ALR_GEOSE
ID ALR_GEOSE Reviewed; 388 AA.
AC P10724;
DT 01-JUL-1989, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 2.
DT 03-AUG-2022, entry version 144.
DE RecName: Full=Alanine racemase {ECO:0000255|HAMAP-Rule:MF_01201};
DE EC=5.1.1.1 {ECO:0000255|HAMAP-Rule:MF_01201, ECO:0000269|PubMed:10079072, ECO:0000269|PubMed:12203980, ECO:0000269|PubMed:12741835};
GN Name=alr; Synonyms=dal;
OS Geobacillus stearothermophilus (Bacillus stearothermophilus).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Geobacillus.
OX NCBI_TaxID=1422;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=2835089; DOI=10.1021/bi00404a033;
RA Tanizawa K., Ohshima A., Scheidegger A., Inagaki K., Tanaka H., Soda K.;
RT "Thermostable alanine racemase from Bacillus stearothermophilus: DNA and
RT protein sequence determination and secondary structure prediction.";
RL Biochemistry 27:1311-1316(1988).
RN [2]
RP PROTEIN SEQUENCE OF 31-43.
RX PubMed=2496744; DOI=10.1021/bi00428a004;
RA Faraci W.S., Walsh C.T.;
RT "Mechanism of inactivation of alanine racemase by beta, beta, beta-
RT trifluoroalanine.";
RL Biochemistry 28:431-437(1989).
RN [3]
RP PROTEIN SEQUENCE OF 36-43.
RX PubMed=3730360; DOI=10.1021/bi00359a029;
RA Badet B., Inagaki K., Soda K., Walsh C.T.;
RT "Time-dependent inhibition of Bacillus stearothermophilus alanine racemase
RT by (1-aminoethyl)phosphonate isomers by isomerization to noncovalent slowly
RT dissociating enzyme-(1-aminoethyl)phosphonate complexes.";
RL Biochemistry 25:3275-3282(1986).
RN [4]
RP MUTAGENESIS OF ARG-219.
RX PubMed=10194319; DOI=10.1021/bi982924t;
RA Sun S., Toney M.D.;
RT "Evidence for a two-base mechanism involving tyrosine-265 from arginine-219
RT mutants of alanine racemase.";
RL Biochemistry 38:4058-4065(1999).
RN [5]
RP FUNCTION, ACTIVE SITES, AND MUTAGENESIS.
RX PubMed=10502689; DOI=10.1093/oxfordjournals.jbchem.a022517;
RA Watanabe A., Yoshimura T., Mikami B., Esaki N.;
RT "Tyrosine 265 of alanine racemase serves as a base abstracting alpha-
RT hydrogen from L-alanine: the counterpart residue to lysine 39 specific to
RT D-alanine.";
RL J. Biochem. 126:781-786(1999).
RN [6]
RP FUNCTION, CATALYTIC ACTIVITY, AND MUTAGENESIS OF TYR-354.
RX PubMed=12203980;
RX DOI=10.1002/1439-7633(20020802)3:8<789::aid-cbic789>3.0.co;2-d;
RA Patrick W.M., Weisner J., Blackburn J.M.;
RT "Site-directed mutagenesis of Tyr354 in Geobacillus stearothermophilus
RT alanine racemase identifies a role in controlling substrate specificity and
RT a possible role in the evolution of antibiotic resistance.";
RL ChemBioChem 3:789-792(2002).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) IN COMPLEX WITH PYRIDOXAL PHOSPHATE,
RP COFACTOR, SUBUNIT, PYRIDOXAL PHOSPHATE AT LYS-39, AND SEQUENCE REVISION.
RX PubMed=9063881; DOI=10.1021/bi961856c;
RA Shaw J.P., Petsko G.A., Ringe D.;
RT "Determination of the structure of alanine racemase from Bacillus
RT stearothermophilus at 1.9-A resolution.";
RL Biochemistry 36:1329-1342(1997).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) IN COMPLEX WITH PYRIDOXAL PHOSPHATE
RP AND L-ALA PHOSPHONATE, COFACTOR, AND ACTIVE SITE.
