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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)DescriptionActionsGraphical viewLength
    Binding sitei56Substrate1
    Binding sitei161Substrate1
    Active sitei163Proton donor/acceptorBy similarity1
    Metal bindingi193Magnesium1
    Metal bindingi218Magnesium1
    Metal bindingi241Magnesium1
    Active sitei265Proton donor/acceptorBy similarity1
    Binding sitei294Substrate; via carbonyl oxygen1

    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

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-18940.

    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
    Proteomesi
    • UP000006230 Componenti: Unassembled WGS sequence

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00004252781 – 3674-hydroxyproline betaine 2-epimeraseAdd BLAST367

    Interactioni

    Protein-protein interaction databases

    DIPiDIP-60607N.
    STRINGi314265.R2601_01638.

    Structurei

    Secondary structure

    1367
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi2 – 15Combined sources14
    Beta strandi27 – 39Combined sources13
    Beta strandi44 – 49Combined sources6
    Beta strandi52 – 58Combined sources7
    Helixi61 – 73Combined sources13
    Turni74 – 77Combined sources4
    Beta strandi79 – 81Combined sources3
    Helixi82 – 92Combined sources11
    Helixi97 – 115Combined sources19
    Helixi119 – 122Combined sources4
    Beta strandi129 – 132Combined sources4
    Beta strandi134 – 137Combined sources4
    Helixi142 – 155Combined sources14
    Beta strandi158 – 163Combined sources6
    Helixi169 – 183Combined sources15
    Beta strandi189 – 193Combined sources5
    Helixi200 – 209Combined sources10
    Beta strandi215 – 219Combined sources5
    Beta strandi221 – 223Combined sources3
    Helixi224 – 230Combined sources7
    Helixi231 – 233Combined sources3
    Beta strandi238 – 241Combined sources4
    Helixi247 – 255Combined sources9
    Beta strandi260 – 262Combined sources3
    Helixi266 – 269Combined sources4
    Helixi272 – 285Combined sources14
    Helixi298 – 308Combined sources11
    Helixi313 – 315Combined sources3
    Beta strandi316 – 318Combined sources3
    Helixi323 – 325Combined sources3
    Turni332 – 334Combined sources3
    Beta strandi342 – 344Combined sources3
    Beta strandi348 – 350Combined sources3
    Turni357 – 360Combined sources4
    Beta strandi364 – 367Combined sources4

    3D structure databases

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

    Miscellaneous databases

    EvolutionaryTraceiQ0FPQ4.

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4107WEA. Bacteria.
    ENOG41107K3. LUCA.
    OrthoDBiPOG091H04PO.

    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.
    PfamiPF13378. MR_MLE_C. 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
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2PMQX-ray1.72A/B2-367[»]
    4H2HX-ray1.70A/B/C/D/E/F/G/H2-367[»]
    ProteinModelPortaliQ0FPQ4.
    SMRiQ0FPQ4.
    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.

    Phylogenomic databases

    eggNOGiENOG4107WEA. Bacteria.
    ENOG41107K3. LUCA.
    OrthoDBiPOG091H04PO.

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-18940.

    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.
    PfamiPF13378. MR_MLE_C. 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...

    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: November 2, 2016
    This is version 47 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. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. 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.