ALR1_ECOLI
ID ALR1_ECOLI Reviewed; 359 AA.
AC P0A6B4; P29743; P78136; Q2M6Q1;
DT 07-JUN-2005, integrated into UniProtKB/Swiss-Prot.
DT 07-JUN-2005, sequence version 1.
DT 03-AUG-2022, entry version 130.
DE RecName: Full=Alanine racemase, biosynthetic {ECO:0000305|PubMed:18434499};
DE EC=5.1.1.1 {ECO:0000269|PubMed:18434499};
GN Name=alr {ECO:0000303|PubMed:18434499, ECO:0000303|PubMed:8335265};
GN OrderedLocusNames=b4053, JW4013;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=8335265; DOI=10.1016/0378-1119(93)90690-5;
RA Lilley P.E., Stamford N.P., Vasudevan S.G., Dixon N.E.;
RT "The 92-min region of the Escherichia coli chromosome: location and cloning
RT of the ubiA and alr genes.";
RL Gene 129:9-16(1993).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=8265357; DOI=10.1093/nar/21.23.5408;
RA Blattner F.R., Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L.;
RT "Analysis of the Escherichia coli genome. IV. DNA sequence of the region
RT from 89.2 to 92.8 minutes.";
RL Nucleic Acids Res. 21:5408-5417(1993).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-22.
RX PubMed=6323420; DOI=10.1016/s0021-9258(17)43626-x;
RA Nakayama N., Arai N., Bond M.W., Kaziro Y., Arai K.;
RT "Nucleotide sequence of dnaB and the primary structure of the dnaB protein
RT from Escherichia coli.";
RL J. Biol. Chem. 259:97-101(1984).
RN [6]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 320-359.
RC STRAIN=K12;
RX PubMed=3907634; DOI=10.1016/0006-291x(85)91851-0;
RA Kuramitsu S., Inoue K., Ogawa T., Ogawa H., Kagamiyama H.;
RT "Aromatic amino acid aminotransferase of Escherichia coli: nucleotide
RT sequence of the tyrB gene.";
RL Biochem. Biophys. Res. Commun. 133:134-139(1985).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (2.40 ANGSTROMS) IN COMPLEXES WITH D-CYCLOSERINE AND
RP PYRIDOXAL PHOSPHATE, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL
RP PROPERTIES, COFACTOR, SUBUNIT, PYRIDOXAL PHOSPHATE AT LYS-34, MUTAGENESIS
RP OF ASP-164; GLU-165; PRO-219 AND GLU-221, AND CARBOXYLATION AT LYS-122.
RX PubMed=18434499; DOI=10.1110/ps.083495908;
RA Wu D., Hu T., Zhang L., Chen J., Du J., Ding J., Jiang H., Shen X.;
RT "Residues Asp164 and Glu165 at the substrate entryway function potently in
RT substrate orientation of alanine racemase from E. coli: Enzymatic
RT characterization with crystal structure analysis.";
RL Protein Sci. 17:1066-1076(2008).
CC -!- FUNCTION: Catalyzes the interconversion of L-alanine and D-alanine.
CC Provides the D-alanine required for cell wall biosynthesis.
CC {ECO:0000269|PubMed:18434499}.
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:18434499};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000269|PubMed:18434499};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.31 mM for D-alanine {ECO:0000269|PubMed:18434499};
CC KM=1.00 mM for L-alanine {ECO:0000269|PubMed:18434499};
CC -!- PATHWAY: Amino-acid biosynthesis; D-alanine biosynthesis; D-alanine
CC from L-alanine: step 1/1. {ECO:0000269|PubMed:18434499}.
CC -!- PATHWAY: Cell wall biogenesis; peptidoglycan biosynthesis.
CC {ECO:0000305|PubMed:18434499}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:18434499}.
CC -!- SIMILARITY: Belongs to the alanine racemase family. {ECO:0000255|HAMAP-
CC Rule:MF_01201}.
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DR EMBL; U00006; AAC43147.1; -; Genomic_DNA.
DR EMBL; U00096; AAC77023.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE78055.1; -; Genomic_DNA.
DR EMBL; K01174; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; M12047; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR PIR; D65213; PC1296.
DR RefSeq; NP_418477.1; NC_000913.3.
DR RefSeq; WP_001147328.1; NZ_STEB01000022.1.
DR PDB; 2RJG; X-ray; 2.40 A; A/B/C/D=1-359.
DR PDB; 2RJH; X-ray; 2.40 A; A/B/C/D=1-359.
