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Protein

Alanine racemase, biosynthetic

Gene

alr

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Catalyzes the interconversion of L-alanine and D-alanine. Provides the D-alanine required for cell wall biosynthesis.1 Publication

Catalytic activityi

L-alanine = D-alanine.1 Publication

Cofactori

pyridoxal 5'-phosphate1 Publication

Kineticsi

  1. KM=0.31 mM for D-alanine1 Publication
  2. KM=1.00 mM for L-alanine1 Publication

    Pathwayi: D-alanine biosynthesis

    This protein is involved in step 1 of the subpathway that synthesizes D-alanine from L-alanine.1 Publication
    Proteins known to be involved in this subpathway in this organism are:
    1. Alanine racemase, biosynthetic (alr)
    This subpathway is part of the pathway D-alanine biosynthesis, which is itself part of Amino-acid biosynthesis.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes D-alanine from L-alanine, the pathway D-alanine biosynthesis and in Amino-acid biosynthesis.

    Pathwayi: peptidoglycan biosynthesis

    This protein is involved in the pathway peptidoglycan biosynthesis, which is part of Cell wall biogenesis.1 Publication
    View all proteins of this organism that are known to be involved in the pathway peptidoglycan biosynthesis and in Cell wall biogenesis.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Active sitei34Proton acceptor; specific for D-alanineUniRule annotation1
    Binding sitei129Substrate1 Publication1
    Active sitei255Proton acceptor; specific for L-alanineUniRule annotation1
    Binding sitei303Substrate; via amide nitrogen1 Publication1

    GO - Molecular functioni

    • alanine racemase activity Source: EcoCyc
    • pyridoxal phosphate binding Source: EcoCyc

    GO - Biological processi

    Keywordsi

    Molecular functionIsomerase
    Biological processCell shape, Cell wall biogenesis/degradation, Peptidoglycan synthesis
    LigandPyridoxal phosphate

    Enzyme and pathway databases

    BioCyciEcoCyc:ALARACEBIOSYN-MONOMER
    MetaCyc:ALARACEBIOSYN-MONOMER
    BRENDAi5.1.1.1 2026
    SABIO-RKiP0A6B4
    UniPathwayiUPA00042; UER00497
    UPA00219

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Alanine racemase, biosynthetic1 Publication (EC:5.1.1.11 Publication)
    Gene namesi
    Name:alr2 Publications
    Ordered Locus Names:b4053, JW4013
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG10001 alr

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi164D → A: Slightly reduces affinity for D-Ala and L-Ala. 1 Publication1
    Mutagenesisi164D → K: Reduces catalytic activity. Slightly reduces affinity for D-Ala and L-Ala. 1 Publication1
    Mutagenesisi165E → A: Slightly reduces affinity for D-Ala and L-Ala. 1 Publication1
    Mutagenesisi165E → K: Reduces catalytic activity. Slightly reduces affinity for D-Ala and L-Ala. 1 Publication1
    Mutagenesisi219P → A: No effect on catalytic activity. No effect on affinity for D-Ala and L-Ala. 1 Publication1
    Mutagenesisi221E → A, K or P: Slightly increases catalytic activity. Slightly increases affinity for D-Ala and L-Ala. 1 Publication1

    Chemistry databases

    ChEMBLiCHEMBL2833

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001145141 – 359Alanine racemase, biosyntheticAdd BLAST359

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Modified residuei34N6-(pyridoxal phosphate)lysine1 Publication1
    Modified residuei122N6-carboxylysine1 Publication1

    Proteomic databases

    PaxDbiP0A6B4
    PRIDEiP0A6B4

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Protein-protein interaction databases

    BioGridi4260823, 598 interactors
    IntActiP0A6B4, 6 interactors
    STRINGi316385.ECDH10B_4242

    Chemistry databases

    BindingDBiP0A6B4

    Structurei

    Secondary structure

    1359
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi4 – 9Combined sources6
    Helixi10 – 23Combined sources14
    Beta strandi27 – 32Combined sources6
    Helixi34 – 38Combined sources5
    Helixi42 – 48Combined sources7
    Beta strandi53 – 59Combined sources7
    Helixi60 – 68Combined sources9
    Beta strandi75 – 77Combined sources3
    Helixi84 – 86Combined sources3
    Helixi87 – 92Combined sources6
    Beta strandi95 – 99Combined sources5
    Helixi102 – 110Combined sources9
    Beta strandi119 – 123Combined sources5
    Beta strandi125 – 127Combined sources3
    Beta strandi129 – 132Combined sources4
    Helixi134 – 145Combined sources12
    Beta strandi148 – 150Combined sources3
    Beta strandi155 – 157Combined sources3
    Helixi170 – 182Combined sources13
    Helixi194 – 199Combined sources6
    Helixi201 – 203Combined sources3
    Beta strandi205 – 208Combined sources4
    Helixi212 – 215Combined sources4
    Beta strandi221 – 223Combined sources3
    Helixi226 – 229Combined sources4
    Beta strandi235 – 247Combined sources13
    Beta strandi252 – 254Combined sources3
    Helixi255 – 257Combined sources3
    Beta strandi265 – 271Combined sources7
    Turni274 – 277Combined sources4
    Beta strandi287 – 290Combined sources4
    Beta strandi293 – 297Combined sources5
    Beta strandi303 – 309Combined sources7
    Beta strandi321 – 326Combined sources6
    Helixi331 – 338Combined sources8
    Helixi342 – 347Combined sources6
    Beta strandi353 – 358Combined sources6

