBOXYLATION AT LYS-122.
RX PubMed=14674749; DOI=10.1021/bi030165v;
RA LeMagueres P., Im H., Dvorak A., Strych U., Benedik M.J., Krause K.L.;
RT "Crystal structure at 1.45 A resolution of alanine racemase from a
RT pathogenic bacterium, Pseudomonas aeruginosa, contains both internal and
RT external aldimine forms.";
RL Biochemistry 42:14752-14761(2003).
CC -!- FUNCTION: Isomerizes L-alanine to D-alanine which is then oxidized to
CC pyruvate by DadA. {ECO:0000269|PubMed:10977898}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-alanine = D-alanine; Xref=Rhea:RHEA:20249,
CC ChEBI:CHEBI:57416, ChEBI:CHEBI:57972; EC=5.1.1.1;
CC Evidence={ECO:0000269|PubMed:10977898};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000269|PubMed:14674749};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1.40 mM for D-alanine {ECO:0000269|PubMed:10977898};
CC KM=1.40 mM for L-alanine {ECO:0000269|PubMed:10977898};
CC Vmax=134 umol/min/mg enzyme toward D-alanine
CC {ECO:0000269|PubMed:10977898};
CC Vmax=155 umol/min/mg enzyme toward L-alanine
CC {ECO:0000269|PubMed:10977898};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:14674749}.
CC -!- SIMILARITY: Belongs to the alanine racemase family. {ECO:0000255|HAMAP-
CC Rule:MF_01201}.
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DR EMBL; AF165881; AAD47081.1; -; Genomic_DNA.
DR EMBL; AE004091; AAG08687.1; -; Genomic_DNA.
DR PIR; F82982; F82982.
DR RefSeq; NP_253989.1; NC_002516.2.
DR RefSeq; WP_003114351.1; NZ_QZGE01000020.1.
DR PDB; 1RCQ; X-ray; 1.45 A; A=1-357.
DR PDBsum; 1RCQ; -.
DR AlphaFoldDB; Q9HTQ2; -.
DR SMR; Q9HTQ2; -.
DR STRING; 208964.PA5302; -.
DR DrugBank; DB03252; D-Lysine.
DR DrugBank; DB03801; Lysine Nz-Carboxylic Acid.
DR PaxDb; 208964-PA5302; -.
DR GeneID; 878055; -.
DR KEGG; pae:PA5302; -.
DR PATRIC; fig|208964.12.peg.5556; -.
DR PseudoCAP; PA5302; -.
DR HOGENOM; CLU_028393_1_0_6; -.
DR InParanoid; Q9HTQ2; -.
DR OrthoDB; 9813814at2; -.
DR PhylomeDB; Q9HTQ2; -.
DR BioCyc; PAER208964:G1FZ6-5423-MONOMER; -.
DR BRENDA; 5.1.1.1; 5087.
DR SABIO-RK; Q9HTQ2; -.
DR EvolutionaryTrace; Q9HTQ2; -.
DR Proteomes; UP000002438; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0008784; F:alanine racemase activity; IDA:PseudoCAP.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IBA:GO_Central.
DR GO; GO:0030632; P:D-alanine biosynthetic process; IBA:GO_Central.
DR CDD; cd06827; PLPDE_III_AR_proteobact; 1.
DR Gene3D; 3.20.20.10; Alanine racemase; 1.
DR HAMAP; MF_01201; Ala_racemase; 1.
DR InterPro; IPR000821; Ala_racemase.
DR InterPro; IPR009006; Ala_racemase/Decarboxylase_C.
DR InterPro; IPR011079; Ala_racemase_C.
DR InterPro; IPR001608; Ala_racemase_N.
DR InterPro; IPR020622; Ala_racemase_pyridoxalP-BS.
DR InterPro; IPR029066; PLP-binding_barrel.
DR NCBIfam; TIGR00492; alr; 1.
DR PANTHER; PTHR30511; ALANINE RACEMASE; 1.
DR PANTHER; PTHR30511:SF0; ALANINE RACEMASE, CATABOLIC-RELATED; 1.
DR Pfam; PF00842; Ala_racemase_C; 1.
DR Pfam; PF01168; Ala_racemase_N; 1.
DR PRINTS; PR00992; ALARACEMASE.
DR SMART; SM01005; Ala_racemase_C; 1.
DR SUPFAM; SSF50621; Alanine racemase C-terminal domain-like; 1.
DR SUPFAM; SSF51419; PLP-binding barrel; 1.
DR PROSITE; PS00395; ALANINE_RACEMASE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Isomerase; Pyridoxal phosphate; Reference proteome.