DR PDB; 3B8T; X-ray; 3.00 A; A/B/C/D=1-359.
DR PDB; 3B8U; X-ray; 3.00 A; A/B/C/D=1-359.
DR PDB; 3B8V; X-ray; 2.60 A; A/B/C/D=1-359.
DR PDB; 3B8W; X-ray; 2.70 A; A/B/C/D=1-359.
DR PDB; 4WR3; X-ray; 1.90 A; A/B/C/D=1-359.
DR PDB; 4XBJ; X-ray; 2.25 A; A/B/C/D=1-359.
DR PDBsum; 2RJG; -.
DR PDBsum; 2RJH; -.
DR PDBsum; 3B8T; -.
DR PDBsum; 3B8U; -.
DR PDBsum; 3B8V; -.
DR PDBsum; 3B8W; -.
DR PDBsum; 4WR3; -.
DR PDBsum; 4XBJ; -.
DR AlphaFoldDB; P0A6B4; -.
DR SMR; P0A6B4; -.
DR BioGRID; 4260823; 598.
DR IntAct; P0A6B4; 6.
DR STRING; 511145.b4053; -.
DR BindingDB; P0A6B4; -.
DR ChEMBL; CHEMBL2833; -.
DR jPOST; P0A6B4; -.
DR PaxDb; P0A6B4; -.
DR PRIDE; P0A6B4; -.
DR EnsemblBacteria; AAC77023; AAC77023; b4053.
DR EnsemblBacteria; BAE78055; BAE78055; BAE78055.
DR GeneID; 66672033; -.
DR GeneID; 948564; -.
DR KEGG; ecj:JW4013; -.
DR KEGG; eco:b4053; -.
DR PATRIC; fig|1411691.4.peg.2654; -.
DR EchoBASE; EB0001; -.
DR eggNOG; COG0787; Bacteria.
DR HOGENOM; CLU_028393_1_0_6; -.
DR InParanoid; P0A6B4; -.
DR OMA; WEILCGF; -.
DR PhylomeDB; P0A6B4; -.
DR BioCyc; EcoCyc:ALARACEBIOSYN-MON; -.
DR BioCyc; MetaCyc:ALARACEBIOSYN-MON; -.
DR BRENDA; 5.1.1.1; 2026.
DR SABIO-RK; P0A6B4; -.
DR UniPathway; UPA00042; UER00497.
DR UniPathway; UPA00219; -.
DR EvolutionaryTrace; P0A6B4; -.
DR PRO; PR:P0A6B4; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0008784; F:alanine racemase activity; IBA:GO_Central.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IBA:GO_Central.
DR GO; GO:0071555; P:cell wall organization; IEA:UniProtKB-KW.
DR GO; GO:0030632; P:D-alanine biosynthetic process; IBA:GO_Central.
DR GO; GO:0009252; P:peptidoglycan biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0008360; P:regulation of cell shape; IEA:UniProtKB-KW.
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; Cell shape; Cell wall biogenesis/degradation; Isomerase;
KW Peptidoglycan synthesis; Pyridoxal phosphate; Reference proteome.
FT CHAIN 1..359
FT /note="Alanine racemase, biosynthetic"
FT /id="PRO_0000114514"
FT ACT_SITE 34
FT /note="Proton acceptor; specific for D-alanine"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01201"
FT ACT_SITE 255
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:18434499"
FT BINDING 303
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:18434499"
FT MOD_RES 34
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000269|PubMed:18434499"
FT MOD_RES 122
FT /note="N6-carboxylysine"
FT /evidence="ECO:0000269|PubMed:18434499"
FT MUTAGEN 164
FT /note="D->A: Slightly reduces affinity for D-Ala and L-
FT Ala."
FT /evidence="ECO:0000269|PubMed:18434499"
FT MUTAGEN 164
FT /note="D->K: Reduces catalytic activity. Slightly reduces
FT affinity for D-Ala and L-Ala."
FT /evidence="ECO:0000269|PubMed:18434499"
FT MUTAGEN 165
FT /note="E->A: Slightly reduces affinity for D-Ala and L-
FT Ala."
FT /evidence="ECO:0000269|PubMed:18434499"
FT MUTAGEN 165
FT /note="E->K: Reduces catalytic activity. Slightly reduces
FT affinity for D-Ala and L-Ala."
FT /evidence="ECO:0000269|PubMed:18434499"
FT MUTAGEN 219
FT /note="P->A: No effect on catalytic activity. No effect on
FT affinity for D-Ala and L-Ala."