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2RJGX-ray2.40A/B/C/D1-359[»]
    2RJHX-ray2.40A/B/C/D1-359[»]
    3B8TX-ray3.00A/B/C/D1-359[»]
    3B8UX-ray3.00A/B/C/D1-359[»]
    3B8VX-ray2.60A/B/C/D1-359[»]
    3B8WX-ray2.70A/B/C/D1-359[»]
    4WR3X-ray1.90A/B/C/D1-359[»]
    4XBJX-ray2.25A/B/C/D1-359[»]
    ProteinModelPortaliP0A6B4
    SMRiP0A6B4
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP0A6B4

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the alanine racemase family.UniRule annotation

    Phylogenomic databases

    eggNOGiENOG4105CJ4 Bacteria
    COG0787 LUCA
    HOGENOMiHOG000031446
    InParanoidiP0A6B4
    KOiK01775
    OMAiWEILCGF
    PhylomeDBiP0A6B4

    Family and domain databases

    Gene3Di2.40.37.10, 2 hits
    3.20.20.10, 1 hit
    HAMAPiMF_01201 Ala_racemase, 1 hit
    InterProiView protein in InterPro
    IPR000821 Ala_racemase
    IPR009006 Ala_racemase/Decarboxylase_C
    IPR011079 Ala_racemase_C
    IPR001608 Ala_racemase_N
    IPR020622 Ala_racemase_pyridoxalP-BS
    IPR029066 PLP-binding_barrel
    PfamiView protein in Pfam
    PF00842 Ala_racemase_C, 1 hit
    PF01168 Ala_racemase_N, 1 hit
    PRINTSiPR00992 ALARACEMASE
    SMARTiView protein in SMART
    SM01005 Ala_racemase_C, 1 hit
    SUPFAMiSSF50621 SSF50621, 1 hit
    SSF51419 SSF51419, 1 hit
    TIGRFAMsiTIGR00492 alr, 1 hit
    PROSITEiView protein in PROSITE
    PS00395 ALANINE_RACEMASE, 1 hit

    Sequencei

    Sequence statusi: Complete.

    P0A6B4-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MQAATVVINR RALRHNLQRL RELAPASKMV AVVKANAYGH GLLETARTLP
    60 70 80 90 100
    DADAFGVARL EEALRLRAGG ITKPVLLLEG FFDARDLPTI SAQHFHTAVH
    110 120 130 140 150
    NEEQLAALEE ASLDEPVTVW MKLDTGMHRL GVRPEQAEAF YHRLTQCKNV
    160 170 180 190 200
    RQPVNIVSHF ARADEPKCGA TEKQLAIFNT FCEGKPGQRS IAASGGILLW
    210 220 230 240 250
    PQSHFDWVRP GIILYGVSPL EDRSTGADFG CQPVMSLTSS LIAVREHKAG
    260 270 280 290 300
    EPVGYGGTWV SERDTRLGVV AMGYGDGYPR AAPSGTPVLV NGREVPIVGR
    310 320 330 340 350
    VAMDMICVDL GPQAQDKAGD PVILWGEGLP VERIAEMTKV SAYELITRLT

    SRVAMKYVD
    Length:359
    Mass (Da):39,153
    Last modified:June 7, 2005 - v1
    Checksum:iFDE9B438115342C2
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U00006 Genomic DNA Translation: AAC43147.1
    U00096 Genomic DNA Translation: AAC77023.1
    AP009048 Genomic DNA Translation: BAE78055.1
    K01174 Genomic DNA No translation available.
    M12047 Genomic DNA No translation available.
    PIRiD65213 PC1296
    RefSeqiNP_418477.1, NC_000913.3
    WP_001147328.1, NZ_LN832404.1

    Genome annotation databases

    EnsemblBacteriaiAAC77023; AAC77023; b4053
    BAE78055; BAE78055; BAE78055
    GeneIDi948564
    KEGGiecj:JW4013
    eco:b4053
    PATRICifig|1411691.4.peg.2654

    Similar proteinsi

    Entry informationi

    Entry nameiALR1_ECOLI
    AccessioniPrimary (citable) accession number: P0A6B4
    Secondary accession number(s): P29743, P78136, Q2M6Q1
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 7, 2005
    Last sequence update: June 7, 2005
    Last modified: March 28, 2018
    This is version 109 of the entry and version 1 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome
    UniProt is an ELIXIR core data resource
    Main funding by: National Institutes of Health