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A1B198 (HPBD_PARDP) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 42. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
4-hydroxyproline betaine 2-epimerase

Short name=Hyp-B 2-epimerase
EC=5.1.1.-
Alternative name(s):
(4R)-4-hydroxyproline betaine 2-epimerase
Gene names
Name:hpbD
Ordered Locus Names:Pden_1187
OrganismParacoccus denitrificans (strain Pd 1222) [Complete proteome] [HAMAP]
Taxonomic identifier318586 [NCBI]
Taxonomic lineageBacteriaProteobacteriaAlphaproteobacteriaRhodobacteralesRhodobacteraceaeParacoccus

Protein attributes

Sequence length369 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.2

Catalytic activity

Trans-4-hydroxy-L-proline betaine = cis-4-hydroxy-D-proline betaine. Ref.2

Cofactor

Binds 1 magnesium ion per subunit. Ref.3

Induction

Up-regulated by tHyp-B and cHyp-B. Repressed by high salt concentration. Ref.2

Disruption phenotype

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. Ref.2

Sequence similarities

Belongs to the mandelate racemase/muconate lactonizing enzyme family.

Biophysicochemical properties

Kinetic parameters:

kcat is 110 sec(-1) with trans-4-hydroxy-L-proline betaine as substrate and 68 sec(-1) with L-proline betaine as substrate.

KM=64 mM for trans-4-hydroxy-L-proline betaine Ref.2

KM=34 mM for L-proline betaine

Ontologies

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 3693694-hydroxyproline betaine 2-epimerase
PRO_0000425279

Sites

Active site1641Proton donor/acceptor By similarity
Active site2661Proton donor/acceptor By similarity
Metal binding1941Magnesium
Metal binding2191Magnesium
Metal binding2421Magnesium
Binding site561Substrate
Binding site1621Substrate
Binding site2951Substrate; via carbonyl oxygen

Secondary structure

..................................................................... 369
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
A1B198 [UniParc].

Last modified January 23, 2007. Version 1.
Checksum: 31E3E18DBDF60A5A

FASTA36939,382
        10         20         30         40         50         60 
MKIAEIHVYA HDLPVKDGPY TIASSTVWSL QTTLVKIVAD SGLAGWGETC PVGPTYAPSH 

        70         80         90        100        110        120 
ALGARAALAE MAPGLIGANP LQPLVLRRRM DGLLCGHNYA KAAIDIAAYD LMGKHYGVRV 

       130        140        150        160        170        180 
ADLLGGVAAE RVPSYYATGI GQPDEIARIA AEKVAEGFPR LQIKIGGRPV EIDIETVRKV 

       190        200        210        220        230        240 
WERIRGTGTR LAVDGNRSLP SRDALRLSRE CPEIPFVLEQ PCNTLEEIAA IRGRVQHGIY 

       250        260        270        280        290        300 
LDESGEDLST VIRAAGQGLC DGFGMKLTRI GGLQQMAAFR DICEARALPH SCDDAWGGDI 

       310        320        330        340        350        360 
IAAACTHIGA TVQPRLNEGV WVAQPYIAQP YDEENGIRIA GGHIDLPKGP GLGITPDESL 


FGPPVASFS 

« Hide

References

« Hide 'large scale' references
[1]"Complete sequence of chromosome 1 of Paracoccus denitrificans PD1222."
Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S., Munk A.C., Brettin T., Bruce D., Han C., Tapia R., Gilna P., Schmutz J. expand/collapse author list , Larimer F., Land M., Hauser L., Kyrpides N., Lykidis A., Spiro S., Richardson D.J., Moir J.W.B., Ferguson S.J., van Spanning R.J.M., Richardson P.
Submitted (DEC-2006) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: Pd 1222.
[2]"Discovery of new enzymes and metabolic pathways by using structure and genome context."
Zhao S., Kumar R., Sakai A., Vetting M.W., Wood B.M., Brown S., Bonanno J.B., Hillerich B.S., Seidel R.D., Babbitt P.C., Almo S.C., Sweedler J.V., Gerlt J.A., Cronan J.E., Jacobson M.P.
Nature 502:698-702(2013) [PubMed] [Europe PMC] [Abstract]
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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
CP000489 Genomic DNA. Translation: ABL69292.1.
RefSeqYP_914988.1. NC_008686.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
4E8GX-ray2.00A/B2-369[»]
4IZGX-ray1.70A/B1-369[»]
4J1OX-ray1.60A/B1-369[»]
ProteinModelPortalA1B198.
SMRA1B198. Positions 2-367.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING318586.Pden_1187.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaABL69292; ABL69292; Pden_1187.
GeneID4580070.
KEGGpde:Pden_1187.
PATRIC22853539. VBIParDen97112_1164.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG4948.
HOGENOMHOG000140215.
OMARRVDRIN.

Enzyme and pathway databases

BioCycPDEN318586:GCVQ-1200-MONOMER.

Family and domain databases

Gene3D3.20.20.120. 1 hit.
3.30.390.10. 1 hit.
InterProIPR029065. Enolase_C-like.
IPR029017. Enolase_N_like.
IPR013342. Mandelate_racemase_C.
IPR013341. Mandelate_racemase_N.
IPR001354. MR_MLE.
[Graphical view]
PANTHERPTHR13794. PTHR13794. 1 hit.
PfamPF01188. MR_MLE. 1 hit.
PF02746. MR_MLE_N. 1 hit.
[Graphical view]
SMARTSM00922. MR_MLE. 1 hit.
[Graphical view]
SUPFAMSSF51604. SSF51604. 1 hit.
SSF54826. SSF54826. 1 hit.
ProtoNetSearch...

Entry information

Entry nameHPBD_PARDP
AccessionPrimary (citable) accession number: A1B198
Entry history
Integrated into UniProtKB/Swiss-Prot: February 19, 2014
Last sequence update: January 23, 2007
Last modified: June 11, 2014
This is version 42 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references