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Protein

4-hydroxyproline betaine 2-epimerase

Gene

hpbD

Organism
Pelagibaca bermudensis (strain JCM 13377 / KCTC 12554 / HTCC2601)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the 2-epimerization of trans-4-hydroxy-L-proline betaine (tHyp-B) to cis-4-hydroxy-D-proline betaine (cHyp-B). Is involved in a catabolic pathway that degrades tHyp-B to alpha-ketoglutarate. This pathway would permit the utilization of tHyp-B as a carbon and nitrogen source in the absence of osmotic stress, since tHyp-B functions as an osmolyte and is not catabolized when it is needed as osmoprotectant. To a lesser extent, can also catalyze the racemization of L-proline betaine.1 Publication

Catalytic activityi

Trans-4-hydroxy-L-proline betaine = cis-4-hydroxy-D-proline betaine.1 Publication

Cofactori

Mg2+1 PublicationNote: Binds 1 Mg2+ ion per subunit.1 Publication

Kineticsi

kcat is 330 sec(-1) with trans-4-hydroxy-L-proline betaine as substrate and 5.3 sec(-1) with L-proline betaine as substrate.

  1. KM=42 mM for trans-4-hydroxy-L-proline betaine1 Publication
  2. KM=8 mM for L-proline betaine1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei56 – 561Substrate
    Binding sitei161 – 1611Substrate
    Active sitei163 – 1631Proton donor/acceptorBy similarity
    Metal bindingi193 – 1931Magnesium
    Metal bindingi218 – 2181Magnesium
    Metal bindingi241 – 2411Magnesium
    Active sitei265 – 2651Proton donor/acceptorBy similarity
    Binding sitei294 – 2941Substrate; via carbonyl oxygen

    GO - Molecular functioni

    • magnesium ion binding Source: UniProtKB
    • racemase activity, acting on amino acids and derivatives Source: UniProtKB
    • racemase and epimerase activity, acting on amino acids and derivatives Source: CACAO

    GO - Biological processi

    • amino-acid betaine catabolic process Source: UniProtKB
    Complete GO annotation...

    Keywords - Molecular functioni

    Isomerase

    Keywords - Ligandi

    Magnesium, Metal-binding

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    4-hydroxyproline betaine 2-epimerase (EC:5.1.1.-)
    Short name:
    Hyp-B 2-epimerase
    Alternative name(s):
    (4R)-4-hydroxyproline betaine 2-epimerase
    Gene namesi
    Name:hpbD
    ORF Names:R2601_01638
    OrganismiPelagibaca bermudensis (strain JCM 13377 / KCTC 12554 / HTCC2601)
    Taxonomic identifieri314265 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhodobacteralesRhodobacteraceaePelagibaca

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 3673674-hydroxyproline betaine 2-epimerasePRO_0000425278Add
    BLAST

    Interactioni

    Protein-protein interaction databases

    DIPiDIP-60607N.
    STRINGi314265.R2601_01638.

    Structurei

    Secondary structure

    1
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi2 – 1514Combined sources
    Beta strandi27 – 3913Combined sources
    Beta strandi44 – 496Combined sources
    Beta strandi52 – 587Combined sources
    Helixi61 – 7313Combined sources
    Turni74 – 774Combined sources
    Beta strandi79 – 813Combined sources
    Helixi82 – 9211Combined sources
    Helixi97 – 11519Combined sources
    Helixi119 – 1224Combined sources
    Beta strandi129 – 1324Combined sources
    Beta strandi134 – 1374Combined sources
    Helixi142 – 15514Combined sources
    Beta strandi158 – 1636Combined sources
    Helixi169 – 18315Combined sources
    Beta strandi189 – 1935Combined sources
    Helixi200 – 20910Combined sources
    Beta strandi215 – 2195Combined sources
    Beta strandi221 – 2233Combined sources
    Helixi224 – 2307Combined sources
    Helixi231 – 2333Combined sources
    Beta strandi238 – 2414Combined sources
    Helixi247 – 2559Combined sources
    Beta strandi260 – 2623Combined sources
    Helixi266 – 2694Combined sources
    Helixi272 – 28514Combined sources
    Helixi298 – 30811Combined sources
    Helixi313 – 3153Combined sources
    Beta strandi316 – 3183Combined sources
    Helixi323 – 3253Combined sources
    Turni332 – 3343Combined sources
    Beta strandi342 – 3443Combined sources
    Beta strandi348 – 3503Combined sources
    Turni357 – 3604Combined sources
    Beta strandi364 – 3674Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2PMQX-ray1.72A/B2-367[»]
    4H2HX-ray1.70A/B/C/D/E/F/G/H2-367[»]
    ProteinModelPortaliQ0FPQ4.
    SMRiQ0FPQ4. Positions 2-367.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ0FPQ4.