RX PubMed=9671513; DOI=10.1021/bi980692s;
RA Stamper C.G., Morollo A.A., Ringe D.;
RT "Reaction of alanine racemase with 1-aminoethylphosphonic acid forms a
RT stable external aldimine.";
RL Biochemistry 37:10438-10445(1998).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS)IN COMPLEX WITH PYRIDOXAL PHOSPHATE
RP AND PROPIONATE, CATALYTIC ACTIVITY, SUBUNIT, COFACTOR, PYRIDOXAL PHOSPHATE
RP AT LYS-39, ACTIVITY REGULATION, AND CARBOXYLATION AT LYS-129.
RC STRAIN=ATCC 12980 / DSM 22 / CCM 2062 / JCM 2501 / NBRC 12550 / NCIMB 8923
RC / NCTC 10339 / R-35646 / VKM B-510;
RX PubMed=10079072; DOI=10.1021/bi9822729;
RA Morollo A.A., Petsko G.A., Ringe D.;
RT "Structure of a Michaelis complex analogue: propionate binds in the
RT substrate carboxylate site of alanine racemase.";
RL Biochemistry 38:3293-3301(1999).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) IN COMPLEX WITH D-ALANINE
RP PHOSPHONATE, AND CARBOXYLATION AT LYS-129.
RA Stamper G.F., Ringe D.;
RT "Crystal structure of alanine racemase in complex with D-alanine
RT phosphonate.";
RL Submitted (SEP-2000) to the PDB data bank.
RN [11]
RP X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) IN COMPLEXES WITH
RP N-(5'-PHOSPHOPYRIDOXYL)-D-ALANINE AND N-(5'-PHOSPHOPYRIDOXYL)-L-ALANINE,
RP COFACTOR, ACTIVE SITE, PYRIDOXAL PHOSPHATE AT LYS-39, AND CARBOXYLATION AT
RP LYS-129.
RX PubMed=11886871; DOI=10.1074/jbc.m201615200;
RA Watanabe A., Yoshimura T., Mikami B., Hayashi H., Kagamiyama H., Esaki N.;
RT "Reaction mechanism of alanine racemase from Bacillus stearothermophilus:
RT x-ray crystallographic studies of the enzyme bound with N-(5'-
RT phosphopyridoxyl)alanine.";
RL J. Biol. Chem. 277:19166-19172(2002).
RN [12]
RP X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) IN COMPLEXES WITH PYRIDOXAL
RP PHOSPHATE AND CYCLOSERINE, CATALYTIC ACTIVITY, ACTIVITY REGULATION,
RP COFACTOR, ACTIVE SITE, AND CARBOXYLATION AT LYS-129.
RX PubMed=12741835; DOI=10.1021/bi027022d;
RA Fenn T.D., Stamper G.F., Morollo A.A., Ringe D.;
RT "A side reaction of alanine racemase: transamination of cycloserine.";
RL Biochemistry 42:5775-5783(2003).
RN [13]
RP X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) IN COMPLEX WITH CYCLOSERINE AND
RP PYRIDOXAL PHOSPHATE, COFACTOR, SUBUNIT, PYRIDOXAL PHOSPHATE AT LYS-39,
RP MUTAGENESIS OF TYR-265, ACTIVITY REGULATION, ACTIVE SITE, AND CARBOXYLATION
RP AT LYS-129.
RX PubMed=15807525; DOI=10.1021/bi047842l;
RA Fenn T.D., Holyoak T., Stamper G.F., Ringe D.;
RT "Effect of a Y265F mutant on the transamination-based cycloserine
RT inactivation of alanine racemase.";
RL Biochemistry 44:5317-5327(2005).
CC -!- FUNCTION: Catalyzes the interconversion of L-alanine and D-alanine.
CC Also weakly active on serine. {ECO:0000269|PubMed:10502689,
CC ECO:0000269|PubMed:12203980}.
