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Protein

4-pyridoxolactonase

Gene

mlr6805

Organism
Rhizobium loti (strain MAFF303099) (Mesorhizobium loti)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in the degradation of pyridoxine or pyridoxamine (free, phosphate-unbound, forms of vitamin B6). Hydrolyzes 4-pyridoxolactone to 4-pyridoxic acid. Has lower activity toward N-hexanoyl-D,L-homoserine lactone, but is not active toward 5-pyridoxolactone and gamma-butyrolactone.2 Publications

Catalytic activityi

4-pyridoxolactone + H2O = 4-pyridoxate.2 Publications

Cofactori

Zn2+2 PublicationsNote: Binds 2 Zn2+ ions per subunit.2 Publications

Enzyme regulationi

Inhibited by Hg2+.1 Publication

Kineticsi

  1. KM=7.98 µM for 4-pyridoxolactone1 Publication
  2. KM=319 µM for 4-pyridoxic acid1 Publication

    pH dependencei

    Optimum pH is 7.5. Retains 36% of maximum activity at pH 5.0 and 10% of maximum activity at pH 9.5.1 Publication

    Temperature dependencei

    Optimum temperature is 60-70 degrees Celsius. Stable for 10 minutes at 50 degrees Celsius or lower, 64% of activity remains following 10 minutes incubation at 55 degrees Celsius and 14% of activity remains following 10 minutes incubation at 60 degrees Celsius.1 Publication

    Pathwayi: B6 vitamer degradation

    This protein is involved in step 2 of the subpathway that synthesizes 4-pyridoxate from pyridoxal.1 Publication
    Proteins known to be involved in the 2 steps of the subpathway in this organism are:
    1. Pyridoxal 4-dehydrogenase (pldh-t)
    2. 4-pyridoxolactonase (mlr6805)
    This subpathway is part of the pathway B6 vitamer degradation, which is itself part of Cofactor degradation.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes 4-pyridoxate from pyridoxal, the pathway B6 vitamer degradation and in Cofactor degradation.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Metal bindingi96Zinc 1; via tele nitrogen; catalytic1 Publication1
    Metal bindingi98Zinc 1; via pros nitrogen; catalytic1 Publication1
    Active sitei100Proton donor/acceptorSequence analysis1
    Metal bindingi100Zinc 2; catalytic1 Publication1
    Metal bindingi101Zinc 2; via tele nitrogen; catalytic1 Publication1
    Metal bindingi185Zinc 1; via tele nitrogen; catalytic1 Publication1
    Metal bindingi207Zinc 1; catalytic1 Publication1
    Metal bindingi207Zinc 2; catalytic1 Publication1
    Metal bindingi252Zinc 2; via tele nitrogen; catalytic1 Publication1

    GO - Molecular functioni

    • 4-pyridoxolactonase activity Source: UniProtKB
    • metal ion binding Source: UniProtKB-KW

    GO - Biological processi

    • vitamin B6 catabolic process Source: UniProtKB
    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Ligandi

    Metal-binding, Zinc

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-13149.
    UniPathwayiUPA00192; UER00589.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    4-pyridoxolactonaseImported (EC:3.1.1.27)
    Gene namesi
    Ordered Locus Names:mlr6805
    OrganismiRhizobium loti (strain MAFF303099) (Mesorhizobium loti)
    Taxonomic identifieri266835 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesPhyllobacteriaceaeMesorhizobium
    Proteomesi
    • UP000000552 Componenti: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Initiator methionineiRemoved1 Publication
    ChainiPRO_00004030572 – 2684-pyridoxolactonase1 PublicationAdd BLAST267

    Interactioni

    Subunit structurei

    Homodimer.2 Publications

    Protein-protein interaction databases

    STRINGi266835.mlr6805.

    Structurei

    Secondary structure

    1268
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi5 – 17Combined sources13
    Helixi18 – 21Combined sources4
    Turni22 – 25Combined sources4
    Beta strandi29 – 42Combined sources14
    Beta strandi45 – 49Combined sources5
    Helixi55 – 61Combined sources7
    Helixi63 – 65Combined sources3
    Helixi71 – 73Combined sources3
    Helixi75 – 81Combined sources7
    Helixi86 – 88Combined sources3
    Beta strandi91 – 93Combined sources3
    Helixi99 – 101Combined sources3
    Turni102 – 104Combined sources3
    Helixi105 – 107Combined sources3
    Beta strandi111 – 116Combined sources6
    Helixi119 – 124Combined sources6
    Helixi128 – 130Combined sources3
    Turni131 – 134Combined sources4
    Helixi141 – 147Combined sources7
    Helixi150 – 152Combined sources3
    Helixi160 – 162Combined sources3
    Beta strandi164 – 167Combined sources4
    Beta strandi169 – 174Combined sources6
    Beta strandi177 – 181Combined sources5
    Beta strandi184 – 186Combined sources3
    Beta strandi190 – 194Combined sources5
    Beta strandi197 – 199Combined sources3
    Beta strandi202 – 206Combined sources5
    Helixi212 – 217Combined sources6
    Helixi227 – 244Combined sources18
    Beta strandi247 – 252Combined sources6
    Helixi254 – 257Combined sources4

