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Q0FPQ4

- HPBD_PELBH

UniProt

Q0FPQ4 - HPBD_PELBH

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Protein

4-hydroxyproline betaine 2-epimerase

Gene
hpbD, R2601_01638
Organism
Pelagibaca bermudensis (strain JCM 13377 / KCTC 12554 / HTCC2601)
Status
Reviewed - Annotation score: 4 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. To a lesser extent, 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 330 sec(-1) with trans-4-hydroxy-L-proline betaine as substrate and 5.3 sec(-1) with L-proline betaine as substrate.

  1. KM=42 mM for trans-4-hydroxy-L-proline betaine1 Publication
  2. KM=8 mM for L-proline betaine

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei56 – 561Substrate
Binding sitei161 – 1611Substrate
Active sitei163 – 1631Proton donor/acceptor By similarity
Metal bindingi193 – 1931Magnesium
Metal bindingi218 – 2181Magnesium
Metal bindingi241 – 2411Magnesium
Active sitei265 – 2651Proton donor/acceptor By similarity
Binding sitei294 – 2941Substrate; via carbonyl oxygen

GO - Molecular functioni

  1. magnesium ion binding Source: UniProtKB
  2. racemase activity, acting on amino acids and derivatives Source: UniProtKB

GO - Biological processi

  1. amino-acid betaine catabolic process Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Isomerase

Keywords - Ligandi

Magnesium, Metal-binding

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
ORF Names:R2601_01638
OrganismiPelagibaca bermudensis (strain JCM 13377 / KCTC 12554 / HTCC2601)
Taxonomic identifieri314265 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhodobacteralesRhodobacteraceaePelagibaca

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 3673674-hydroxyproline betaine 2-epimerasePRO_0000425278Add
BLAST

Interactioni

Protein-protein interaction databases

DIPiDIP-60607N.

Structurei

Secondary structure

1
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 1514
Beta strandi27 – 3913
Beta strandi44 – 496
Beta strandi52 – 587
Helixi61 – 7313
Turni74 – 774
Beta strandi79 – 813
Helixi82 – 9211
Helixi97 – 11519
Helixi119 – 1224
Beta strandi129 – 1324
Beta strandi134 – 1374
Helixi142 – 15514
Beta strandi158 – 1636
Helixi169 – 18315
Beta strandi189 – 1935
Helixi200 – 20910
Beta strandi215 – 2195
Beta strandi221 – 2233
Helixi224 – 2307
Helixi231 – 2333
Beta strandi238 – 2414
Helixi247 – 2559
Beta strandi260 – 2623
Helixi266 – 2694
Helixi272 – 28514
Helixi298 – 30811
Helixi313 – 3153
Beta strandi316 – 3183
Helixi323 – 3253
Turni332 – 3343
Beta strandi342 – 3443
Beta strandi348 – 3503
Turni357 – 3604
Beta strandi364 – 3674

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2PMQX-ray1.72A/B2-367[»]
4H2HX-ray1.70A/B/C/D/E/F/G/H2-367[»]
ProteinModelPortaliQ0FPQ4.
SMRiQ0FPQ4. Positions 2-367.

Miscellaneous databases

EvolutionaryTraceiQ0FPQ4.

Family & Domainsi

Sequence similaritiesi

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.

Q0FPQ4-1 [UniParc]FASTAAdd to Basket

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MKIAEIQLFQ HDLPVVNGPY RIASGDVWSL TTTIVKIIAE DGTIGWGETC    50
PVGPTYAEAH AGGALAALEV LASGLAGAEA LPLPLHTRMD SLLCGHNYAK 100
SALDIAVHDL WGKRLGVPVH ELLGGALTDS VSSYYSLGVM EPDEAARQAL 150
EKQREGYSRL QVKLGARPIE IDIEAIRKVW EAVRGTGIAL AADGNRGWTT 200
RDALRFSREC PDIPFVMEQP CNSFEDLEAI RPLCHHALYM DEDGTSLNTV 250
ITAAATSLVD GFGMKVSRIG GLQHMRAFRD FCAARNLPHT CDDAWGGDIV 300
SAACTHIAST VLPRLMEGAW LAQPYVAEHY DAENGVRIEG GRIRVPQGPG 350
LGLTIDPERF GPPLFSA 367
Length:367
Mass (Da):39,558
Last modified:October 17, 2006 - v1
Checksum:i6377860F2A17B87E
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AATQ01000017 Genomic DNA. Translation: EAU46159.1.

Genome annotation databases

EnsemblBacteriaiEAU46159; EAU46159; R2601_01638.
PATRICi28150214. VBIRosSp73948_3937.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AATQ01000017 Genomic DNA. Translation: EAU46159.1 .

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2PMQ X-ray 1.72 A/B 2-367 [» ]
4H2H X-ray 1.70 A/B/C/D/E/F/G/H 2-367 [» ]
ProteinModelPortali Q0FPQ4.
SMRi Q0FPQ4. Positions 2-367.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-60607N.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai EAU46159 ; EAU46159 ; R2601_01638 .
PATRICi 28150214. VBIRosSp73948_3937.

Miscellaneous databases

EvolutionaryTracei Q0FPQ4.

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. "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. 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.

Entry informationi

Entry nameiHPBD_PELBH
AccessioniPrimary (citable) accession number: Q0FPQ4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 19, 2014
Last sequence update: October 17, 2006
Last modified: June 11, 2014
This is version 31 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

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

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