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:0000255|HAMAP-Rule:MF_01201,
CC ECO:0000269|PubMed:10079072, ECO:0000269|PubMed:12203980,
CC ECO:0000269|PubMed:12741835};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01201,
CC ECO:0000269|PubMed:10079072, ECO:0000269|PubMed:11886871,
CC ECO:0000269|PubMed:12741835, ECO:0000269|PubMed:15807525,
CC ECO:0000269|PubMed:9063881, ECO:0000269|PubMed:9671513};
CC -!- ACTIVITY REGULATION: Inhibited by acetate and propionate. Irreversibly
CC inhibited by cycloserine. {ECO:0000269|PubMed:10079072,
CC ECO:0000269|PubMed:12741835, ECO:0000269|PubMed:15807525}.
CC -!- PATHWAY: Amino-acid biosynthesis; D-alanine biosynthesis; D-alanine
CC from L-alanine: step 1/1. {ECO:0000255|HAMAP-Rule:MF_01201}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:10079072,
CC ECO:0000269|PubMed:15807525, ECO:0000269|PubMed:9063881,
CC ECO:0000269|PubMed:9671513, ECO:0000269|Ref.10}.
CC -!- SIMILARITY: Belongs to the alanine racemase family. {ECO:0000255|HAMAP-
CC Rule:MF_01201}.
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DR EMBL; M19142; AAA22220.1; -; Genomic_DNA.
DR PIR; A29984; A29984.
DR PDB; 1BD0; X-ray; 1.60 A; A/B=1-388.
DR PDB; 1EPV; X-ray; 2.20 A; A/B=2-388.
DR PDB; 1FTX; X-ray; 2.20 A; A/B=2-388.
DR PDB; 1L6F; X-ray; 2.00 A; A/B=1-388.
DR PDB; 1L6G; X-ray; 2.00 A; A/B=1-388.
DR PDB; 1NIU; X-ray; 2.20 A; A/B=1-388.
DR PDB; 1SFT; X-ray; 1.90 A; A/B=1-388.
DR PDB; 1XQK; X-ray; 1.95 A; A/B=1-388.
DR PDB; 1XQL; X-ray; 1.80 A; A/B=1-388.
DR PDB; 2SFP; X-ray; 1.90 A; A/B=1-388.
DR PDB; 3UW6; X-ray; 2.30 A; A/B/C=1-388.
DR PDB; 4ILS; X-ray; 2.50 A; A/B/C=1-388.
DR PDBsum; 1BD0; -.
DR PDBsum; 1EPV; -.
DR PDBsum; 1FTX; -.
DR PDBsum; 1L6F; -.
DR PDBsum; 1L6G; -.
DR PDBsum; 1NIU; -.
DR PDBsum; 1SFT; -.
DR PDBsum; 1XQK; -.
DR PDBsum; 1XQL; -.
DR PDBsum; 2SFP; -.
DR PDBsum; 3UW6; -.
DR PDBsum; 4ILS; -.
DR AlphaFoldDB; P10724; -.
DR SMR; P10724; -.
DR ChEMBL; CHEMBL1075086; -.
DR DrugBank; DB02038; D-[3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-ylmethyl]-N,O-cycloserylamide.
DR DrugBank; DB03801; Lysine Nz-Carboxylic Acid.
DR DrugBank; DB01993; N-(5'-Phosphopyridoxyl)-D-Alanine.
DR DrugBank; DB04467; N-(5'-phosphopyridoxyl)-L-alanine.
DR DrugBank; DB03097; PMP-hydroxyisoxazole, pyridoxamine-5-phosphate-hydroxyisoxazole.
DR DrugBank; DB03766; Propanoic acid.
DR DrugBank; DB02142; Pyridoxamine-5'-Phosphate.
DR DrugBank; DB03327; {1-[(3-Hydroxy-Methyl-5-Phosphonooxy-Methyl-Pyridin-4-Ylmethyl)-Amino]-Ethyl}-Phosphonic Acid.
DR BRENDA; 5.1.1.1; 623.
DR SABIO-RK; P10724; -.
DR UniPathway; UPA00042; UER00497.
DR EvolutionaryTrace; P10724; -.
DR GO; GO:0008784; F:alanine racemase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IEA:UniProtKB-UniRule.
DR GO; GO:0030632; P:D-alanine biosynthetic process; IEA:UniProtKB-UniPathway.
DR Gene3D; 2.40.37.10; -; 1.
