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Q0FPQ4 (HPBD_PELBH) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 30. 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
ORF Names:R2601_01638
OrganismPelagibaca bermudensis (strain JCM 13377 / KCTC 12554 / HTCC2601)
Taxonomic identifier314265 [NCBI]
Taxonomic lineageBacteriaProteobacteriaAlphaproteobacteriaRhodobacteralesRhodobacteraceaePelagibaca

Protein attributes

Sequence length367 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. To a lesser extent, 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.2

Sequence similarities

Belongs to the mandelate racemase/muconate lactonizing enzyme family.

Biophysicochemical properties

Kinetic parameters:

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.

KM=42 mM for trans-4-hydroxy-L-proline betaine Ref.2

KM=8 mM for L-proline betaine

Ontologies

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 3673674-hydroxyproline betaine 2-epimerase
PRO_0000425278

Sites

Active site1631Proton donor/acceptor By similarity
Active site2651Proton donor/acceptor By similarity
Metal binding1931Magnesium
Metal binding2181Magnesium
Metal binding2411Magnesium
Binding site561Substrate
Binding site1611Substrate
Binding site2941Substrate; via carbonyl oxygen

Secondary structure

................................................................. 367
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q0FPQ4 [UniParc].

Last modified October 17, 2006. Version 1.
Checksum: 6377860F2A17B87E

FASTA36739,558
        10         20         30         40         50         60 
MKIAEIQLFQ HDLPVVNGPY RIASGDVWSL TTTIVKIIAE DGTIGWGETC PVGPTYAEAH 

        70         80         90        100        110        120 
AGGALAALEV LASGLAGAEA LPLPLHTRMD SLLCGHNYAK SALDIAVHDL WGKRLGVPVH 

       130        140        150        160        170        180 
ELLGGALTDS VSSYYSLGVM EPDEAARQAL EKQREGYSRL QVKLGARPIE IDIEAIRKVW 

       190        200        210        220        230        240 
EAVRGTGIAL AADGNRGWTT RDALRFSREC PDIPFVMEQP CNSFEDLEAI RPLCHHALYM 

       250        260        270        280        290        300 
DEDGTSLNTV ITAAATSLVD GFGMKVSRIG GLQHMRAFRD FCAARNLPHT CDDAWGGDIV 

       310        320        330        340        350        360 
SAACTHIAST VLPRLMEGAW LAQPYVAEHY DAENGVRIEG GRIRVPQGPG LGLTIDPERF 


GPPLFSA 

« Hide

References

[1]"Genome sequences of Pelagibaca bermudensis HTCC2601T and Maritimibacter alkaliphilus HTCC2654T, the type strains of two marine Roseobacter genera."
Thrash J.C., Cho J.C., Ferriera S., Johnson J., Vergin K.L., Giovannoni S.J.
J. Bacteriol. 192:5552-5553(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: JCM 13377 / KCTC 12554 / HTCC2601.
[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: X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) IN COMPLEXES WITH MAGNESIUM AND HYDROXYPROLINE BETAINE, FUNCTION, CATALYTIC ACTIVITY, KINETIC PARAMETERS, COFACTOR, GENE NAME, PATHWAY.
Strain: JCM 13377 / KCTC 12554 / HTCC2601.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AATQ01000017 Genomic DNA. Translation: EAU46159.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2PMQX-ray1.72A/B2-367[»]
4H2HX-ray1.70A/B/C/D/E/F/G/H2-367[»]
ProteinModelPortalQ0FPQ4.
SMRQ0FPQ4. Positions 2-367.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-60607N.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaEAU46159; EAU46159; R2601_01638.
PATRIC28150214. VBIRosSp73948_3937.

Family and domain databases

InterProIPR013342. 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]
ProtoNetSearch...

Other

EvolutionaryTraceQ0FPQ4.

Entry information

Entry nameHPBD_PELBH
AccessionPrimary (citable) accession number: Q0FPQ4
Entry history
Integrated into UniProtKB/Swiss-Prot: February 19, 2014
Last sequence update: October 17, 2006
Last modified: April 16, 2014
This is version 30 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