FT /evidence="ECO:0000269|PubMed:18434499"
FT MUTAGEN 221
FT /note="E->A,K,P: Slightly increases catalytic activity.
FT Slightly increases affinity for D-Ala and L-Ala."
FT /evidence="ECO:0000269|PubMed:18434499"
FT STRAND 4..9
FT /evidence="ECO:0007829|PDB:4WR3"
FT HELIX 10..23
FT /evidence="ECO:0007829|PDB:4WR3"
FT STRAND 27..32
FT /evidence="ECO:0007829|PDB:4WR3"
FT HELIX 34..38
FT /evidence="ECO:0007829|PDB:4WR3"
FT HELIX 42..48
FT /evidence="ECO:0007829|PDB:4WR3"
FT STRAND 53..59
FT /evidence="ECO:0007829|PDB:4WR3"
FT HELIX 60..68
FT /evidence="ECO:0007829|PDB:4WR3"
FT STRAND 75..77
FT /evidence="ECO:0007829|PDB:4WR3"
FT HELIX 84..86
FT /evidence="ECO:0007829|PDB:4WR3"
FT HELIX 87..92
FT /evidence="ECO:0007829|PDB:4WR3"
FT STRAND 95..99
FT /evidence="ECO:0007829|PDB:4WR3"
FT HELIX 102..110
FT /evidence="ECO:0007829|PDB:4WR3"
FT STRAND 119..123
FT /evidence="ECO:0007829|PDB:4WR3"
FT STRAND 125..127
FT /evidence="ECO:0007829|PDB:4XBJ"
FT STRAND 129..132
FT /evidence="ECO:0007829|PDB:4WR3"
FT HELIX 134..145
FT /evidence="ECO:0007829|PDB:4WR3"
FT STRAND 148..150
FT /evidence="ECO:0007829|PDB:2RJG"
FT STRAND 155..157
FT /evidence="ECO:0007829|PDB:4WR3"
FT HELIX 170..182
FT /evidence="ECO:0007829|PDB:4WR3"
FT HELIX 194..199
FT /evidence="ECO:0007829|PDB:4WR3"
FT HELIX 201..203
FT /evidence="ECO:0007829|PDB:4WR3"
FT STRAND 205..208
FT /evidence="ECO:0007829|PDB:4WR3"
FT HELIX 212..215
FT /evidence="ECO:0007829|PDB:4WR3"
FT STRAND 221..223
FT /evidence="ECO:0007829|PDB:4WR3"
FT HELIX 226..229
FT /evidence="ECO:0007829|PDB:4WR3"
FT STRAND 235..247
FT /evidence="ECO:0007829|PDB:4WR3"
FT STRAND 252..254
FT /evidence="ECO:0007829|PDB:4WR3"
FT HELIX 255..257
FT /evidence="ECO:0007829|PDB:4WR3"
FT STRAND 265..271
FT /evidence="ECO:0007829|PDB:4WR3"
FT TURN 274..277
FT /evidence="ECO:0007829|PDB:4WR3"
FT STRAND 287..290
FT /evidence="ECO:0007829|PDB:4WR3"
FT STRAND 293..297
FT /evidence="ECO:0007829|PDB:4WR3"
FT STRAND 303..309
FT /evidence="ECO:0007829|PDB:4WR3"
FT STRAND 321..326
FT /evidence="ECO:0007829|PDB:4WR3"
FT HELIX 331..338
FT /evidence="ECO:0007829|PDB:4WR3"
FT HELIX 342..347
FT /evidence="ECO:0007829|PDB:4WR3"
FT STRAND 353..358
FT /evidence="ECO:0007829|PDB:4WR3"
SQ SEQUENCE 359 AA; 39153 MW; FDE9B438115342C2 CRC64;
MQAATVVINR RALRHNLQRL RELAPASKMV AVVKANAYGH GLLETARTLP DADAFGVARL
EEALRLRAGG ITKPVLLLEG FFDARDLPTI SAQHFHTAVH NEEQLAALEE ASLDEPVTVW
MKLDTGMHRL GVRPEQAEAF YHRLTQCKNV RQPVNIVSHF ARADEPKCGA TEKQLAIFNT
FCEGKPGQRS IAASGGILLW PQSHFDWVRP GIILYGVSPL EDRSTGADFG CQPVMSLTSS
LIAVREHKAG EPVGYGGTWV SERDTRLGVV AMGYGDGYPR AAPSGTPVLV NGREVPIVGR
VAMDMICVDL GPQAQDKAGD PVILWGEGLP VERIAEMTKV SAYELITRLT SRVAMKYVD
