Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

4-hydroxyproline betaine 2-epimerase

Gene

hpbD

Organism
Paracoccus denitrificans (strain Pd 1222)
Status
Reviewed-Annotation score: Annotation score: 5 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. 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 110 sec(-1) with trans-4-hydroxy-L-proline betaine as substrate and 68 sec(-1) with L-proline betaine as substrate.

  1. KM=64 mM for trans-4-hydroxy-L-proline betaine1 Publication
  2. KM=34 mM for L-proline betaine1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei56 – 561Substrate
    Binding sitei162 – 1621Substrate
    Active sitei164 – 1641Proton donor/acceptorBy similarity
    Metal bindingi194 – 1941Magnesium
    Metal bindingi219 – 2191Magnesium
    Metal bindingi242 – 2421Magnesium
    Active sitei266 – 2661Proton donor/acceptorBy similarity
    Binding sitei295 – 2951Substrate; via carbonyl oxygen

    GO - Molecular functioni

    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

    BioCyciPDEN318586:GCVQ-1200-MONOMER.

    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
    Ordered Locus Names:Pden_1187
    OrganismiParacoccus denitrificans (strain Pd 1222)
    Taxonomic identifieri318586 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhodobacteralesRhodobacteraceaeParacoccus
    ProteomesiUP000000361 Componenti: Chromosome 1

    Pathology & Biotechi

    Disruption phenotypei

    Cells lacking this gene grow more slowly than wild-type on tHyp-B as sole carbon source, whereas growth is normal on cHyp-B. When both hpbD and hypF are disrupted, P.denitrificans is unable to utilize tHyp-B or tHyp as sole carbon source.1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 3693694-hydroxyproline betaine 2-epimerasePRO_0000425279Add
    BLAST

    Expressioni

    Inductioni

    Up-regulated by tHyp-B and cHyp-B. Repressed by high salt concentration.1 Publication

    Interactioni

    Protein-protein interaction databases

    STRINGi318586.Pden_1187.

    Structurei

    Secondary structure

    1
    369
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi3 – 1412Combined sources
    Beta strandi20 – 223Combined sources
    Beta strandi25 – 3915Combined sources
    Beta strandi44 – 496Combined sources
    Beta strandi56 – 583Combined sources
    Helixi61 – 7111Combined sources
    Helixi72 – 754Combined sources
    Helixi83 – 919Combined sources
    Helixi98 – 11619Combined sources
    Helixi120 – 1234Combined sources
    Beta strandi130 – 1334Combined sources
    Beta strandi136 – 1383Combined sources
    Helixi143 – 15614Combined sources
    Beta strandi159 – 1646Combined sources
    Helixi170 – 18415Combined sources
    Turni185 – 1884Combined sources
    Beta strandi190 – 1945Combined sources
    Helixi201 – 21010Combined sources
    Beta strandi216 – 2205Combined sources
    Beta strandi222 – 2243Combined sources
    Helixi225 – 2317Combined sources
    Helixi232 – 2343Combined sources
    Beta strandi239 – 2424Combined sources
    Helixi248 – 2569Combined sources
    Beta strandi261 – 2666Combined sources
    Helixi267 – 2704Combined sources
    Helixi273 – 28513Combined sources
    Beta strandi290 – 2934Combined sources
    Helixi299 – 30911Combined sources
    Helixi314 – 3163Combined sources
    Beta strandi317 – 3193Combined sources
    Helixi324 – 3263Combined sources
    Turni333 – 3353Combined sources
    Beta strandi343 – 3453Combined sources
    Beta strandi349 – 3513Combined sources
    Helixi358 – 3603Combined sources
    Beta strandi365 – 3684Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4E8GX-ray2.00A/B2-369[»]
    4IZGX-ray1.70A/B1-369[»]
    4J1OX-ray1.60A/B1-369[»]
    ProteinModelPortaliA1B198.
    SMRiA1B198. Positions 2-367.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiCOG4948.
    HOGENOMiHOG000140215.
    OMAiRRVDRIN.
    OrthoDBiEOG689HPX.

    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.

    A1B198-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MKIAEIHVYA HDLPVKDGPY TIASSTVWSL QTTLVKIVAD SGLAGWGETC
    60 70 80 90 100
    PVGPTYAPSH ALGARAALAE MAPGLIGANP LQPLVLRRRM DGLLCGHNYA
    110 120 130 140 150
    KAAIDIAAYD LMGKHYGVRV ADLLGGVAAE RVPSYYATGI GQPDEIARIA
    160 170 180 190 200
    AEKVAEGFPR LQIKIGGRPV EIDIETVRKV WERIRGTGTR LAVDGNRSLP
    210 220 230 240 250
    SRDALRLSRE CPEIPFVLEQ PCNTLEEIAA IRGRVQHGIY LDESGEDLST
    260 270 280 290 300
    VIRAAGQGLC DGFGMKLTRI GGLQQMAAFR DICEARALPH SCDDAWGGDI
    310 320 330 340 350
    IAAACTHIGA TVQPRLNEGV WVAQPYIAQP YDEENGIRIA GGHIDLPKGP
    360
    GLGITPDESL FGPPVASFS
    Length:369
    Mass (Da):39,382
    Last modified:January 23, 2007 - v1
    Checksum:i31E3E18DBDF60A5A
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    CP000489 Genomic DNA. Translation: ABL69292.1.
    RefSeqiWP_011747512.1. NC_008686.1.
    YP_914988.1. NC_008686.1.

    Genome annotation databases

    EnsemblBacteriaiABL69292; ABL69292; Pden_1187.
    KEGGipde:Pden_1187.
    PATRICi22853539. VBIParDen97112_1164.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    CP000489 Genomic DNA. Translation: ABL69292.1.
    RefSeqiWP_011747512.1. NC_008686.1.
    YP_914988.1. NC_008686.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4E8GX-ray2.00A/B2-369[»]
    4IZGX-ray1.70A/B1-369[»]
    4J1OX-ray1.60A/B1-369[»]
    ProteinModelPortaliA1B198.
    SMRiA1B198. Positions 2-367.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi318586.Pden_1187.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiABL69292; ABL69292; Pden_1187.
    KEGGipde:Pden_1187.
    PATRICi22853539. VBIParDen97112_1164.

    Phylogenomic databases

    eggNOGiCOG4948.
    HOGENOMiHOG000140215.
    OMAiRRVDRIN.
    OrthoDBiEOG689HPX.

    Enzyme and pathway databases

    BioCyciPDEN318586:GCVQ-1200-MONOMER.

    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

    « Hide 'large scale' publications
    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: Pd 1222.
    2. Cited for: FUNCTION, CATALYTIC ACTIVITY, KINETIC PARAMETERS, GENE NAME, INDUCTION, DISRUPTION PHENOTYPE, PATHWAY.
      Strain: Pd 1222.
    3. "Crystal structure of an enolase (mandelate racemase subgroup) from Paracococus denitrificans Pd1222 (target NYSGRC-012907) with bound L-proline betaine (substrate), cis-4OH-D-proline betaine (product), and Mg."
      New York Structural Genomics Research Consortium (NYSGRC)
      Submitted (FEB-2013) to the PDB data bank
      Cited for: X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) IN COMPLEXES WITH MAGNESIUM AND HYDROXYPROLINE BETAINE OR PROLINE BETAINE, COFACTOR.

    Entry informationi

    Entry nameiHPBD_PARDP
    AccessioniPrimary (citable) accession number: A1B198
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 19, 2014
    Last sequence update: January 23, 2007
    Last modified: May 27, 2015
    This is version 51 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

    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.