DR Gene3D; 3.20.20.10; -; 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 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; SSF50621; 1.
DR SUPFAM; SSF51419; SSF51419; 1.
DR TIGRFAMs; TIGR00492; alr; 1.
DR PROSITE; PS00395; ALANINE_RACEMASE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Isomerase; Pyridoxal phosphate.
FT CHAIN 1..388
FT /note="Alanine racemase"
FT /id="PRO_0000114499"
FT ACT_SITE 39
FT /note="Proton acceptor; specific for D-alanine"
FT /evidence="ECO:0000305|PubMed:10502689,
FT ECO:0000305|PubMed:15807525"
FT ACT_SITE 265
FT /note="Proton acceptor; specific for L-alanine"
FT /evidence="ECO:0000305|PubMed:10502689,
FT ECO:0000305|PubMed:15807525"
FT BINDING 136
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:11886871"
FT BINDING 312
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:11886871"
FT MOD_RES 39
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000269|PubMed:11886871,
FT ECO:0000269|PubMed:15807525, ECO:0000269|PubMed:9063881"
FT MOD_RES 129
FT /note="N6-carboxylysine"
FT /evidence="ECO:0000269|PubMed:10079072,
FT ECO:0000269|PubMed:11886871, ECO:0000269|PubMed:12741835,
FT ECO:0000269|PubMed:15807525, ECO:0000269|Ref.10"
FT MUTAGEN 39
FT /note="K->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:10502689"
FT MUTAGEN 166
FT /note="H->A: 6.5-fold decrease in activity."
FT /evidence="ECO:0000269|PubMed:10502689"
FT MUTAGEN 219
FT /note="R->A: 100-fold decrease in activity."
FT /evidence="ECO:0000269|PubMed:10194319"
FT MUTAGEN 219
FT /note="R->E: 1000-fold decrease in activity."
FT /evidence="ECO:0000269|PubMed:10194319"
FT MUTAGEN 219
FT /note="R->K: 4-fold decrease in activity."
FT /evidence="ECO:0000269|PubMed:10194319"
FT MUTAGEN 265
FT /note="Y->A: 5000-fold decrease in activity."
FT /evidence="ECO:0000269|PubMed:15807525"
FT MUTAGEN 265
FT /note="Y->F: Loss of activity."
FT /evidence="ECO:0000269|PubMed:15807525"
FT MUTAGEN 265
FT /note="Y->S: 2000-fold decrease in activity."
FT /evidence="ECO:0000269|PubMed:15807525"
FT MUTAGEN 354
FT /note="Y->A: 54-fold increase in serine racemase activity."
FT /evidence="ECO:0000269|PubMed:12203980"
FT MUTAGEN 354
FT /note="Y->N: 81-fold increase in serine racemase activity."
FT /evidence="ECO:0000269|PubMed:12203980"
FT MUTAGEN 354
FT /note="Y->Q: 51-fold increase in serine racemase activity."
