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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)DescriptionActionsGraphical viewLength
    Binding sitei56Substrate1
    Binding sitei162Substrate1
    Active sitei164Proton donor/acceptorBy similarity1
    Metal bindingi194Magnesium1
    Metal bindingi219Magnesium1
    Metal bindingi242Magnesium1
    Active sitei266Proton donor/acceptorBy similarity1
    Binding sitei295Substrate; via carbonyl oxygen1

    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

    BioCyciMetaCyc:MONOMER-18941.

    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
    Proteomesi
    • UP000000361 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)DescriptionActionsGraphical viewLength
    ChainiPRO_00004252791 – 3694-hydroxyproline betaine 2-epimeraseAdd BLAST369

    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

    1369
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi3 – 14Combined sources12
    Beta strandi20 – 22Combined sources3
    Beta strandi25 – 39Combined sources15
    Beta strandi44 – 49Combined sources6
    Beta strandi56 – 58Combined sources3
    Helixi61 – 71Combined sources11
    Helixi72 – 75Combined sources4
    Helixi83 – 91Combined sources9
    Helixi98 – 116Combined sources19
    Helixi120 – 123Combined sources4
    Beta strandi130 – 133Combined sources4
    Beta strandi136 – 138Combined sources3
    Helixi143 – 156Combined sources14
    Beta strandi159 – 164Combined sources6
    Helixi170 – 184Combined sources15
    Turni185 – 188Combined sources4
    Beta strandi190 – 194Combined sources5
    Helixi201 – 210Combined sources10
    Beta strandi216 – 220Combined sources5
    Beta strandi222 – 224Combined sources3
    Helixi225 – 231Combined sources7
    Helixi232 – 234Combined sources3
    Beta strandi239 – 242Combined sources4
    Helixi248 – 256Combined sources9
    Beta strandi261 – 266Combined sources6
    Helixi267 – 270Combined sources4
    Helixi273 – 285Combined sources13
    Beta strandi290 – 293Combined sources4
    Helixi299 – 309Combined sources11
    Helixi314 – 316Combined sources3
    Beta strandi317 – 319Combined sources3
    Helixi324 – 326Combined sources3
    Turni333 – 335Combined sources3
    Beta strandi343 – 345Combined sources3
    Beta strandi349 – 351Combined sources3
    Helixi358 – 360Combined sources3
    Beta strandi365 – 368Combined sources4

    3D structure databases

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

    Family & Domainsi

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4107WEA. Bacteria.
    ENOG41107K3. LUCA.
    HOGENOMiHOG000140215.
    OMAiGWGETCP.
    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.

    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.

    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.

    3D structure databases

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

    eggNOGiENOG4107WEA. Bacteria.
    ENOG41107K3. LUCA.
    HOGENOMiHOG000140215.
    OMAiGWGETCP.
    OrthoDBiPOG091H04PO.

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-18941.

    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_PARDP
    AccessioniPrimary (citable) accession number: A1B198
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 19, 2014
    Last sequence update: January 23, 2007
    Last modified: November 2, 2016
    This is version 59 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.