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Database: UniProt
Entry: P10724
LinkDB: P10724
Original site: P10724 
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   05-DEC-2018, entry version 134.
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.,
RA   Soda K.;
RT   "Thermostable alanine racemase from Bacillus stearothermophilus: DNA
RT   and protein sequence determination and secondary structure
RT   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
RT   racemase by (1-aminoethyl)phosphonate isomers by isomerization to
RT   noncovalent slowly dissociating enzyme-(1-aminoethyl)phosphonate
RT   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
RT   arginine-219 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
RT   to 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
RT   specificity and a possible role in the evolution of antibiotic
RT   resistance.";
RL   ChemBioChem 3:789-792(2002).
RN   [7]
RP   X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) IN COMPLEX WITH PYRIDOXAL
RP   PHOSPHATE, COFACTOR, SUBUNIT, PYRIDOXAL PHOSPHATE AT LYS-39, AND
RP   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
RP   PHOSPHATE 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
RP   PHOSPHATE AND PROPIONATE, CATALYTIC ACTIVITY, SUBUNIT, COFACTOR,
RP   PYRIDOXAL PHOSPHATE AT LYS-39, ACTIVITY REGULATION, AND CARBAMYLATION
RP   AT LYS-129.
RC   STRAIN=ATCC 12980 / DSM 22 / JCM 2501 / NBRC 12550 / NCIMB 8923 / NCTC
RC   10339 / 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 CARBAMYLATION 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
RP   N-(5'-PHOSPHOPYRIDOXYL)-L-ALANINE, COFACTOR, ACTIVE SITE, PYRIDOXAL
RP   PHOSPHATE AT LYS-39, AND CARBAMYLATION AT LYS-129.
RX   PubMed=11886871; DOI=10.1074/jbc.M201615200;
RA   Watanabe A., Yoshimura T., Mikami B., Hayashi H., Kagamiyama H.,
RA   Esaki N.;
RT   "Reaction mechanism of alanine racemase from Bacillus
RT   stearothermophilus: x-ray crystallographic studies of the enzyme bound
RT   with N-(5'-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 CARBAMYLATION 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
RP   CARBAMYLATION 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-
CC       alanine. Also weakly active on serine.
CC       {ECO:0000269|PubMed:10502689, 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.
CC       Irreversibly inhibited by cycloserine.
CC       {ECO:0000269|PubMed:10079072, ECO:0000269|PubMed:12741835,
CC       ECO:0000269|PubMed:15807525}.
CC   -!- PATHWAY: Amino-acid biosynthesis; D-alanine biosynthesis; D-
CC       alanine from L-alanine: step 1/1. {ECO:0000255|HAMAP-
CC       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.
CC       {ECO:0000255|HAMAP-Rule:MF_01201}.
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   ProteinModelPortal; P10724; -.
DR   SMR; P10724; -.
DR   ChEMBL; CHEMBL1075086; -.
DR   DrugBank; DB03801; Lysine Nz-Carboxylic Acid.
DR   DrugBank; DB01993; N-(5'-Phosphopyridoxyl)-D-Alanine.
DR   DrugBank; DB03766; Propanoic Acid.
DR   DrugBank; DB02142; Pyridoxamine-5'-Phosphate.
DR   DrugBank; DB04467; Pyridoxyl-Alanine-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;
KW   Pyridoxal phosphate.
FT   CHAIN         1    388       Alanine racemase.
FT                                /FTId=PRO_0000114499.
FT   ACT_SITE     39     39       Proton acceptor; specific for D-alanine.
FT                                {ECO:0000305|PubMed:10502689,
FT                                ECO:0000305|PubMed:15807525}.
FT   ACT_SITE    265    265       Proton acceptor; specific for L-alanine.
FT                                {ECO:0000305|PubMed:10502689,
FT                                ECO:0000305|PubMed:15807525}.
FT   BINDING     136    136       Substrate. {ECO:0000269|PubMed:11886871}.
FT   BINDING     312    312       Substrate; via amide nitrogen.
FT                                {ECO:0000269|PubMed:11886871}.
FT   MOD_RES      39     39       N6-(pyridoxal phosphate)lysine.
FT                                {ECO:0000269|PubMed:11886871,
FT                                ECO:0000269|PubMed:15807525,
FT                                ECO:0000269|PubMed:9063881}.
FT   MOD_RES     129    129       N6-carboxylysine.
FT                                {ECO:0000269|PubMed:10079072,
FT                                ECO:0000269|PubMed:11886871,
FT                                ECO:0000269|PubMed:12741835,
FT                                ECO:0000269|PubMed:15807525,
FT                                ECO:0000269|Ref.10}.
FT   MUTAGEN      39     39       K->A: Loss of activity.
FT                                {ECO:0000269|PubMed:10502689}.
FT   MUTAGEN     166    166       H->A: 6.5-fold decrease in activity.
FT                                {ECO:0000269|PubMed:10502689}.
FT   MUTAGEN     219    219       R->A: 100-fold decrease in activity.