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    3AJ3X-ray1.58A1-268[»]
    4KEPX-ray1.83A1-268[»]
    4KEQX-ray2.28A1-268[»]
    ProteinModelPortaliQ988B9.
    SMRiQ988B9.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the metallo-beta-lactamase superfamily.Curated

    Phylogenomic databases

    eggNOGiENOG4107U32. Bacteria.
    ENOG410ZVJD. LUCA.
    HOGENOMiHOG000151734.
    KOiK18610.
    OMAiRANSTFE.
    OrthoDBiPOG091H0MEG.

    Family and domain databases

    Gene3Di3.60.15.10. 1 hit.
    InterProiIPR001279. Metallo-B-lactamas.
    [Graphical view]
    PfamiPF00753. Lactamase_B. 1 hit.
    [Graphical view]
    SMARTiSM00849. Lactamase_B. 1 hit.
    [Graphical view]
    SUPFAMiSSF56281. SSF56281. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    Q988B9-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSDTKVYLLD GGSLVLDGYH VFWNRGPGGE VRFPVYSILI EHAEGRFLID
    60 70 80 90 100
    TGYDYDHVMK VLPFEKPIQE KHQTIPGALG LLGLEPRDID VVVNSHFHFD
    110 120 130 140 150
    HCGGNKYFPH AKKICHRSEV PQACNPQPFE HLGYSDLSFS AEAAEARGAT
    160 170 180 190 200
    AQLLEGTTRA NSTFEGIDGD VDLARGVKLI STPGHSIGHY SLLVEFPRRK
    210 220 230 240 250
    PILFTIDAAY TQKSLETLCQ AAFHIDPVAG VNSMRKVKKL AEDHGAELMY
    260
    SHDMDNFKTY RTGTQFYG
    Length:268
    Mass (Da):29,856
    Last modified:October 1, 2001 - v1
    Checksum:iAC209337C4609D5C
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AB197037 Genomic DNA. Translation: BAE53392.1.
    BA000012 Genomic DNA. Translation: BAB53031.1.
    RefSeqiWP_010914341.1. NC_002678.2.

    Genome annotation databases

    EnsemblBacteriaiBAB53031; BAB53031; BAB53031.
    GeneIDi1229900.
    KEGGimlo:mlr6805.
    PATRICi22485071. VBIMesLot2464_5415.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AB197037 Genomic DNA. Translation: BAE53392.1.
    BA000012 Genomic DNA. Translation: BAB53031.1.
    RefSeqiWP_010914341.1. NC_002678.2.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    3AJ3X-ray1.58A1-268[»]
    4KEPX-ray1.83A1-268[»]
    4KEQX-ray2.28A1-268[»]
    ProteinModelPortaliQ988B9.
    SMRiQ988B9.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi266835.mlr6805.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiBAB53031; BAB53031; BAB53031.
    GeneIDi1229900.
    KEGGimlo:mlr6805.
    PATRICi22485071. VBIMesLot2464_5415.

    Phylogenomic databases

    eggNOGiENOG4107U32. Bacteria.
    ENOG410ZVJD. LUCA.
    HOGENOMiHOG000151734.
    KOiK18610.
    OMAiRANSTFE.
    OrthoDBiPOG091H0MEG.

    Enzyme and pathway databases

    UniPathwayiUPA00192; UER00589.
    BioCyciMetaCyc:MONOMER-13149.

    Family and domain databases

    Gene3Di3.60.15.10. 1 hit.
    InterProiIPR001279. Metallo-B-lactamas.
    [Graphical view]
    PfamiPF00753. Lactamase_B. 1 hit.
    [Graphical view]
    SMARTiSM00849. Lactamase_B. 1 hit.
    [Graphical view]
    SUPFAMiSSF56281. SSF56281. 1 hit.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiPDLA_RHILO
    AccessioniPrimary (citable) accession number: Q988B9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 11, 2011
    Last sequence update: October 1, 2001
    Last modified: November 2, 2016
    This is version 74 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, Direct protein sequencing, Reference proteome

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. 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.