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A1B198

- HPBD_PARDP

UniProt

A1B198 - HPBD_PARDP

Protein

4-hydroxyproline betaine 2-epimerase

Gene

hpbD

Organism
Paracoccus denitrificans (strain Pd 1222)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 44 (01 Oct 2014)
      Sequence version 1 (23 Jan 2007)
      Previous versions | rss
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    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

    Binds 1 magnesium 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

    1. metal ion binding Source: UniProtKB-KW
    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

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

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    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.

    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.

    A1B198-1 [UniParc]FASTAAdd to Basket

    « Hide

    MKIAEIHVYA HDLPVKDGPY TIASSTVWSL QTTLVKIVAD SGLAGWGETC    50
    PVGPTYAPSH ALGARAALAE MAPGLIGANP LQPLVLRRRM DGLLCGHNYA 100
    KAAIDIAAYD LMGKHYGVRV ADLLGGVAAE RVPSYYATGI GQPDEIARIA 150
    AEKVAEGFPR LQIKIGGRPV EIDIETVRKV WERIRGTGTR LAVDGNRSLP 200
    SRDALRLSRE CPEIPFVLEQ PCNTLEEIAA IRGRVQHGIY LDESGEDLST 250
    VIRAAGQGLC DGFGMKLTRI GGLQQMAAFR DICEARALPH SCDDAWGGDI 300
    IAAACTHIGA TVQPRLNEGV WVAQPYIAQP YDEENGIRIA GGHIDLPKGP 350
    GLGITPDESL FGPPVASFS 369
    Length:369
    Mass (Da):39,382
    Last modified:January 23, 2007 - v1
    Checksum:i31E3E18DBDF60A5A
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    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.
    GeneIDi4580070.
    KEGGipde:Pden_1187.
    PATRICi22853539. VBIParDen97112_1164.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP000489 Genomic DNA. Translation: ABL69292.1 .
    RefSeqi WP_011747512.1. NC_008686.1.
    YP_914988.1. NC_008686.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    4E8G X-ray 2.00 A/B 2-369 [» ]
    4IZG X-ray 1.70 A/B 1-369 [» ]
    4J1O X-ray 1.60 A/B 1-369 [» ]
    ProteinModelPortali A1B198.
    SMRi A1B198. Positions 2-367.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 318586.Pden_1187.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai ABL69292 ; ABL69292 ; Pden_1187 .
    GeneIDi 4580070.
    KEGGi pde:Pden_1187.
    PATRICi 22853539. VBIParDen97112_1164.

    Phylogenomic databases

    eggNOGi COG4948.
    HOGENOMi HOG000140215.
    OMAi RRVDRIN.

    Enzyme and pathway databases

    BioCyci PDEN318586:GCVQ-1200-MONOMER.

    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. 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: October 1, 2014
    This is version 44 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