FT                                {ECO:0000269|PubMed:10194319}.
FT   MUTAGEN     219    219       R->E: 1000-fold decrease in activity.
FT                                {ECO:0000269|PubMed:10194319}.
FT   MUTAGEN     219    219       R->K: 4-fold decrease in activity.
FT                                {ECO:0000269|PubMed:10194319}.
FT   MUTAGEN     265    265       Y->A: 5000-fold decrease in activity.
FT                                {ECO:0000269|PubMed:15807525}.
FT   MUTAGEN     265    265       Y->F: Loss of activity.
FT                                {ECO:0000269|PubMed:15807525}.
FT   MUTAGEN     265    265       Y->S: 2000-fold decrease in activity.
FT                                {ECO:0000269|PubMed:15807525}.
FT   MUTAGEN     354    354       Y->A: 54-fold increase in serine racemase
FT                                activity. {ECO:0000269|PubMed:12203980}.
FT   MUTAGEN     354    354       Y->N: 81-fold increase in serine racemase
FT                                activity. {ECO:0000269|PubMed:12203980}.
FT   MUTAGEN     354    354       Y->Q: 51-fold increase in serine racemase
FT                                activity. {ECO:0000269|PubMed:12203980}.
FT   CONFLICT     37     38       VV -> PP (in Ref. 3; AA sequence).
FT                                {ECO:0000305}.
FT   CONFLICT     57     62       AGASRL -> RGPPP (in Ref. 1; AAA22220).
FT                                {ECO:0000305}.
FT   CONFLICT    288    289       WL -> V (in Ref. 1; AAA22220).
FT                                {ECO:0000305}.
FT   STRAND        6     13       {ECO:0000244|PDB:1BD0}.
FT   HELIX        14     27       {ECO:0000244|PDB:1BD0}.
FT   STRAND       33     37       {ECO:0000244|PDB:1BD0}.
FT   HELIX        39     43       {ECO:0000244|PDB:1BD0}.
FT   HELIX        47     57       {ECO:0000244|PDB:1BD0}.
FT   STRAND       61     66       {ECO:0000244|PDB:1BD0}.
FT   HELIX        67     75       {ECO:0000244|PDB:1BD0}.
FT   STRAND       82     84       {ECO:0000244|PDB:1BD0}.
FT   HELIX        90     92       {ECO:0000244|PDB:1BD0}.
FT   HELIX        93     98       {ECO:0000244|PDB:1BD0}.
FT   STRAND      101    105       {ECO:0000244|PDB:1BD0}.
FT   HELIX       108    117       {ECO:0000244|PDB:1BD0}.
FT   STRAND      124    130       {ECO:0000244|PDB:1BD0}.
FT   STRAND      132    134       {ECO:0000244|PDB:1BD0}.
FT   STRAND      136    139       {ECO:0000244|PDB:1BD0}.
FT   HELIX       142    154       {ECO:0000244|PDB:1BD0}.
FT   STRAND      158    164       {ECO:0000244|PDB:1BD0}.
FT   STRAND      172    174       {ECO:0000244|PDB:1XQK}.
FT   HELIX       176    189       {ECO:0000244|PDB:1BD0}.
FT   STRAND      192    194       {ECO:0000244|PDB:1SFT}.
FT   STRAND      197    200       {ECO:0000244|PDB:1BD0}.
FT   HELIX       204    209       {ECO:0000244|PDB:1BD0}.
FT   HELIX       211    213       {ECO:0000244|PDB:1XQL}.
FT   STRAND      217    220       {ECO:0000244|PDB:1BD0}.
FT   HELIX       222    225       {ECO:0000244|PDB:1BD0}.
FT   HELIX       231    236       {ECO:0000244|PDB:1BD0}.
FT   STRAND      245    250       {ECO:0000244|PDB:1BD0}.
FT   STRAND      252    257       {ECO:0000244|PDB:1BD0}.
FT   STRAND      262    264       {ECO:0000244|PDB:1BD0}.
FT   HELIX       265    267       {ECO:0000244|PDB:1BD0}.
FT   STRAND      273    281       {ECO:0000244|PDB:1BD0}.
FT   HELIX       284    286       {ECO:0000244|PDB:1BD0}.
FT   HELIX       290    294       {ECO:0000244|PDB:1BD0}.
FT   STRAND      296    299       {ECO:0000244|PDB:1BD0}.
FT   STRAND      302    308       {ECO:0000244|PDB:1BD0}.
FT   STRAND      315    318       {ECO:0000244|PDB:1BD0}.
FT   STRAND      328    335       {ECO:0000244|PDB:1BD0}.
FT   STRAND      338    340       {ECO:0000244|PDB:1BD0}.
FT   HELIX       342    349       {ECO:0000244|PDB:1BD0}.
FT   HELIX       355    359       {ECO:0000244|PDB:1BD0}.
FT   STRAND      366    370       {ECO:0000244|PDB:1BD0}.
FT   STRAND      373    378       {ECO:0000244|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
//
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