    Family & Domainsi

    Sequence similaritiesi

    Family and domain databases

    Gene3Di3.20.20.120. 1 hit.
    3.30.390.10. 1 hit.
    InterProiIPR029065. Enolase_C-like.
    IPR029017. Enolase_N-like.
    IPR013342. Mandelate_racemase_C.
    IPR013341. Mandelate_racemase_N_dom.
    IPR001354. MR/MLE/MAL.
    [Graphical view]
    PANTHERiPTHR13794. PTHR13794. 1 hit.
    PfamiPF01188. MR_MLE. 1 hit.
    PF02746. MR_MLE_N. 1 hit.
    [Graphical view]
    SMARTiSM00922. MR_MLE. 1 hit.
    [Graphical view]
    SUPFAMiSSF51604. SSF51604. 1 hit.
    SSF54826. SSF54826. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Q0FPQ4-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MKIAEIQLFQ HDLPVVNGPY RIASGDVWSL TTTIVKIIAE DGTIGWGETC
    60 70 80 90 100
    PVGPTYAEAH AGGALAALEV LASGLAGAEA LPLPLHTRMD SLLCGHNYAK
    110 120 130 140 150
    SALDIAVHDL WGKRLGVPVH ELLGGALTDS VSSYYSLGVM EPDEAARQAL
    160 170 180 190 200
    EKQREGYSRL QVKLGARPIE IDIEAIRKVW EAVRGTGIAL AADGNRGWTT
    210 220 230 240 250
    RDALRFSREC PDIPFVMEQP CNSFEDLEAI RPLCHHALYM DEDGTSLNTV
    260 270 280 290 300
    ITAAATSLVD GFGMKVSRIG GLQHMRAFRD FCAARNLPHT CDDAWGGDIV
    310 320 330 340 350
    SAACTHIAST VLPRLMEGAW LAQPYVAEHY DAENGVRIEG GRIRVPQGPG
    360
    LGLTIDPERF GPPLFSA
    Length:367
    Mass (Da):39,558
    Last modified:October 17, 2006 - v1
    Checksum:i6377860F2A17B87E
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AATQ01000017 Genomic DNA. Translation: EAU46159.1.
    RefSeqiWP_007801489.1. NZ_DS022277.1.

    Genome annotation databases

    EnsemblBacteriaiEAU46159; EAU46159; R2601_01638.
    PATRICi28150214. VBIRosSp73948_3937.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AATQ01000017 Genomic DNA. Translation: EAU46159.1.
    RefSeqiWP_007801489.1. NZ_DS022277.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2PMQX-ray1.72A/B2-367[»]
    4H2HX-ray1.70A/B/C/D/E/F/G/H2-367[»]
    ProteinModelPortaliQ0FPQ4.
    SMRiQ0FPQ4. Positions 2-367.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    DIPiDIP-60607N.
    STRINGi314265.R2601_01638.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiEAU46159; EAU46159; R2601_01638.
    PATRICi28150214. VBIRosSp73948_3937.

    Miscellaneous databases

    EvolutionaryTraceiQ0FPQ4.

    Family and domain databases

    Gene3Di3.20.20.120. 1 hit.
    3.30.390.10. 1 hit.
    InterProiIPR029065. Enolase_C-like.
    IPR029017. Enolase_N-like.
    IPR013342. Mandelate_racemase_C.
    IPR013341. Mandelate_racemase_N_dom.
    IPR001354. MR/MLE/MAL.
    [Graphical view]
    PANTHERiPTHR13794. PTHR13794. 1 hit.
    PfamiPF01188. MR_MLE. 1 hit.
    PF02746. MR_MLE_N. 1 hit.
    [Graphical view]
    SMARTiSM00922. MR_MLE. 1 hit.
    [Graphical view]
    SUPFAMiSSF51604. SSF51604. 1 hit.
    SSF54826. SSF54826. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    1. "Genome sequences of Pelagibaca bermudensis HTCC2601T and Maritimibacter alkaliphilus HTCC2654T, the type strains of two marine Roseobacter genera."
      Thrash J.C., Cho J.C., Ferriera S., Johnson J., Vergin K.L., Giovannoni S.J.
      J. Bacteriol. 192:5552-5553(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: JCM 13377 / KCTC 12554 / HTCC2601.
    2. Cited for: X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) IN COMPLEXES WITH MAGNESIUM AND HYDROXYPROLINE BETAINE, FUNCTION, CATALYTIC ACTIVITY, KINETIC PARAMETERS, COFACTOR, GENE NAME, PATHWAY.
      Strain: JCM 13377 / KCTC 12554 / HTCC2601.

    Entry informationi

    Entry nameiHPBD_PELBH
    AccessioniPrimary (citable) accession number: Q0FPQ4
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 19, 2014
    Last sequence update: October 17, 2006
    Last modified: July 22, 2015
    This is version 39 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

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3

    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 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.