FT CHAIN 1..357
FT /note="Alanine racemase, catabolic"
FT /id="PRO_0000114547"
FT ACT_SITE 33
FT /note="Proton acceptor; specific for D-alanine"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01201"
FT ACT_SITE 253
FT /note="Proton acceptor; specific for L-alanine"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01201"
FT BINDING 129
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:14674749"
FT BINDING 301
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01201"
FT MOD_RES 33
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000269|PubMed:14674749"
FT MOD_RES 122
FT /note="N6-carboxylysine"
FT /evidence="ECO:0000269|PubMed:14674749"
FT CONFLICT 138
FT /note="S -> R (in Ref. 1; AAD47081)"
FT /evidence="ECO:0000305"
FT CONFLICT 178
FT /note="A -> S (in Ref. 1; AAD47081)"
FT /evidence="ECO:0000305"
FT CONFLICT 262
FT /note="S -> R (in Ref. 1; AAD47081)"
FT /evidence="ECO:0000305"
FT STRAND 5..9
FT /evidence="ECO:0007829|PDB:1RCQ"
FT HELIX 10..24
FT /evidence="ECO:0007829|PDB:1RCQ"
FT STRAND 26..31
FT /evidence="ECO:0007829|PDB:1RCQ"
FT HELIX 33..37
FT /evidence="ECO:0007829|PDB:1RCQ"
FT HELIX 41..48
FT /evidence="ECO:0007829|PDB:1RCQ"
FT TURN 49..51
FT /evidence="ECO:0007829|PDB:1RCQ"
FT STRAND 53..59
FT /evidence="ECO:0007829|PDB:1RCQ"
FT HELIX 60..68
FT /evidence="ECO:0007829|PDB:1RCQ"
FT STRAND 75..77
FT /evidence="ECO:0007829|PDB:1RCQ"
FT HELIX 84..86
FT /evidence="ECO:0007829|PDB:1RCQ"
FT HELIX 87..92
FT /evidence="ECO:0007829|PDB:1RCQ"
FT STRAND 95..99
FT /evidence="ECO:0007829|PDB:1RCQ"
FT HELIX 102..110
FT /evidence="ECO:0007829|PDB:1RCQ"
FT STRAND 117..123
FT /evidence="ECO:0007829|PDB:1RCQ"
FT STRAND 125..127
FT /evidence="ECO:0007829|PDB:1RCQ"
FT STRAND 129..132
FT /evidence="ECO:0007829|PDB:1RCQ"
FT HELIX 134..146
FT /evidence="ECO:0007829|PDB:1RCQ"
FT STRAND 150..156
FT /evidence="ECO:0007829|PDB:1RCQ"
FT HELIX 169..181
FT /evidence="ECO:0007829|PDB:1RCQ"
FT HELIX 193..198
FT /evidence="ECO:0007829|PDB:1RCQ"
FT STRAND 205..207
FT /evidence="ECO:0007829|PDB:1RCQ"
FT HELIX 211..214
FT /evidence="ECO:0007829|PDB:1RCQ"
FT STRAND 218..221
FT /evidence="ECO:0007829|PDB:1RCQ"
FT HELIX 226..228
FT /evidence="ECO:0007829|PDB:1RCQ"
FT STRAND 233..245
FT /evidence="ECO:0007829|PDB:1RCQ"
FT STRAND 250..252
FT /evidence="ECO:0007829|PDB:1RCQ"
FT HELIX 253..255
FT /evidence="ECO:0007829|PDB:1RCQ"
FT STRAND 260..269
FT /evidence="ECO:0007829|PDB:1RCQ"
FT HELIX 272..274
FT /evidence="ECO:0007829|PDB:1RCQ"
FT STRAND 285..288
FT /evidence="ECO:0007829|PDB:1RCQ"
FT STRAND 291..295
FT /evidence="ECO:0007829|PDB:1RCQ"
FT STRAND 304..307
FT /evidence="ECO:0007829|PDB:1RCQ"
FT STRAND 319..327
FT /evidence="ECO:0007829|PDB:1RCQ"
FT HELIX 329..335
FT /evidence="ECO:0007829|PDB:1RCQ"
FT HELIX 340..345
FT /evidence="ECO:0007829|PDB:1RCQ"
FT STRAND 352..355
FT /evidence="ECO:0007829|PDB:1RCQ"
SQ SEQUENCE 357 AA; 38915 MW; 199F4021D02FFF48 CRC64;
MRPARALIDL QALRHNYRLA REATGARALA VIKADAYGHG AVRCAEALAA EADGFAVACI
EEGLELREAG IRQPILLLEG FFEASELELI VAHDFWCVVH CAWQLEAIER ASLARPLNVW
LKMDSGMHRV GFFPEDFSAA HERLRASGKV AKIVMMSHFS RADELDCPRT EEQLAAFAAA
SQGLEGEISL RNSPAVLGWP KVPSDWVRPG ILLYGATPFE RAHPLADRLR PVMTLESKVI
SVRDLPAGEP VGYGARYSTE RSQRIGVVAM GYADGYPRHA ADGTLVFIDG KPGRLVGRVS
MDMLTVDLTD HPQAGLGSRV ELWGPNVPVG ALAAQFGSIP YQLLCNLKRV PRVYSGA
//
