Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Basket 0
(max 400 entries)x

Your basket is currently empty.

Select item(s) and click on "Add to basket" to create your own collection here
(400 entries max)

Q0FPQ4

- HPBD_PELBH

UniProt

Q0FPQ4 - HPBD_PELBH

Protein

4-hydroxyproline betaine 2-epimerase

Gene

hpbD

Organism
Pelagibaca bermudensis (strain JCM 13377 / KCTC 12554 / HTCC2601)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
    • BLAST
    • Align
    • Format
    • Add to basket
    • History
      Entry version 32 (01 Oct 2014)
      Sequence version 1 (17 Oct 2006)
      Previous versions | rss
    • Help video
    • Feedback
    • Comment

    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

    Binds 1 magnesium 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

    1. magnesium ion binding Source: UniProtKB
    2. racemase activity, acting on amino acids and derivatives Source: UniProtKB

    GO - Biological processi

    1. amino-acid betaine catabolic process Source: UniProtKB

    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.

    Structurei

    Secondary structure

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

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    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.
    IPR001354. MR_MLE.
    [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

    MKIAEIQLFQ HDLPVVNGPY RIASGDVWSL TTTIVKIIAE DGTIGWGETC    50
    PVGPTYAEAH AGGALAALEV LASGLAGAEA LPLPLHTRMD SLLCGHNYAK 100
    SALDIAVHDL WGKRLGVPVH ELLGGALTDS VSSYYSLGVM EPDEAARQAL 150
    EKQREGYSRL QVKLGARPIE IDIEAIRKVW EAVRGTGIAL AADGNRGWTT 200
    RDALRFSREC PDIPFVMEQP CNSFEDLEAI RPLCHHALYM DEDGTSLNTV 250
    ITAAATSLVD GFGMKVSRIG GLQHMRAFRD FCAARNLPHT CDDAWGGDIV 300
    SAACTHIAST VLPRLMEGAW LAQPYVAEHY DAENGVRIEG GRIRVPQGPG 350
    LGLTIDPERF GPPLFSA 367
    Length:367
    Mass (Da):39,558
    Last modified:October 17, 2006 - v1
    Checksum:i6377860F2A17B87E
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AATQ01000017 Genomic DNA. Translation: EAU46159.1.

    Genome annotation databases

    EnsemblBacteriaiEAU46159; EAU46159; R2601_01638.
    PATRICi28150214. VBIRosSp73948_3937.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AATQ01000017 Genomic DNA. Translation: EAU46159.1 .

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2PMQ X-ray 1.72 A/B 2-367 [» ]
    4H2H X-ray 1.70 A/B/C/D/E/F/G/H 2-367 [» ]
    ProteinModelPortali Q0FPQ4.
    SMRi Q0FPQ4. Positions 2-367.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-60607N.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai EAU46159 ; EAU46159 ; R2601_01638 .
    PATRICi 28150214. VBIRosSp73948_3937.

    Miscellaneous databases

    EvolutionaryTracei Q0FPQ4.

    Family and domain databases

    Gene3Di 3.20.20.120. 1 hit.
    3.30.390.10. 1 hit.
    InterProi IPR029065. Enolase_C-like.
    IPR029017. Enolase_N_like.
    IPR013342. Mandelate_racemase_C.
    IPR013341. Mandelate_racemase_N.
    IPR001354. MR_MLE.
    [Graphical view ]
    PANTHERi PTHR13794. PTHR13794. 1 hit.
    Pfami PF01188. MR_MLE. 1 hit.
    PF02746. MR_MLE_N. 1 hit.
    [Graphical view ]
    SMARTi SM00922. MR_MLE. 1 hit.
    [Graphical view ]
    SUPFAMi SSF51604. SSF51604. 1 hit.
    SSF54826. SSF54826. 1 hit.
    ProtoNeti Search...

    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: October 1, 2014
    This is version 32 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