FT /evidence="ECO:0000269|PubMed:12203980"
FT CONFLICT 37..38
FT /note="VV -> PP (in Ref. 3; AA sequence)"
FT /evidence="ECO:0000305"
FT CONFLICT 57..62
FT /note="AGASRL -> RGPPP (in Ref. 1; AAA22220)"
FT /evidence="ECO:0000305"
FT CONFLICT 288..289
FT /note="WL -> V (in Ref. 1; AAA22220)"
FT /evidence="ECO:0000305"
FT STRAND 6..13
FT /evidence="ECO:0007829|PDB:1BD0"
FT HELIX 14..27
FT /evidence="ECO:0007829|PDB:1BD0"
FT STRAND 33..37
FT /evidence="ECO:0007829|PDB:1BD0"
FT HELIX 39..43
FT /evidence="ECO:0007829|PDB:1BD0"
FT HELIX 47..57
FT /evidence="ECO:0007829|PDB:1BD0"
FT STRAND 61..66
FT /evidence="ECO:0007829|PDB:1BD0"
FT HELIX 67..75
FT /evidence="ECO:0007829|PDB:1BD0"
FT STRAND 82..84
FT /evidence="ECO:0007829|PDB:1BD0"
FT HELIX 90..92
FT /evidence="ECO:0007829|PDB:1BD0"
FT HELIX 93..98
FT /evidence="ECO:0007829|PDB:1BD0"
FT STRAND 101..105
FT /evidence="ECO:0007829|PDB:1BD0"
FT HELIX 108..117
FT /evidence="ECO:0007829|PDB:1BD0"
FT STRAND 124..130
FT /evidence="ECO:0007829|PDB:1BD0"
FT STRAND 132..134
FT /evidence="ECO:0007829|PDB:1BD0"
FT STRAND 136..139
FT /evidence="ECO:0007829|PDB:1BD0"
FT HELIX 142..154
FT /evidence="ECO:0007829|PDB:1BD0"
FT STRAND 158..164
FT /evidence="ECO:0007829|PDB:1BD0"
FT STRAND 172..174
FT /evidence="ECO:0007829|PDB:1XQK"
FT HELIX 176..189
FT /evidence="ECO:0007829|PDB:1BD0"
FT STRAND 192..194
FT /evidence="ECO:0007829|PDB:1SFT"
FT STRAND 197..200
FT /evidence="ECO:0007829|PDB:1BD0"
FT HELIX 204..209
FT /evidence="ECO:0007829|PDB:1BD0"
FT HELIX 211..213
FT /evidence="ECO:0007829|PDB:1XQL"
FT STRAND 217..220
FT /evidence="ECO:0007829|PDB:1BD0"
FT HELIX 222..225
FT /evidence="ECO:0007829|PDB:1BD0"
FT HELIX 231..236
FT /evidence="ECO:0007829|PDB:1BD0"
FT STRAND 245..250
FT /evidence="ECO:0007829|PDB:1BD0"
FT STRAND 252..257
FT /evidence="ECO:0007829|PDB:1BD0"
FT STRAND 262..264
FT /evidence="ECO:0007829|PDB:1BD0"
FT HELIX 265..267
FT /evidence="ECO:0007829|PDB:1BD0"
FT STRAND 273..281
FT /evidence="ECO:0007829|PDB:1BD0"
FT HELIX 284..286
FT /evidence="ECO:0007829|PDB:1BD0"
FT HELIX 290..294
FT /evidence="ECO:0007829|PDB:1BD0"
FT STRAND 296..299
FT /evidence="ECO:0007829|PDB:1BD0"
FT STRAND 302..308
FT /evidence="ECO:0007829|PDB:1BD0"
FT STRAND 315..318
FT /evidence="ECO:0007829|PDB:1BD0"
FT STRAND 328..335
FT /evidence="ECO:0007829|PDB:1BD0"
FT STRAND 338..340
FT /evidence="ECO:0007829|PDB:1BD0"
FT HELIX 342..349
FT /evidence="ECO:0007829|PDB:1BD0"
FT HELIX 355..359
FT /evidence="ECO:0007829|PDB:1BD0"
FT STRAND 366..370
FT /evidence="ECO:0007829|PDB:1BD0"
FT STRAND 373..378
FT /evidence="ECO:0007829|PDB:1BD0"
SQ SEQUENCE 388 AA; 43593 MW; F54AA581F135EA7A CRC64;
MNDFHRDTWA EVDLDAIYDN VENLRRLLPD DTHIMAVVKA NAYGHGDVQV ARTALEAGAS
RLAVAFLDEA LALREKGIEA PILVLGASRP ADAALAAQQR IALTVFRSDW LEEASALYSG
PFPIHFHLKM DTGMGRLGVK DEEETKRIVA LIERHPHFVL EGLYTHFATA DEVNTDYFSY
QYTRFLHMLE WLPSRPPLVH CANSAASLRF PDRTFNMVRF GIAMYGLAPS PGIKPLLPYP
LKEAFSLHSR LVHVKKLQPG EKVSYGATYT AQTEEWIGTI PIGYADGWLR RLQHFHVLVD
GQKAPIVGRI CMDQCMIRLP GPLPVGTKVT LIGRQGDEVI SIDDVARHLE TINYEVPCTI
SYRVPRIFFR HKRIMEVRNA IGRGESSA
