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Protein

Alanine racemase, biosynthetic

Gene

alr

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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

    Complete GO annotation...

    Keywords - Molecular functioni

    Isomerase

    Keywords - Biological processi

    Cell shape, Cell wall biogenesis/degradation, Peptidoglycan synthesis

    Keywords - Ligandi

    Pyridoxal phosphate

    Enzyme and pathway databases

    BioCyciEcoCyc:ALARACEBIOSYN-MONOMER.
    ECOL316407:JW4013-MONOMER.
    MetaCyc:ALARACEBIOSYN-MONOMER.
    BRENDAi5.1.1.1. 2026.
    SABIO-RKP0A6B4.
    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.
    STRINGi511145.b4053.

    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.
    OMAiTHAKNQM.
    PhylomeDBiP0A6B4.

    Family and domain databases

    Gene3Di2.40.37.10. 1 hit.
    3.20.20.10. 1 hit.
    HAMAPiMF_01201. Ala_racemase. 1 hit.
    InterProiIPR000821. Ala_racemase.
    IPR009006. Ala_racemase/Decarboxylase_C.
    IPR011079. Ala_racemase_C.
    IPR001608. Ala_racemase_N.
    IPR020622. Ala_racemase_pyridoxalP-BS.
    IPR029066. PLP-binding_barrel.
    [Graphical view]
    PfamiPF00842. Ala_racemase_C. 1 hit.
    PF01168. Ala_racemase_N. 1 hit.
    [Graphical view]
    PRINTSiPR00992. ALARACEMASE.
    SMARTiSM01005. Ala_racemase_C. 1 hit.
    [Graphical view]
    SUPFAMiSSF50621. SSF50621. 1 hit.
    SSF51419. SSF51419. 1 hit.
    TIGRFAMsiTIGR00492. alr. 1 hit.
    PROSITEiPS00395. ALANINE_RACEMASE. 1 hit.
    [Graphical view]

    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.
    PATRICi32123645. VBIEscCol129921_4171.

    Cross-referencesi

    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.

    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...

    Protein-protein interaction databases

    BioGridi4260823. 598 interactors.
    IntActiP0A6B4. 6 interactors.
    STRINGi511145.b4053.

    Chemistry databases

    BindingDBiP0A6B4.
    ChEMBLiCHEMBL2833.

    Proteomic databases

    PaxDbiP0A6B4.
    PRIDEiP0A6B4.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC77023; AAC77023; b4053.
    BAE78055; BAE78055; BAE78055.
    GeneIDi948564.
    KEGGiecj:JW4013.
    eco:b4053.
    PATRICi32123645. VBIEscCol129921_4171.

    Organism-specific databases

    EchoBASEiEB0001.
    EcoGeneiEG10001. alr.

    Phylogenomic databases

    eggNOGiENOG4105CJ4. Bacteria.
    COG0787. LUCA.
    HOGENOMiHOG000031446.
    InParanoidiP0A6B4.
    KOiK01775.
    OMAiTHAKNQM.
    PhylomeDBiP0A6B4.

    Enzyme and pathway databases

    UniPathwayiUPA00042; UER00497.
    UPA00219.
    BioCyciEcoCyc:ALARACEBIOSYN-MONOMER.
    ECOL316407:JW4013-MONOMER.
    MetaCyc:ALARACEBIOSYN-MONOMER.
    BRENDAi5.1.1.1. 2026.
    SABIO-RKP0A6B4.

    Miscellaneous databases

    EvolutionaryTraceiP0A6B4.
    PROiP0A6B4.

    Family and domain databases

    Gene3Di2.40.37.10. 1 hit.
    3.20.20.10. 1 hit.
    HAMAPiMF_01201. Ala_racemase. 1 hit.
    InterProiIPR000821. Ala_racemase.
    IPR009006. Ala_racemase/Decarboxylase_C.
    IPR011079. Ala_racemase_C.
    IPR001608. Ala_racemase_N.
    IPR020622. Ala_racemase_pyridoxalP-BS.
    IPR029066. PLP-binding_barrel.
    [Graphical view]
    PfamiPF00842. Ala_racemase_C. 1 hit.
    PF01168. Ala_racemase_N. 1 hit.
    [Graphical view]
    PRINTSiPR00992. ALARACEMASE.
    SMARTiSM01005. Ala_racemase_C. 1 hit.
    [Graphical view]
    SUPFAMiSSF50621. SSF50621. 1 hit.
    SSF51419. SSF51419. 1 hit.
    TIGRFAMsiTIGR00492. alr. 1 hit.
    PROSITEiPS00395. ALANINE_RACEMASE. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiALR1_ECOLI
    AccessioniPrimary (citable) accession number: P0A6B4
    Secondary accession number(s): P29743, P78136, Q2M6Q1
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 7, 2005
    Last sequence update: June 7, 2005
    Last modified: November 2, 2016
    This is version 104 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. SIMILARITY comments
      Index of protein domains and families

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.