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A1B198

- HPBD_PARDP

UniProt

A1B198 - HPBD_PARDP

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Protein
4-hydroxyproline betaine 2-epimerase
Gene
hpbD, Pden_1187
Organism
Paracoccus denitrificans (strain Pd 1222)
Status
Reviewed - 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

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 betaine

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei56 – 561Substrate
Binding sitei162 – 1621Substrate
Active sitei164 – 1641Proton donor/acceptor By similarity
Metal bindingi194 – 1941Magnesium
Metal bindingi219 – 2191Magnesium
Metal bindingi242 – 2421Magnesium
Active sitei266 – 2661Proton donor/acceptor By 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
Complete GO annotation...

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-epimerase
PRO_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

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.

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

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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

« Hide 'large scale' publications
  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: September 3, 2014
This is version 43 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

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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