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A1B198

- HPBD_PARDP

UniProt

A1B198 - HPBD_PARDP

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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

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

Mg2+1 PublicationNote: Binds 1 Mg(2+) 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
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-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 – 1412Combined sources
Beta strandi20 – 223Combined sources
Beta strandi25 – 3915Combined sources
Beta strandi44 – 496Combined sources
Beta strandi56 – 583Combined sources
Helixi61 – 7111Combined sources
Helixi72 – 754Combined sources
Helixi83 – 919Combined sources
Helixi98 – 11619Combined sources
Helixi120 – 1234Combined sources
Beta strandi130 – 1334Combined sources
Beta strandi136 – 1383Combined sources
Helixi143 – 15614Combined sources
Beta strandi159 – 1646Combined sources
Helixi170 – 18415Combined sources
Turni185 – 1884Combined sources
Beta strandi190 – 1945Combined sources
Helixi201 – 21010Combined sources
Beta strandi216 – 2205Combined sources
Beta strandi222 – 2243Combined sources
Helixi225 – 2317Combined sources
Helixi232 – 2343Combined sources
Beta strandi239 – 2424Combined sources
Helixi248 – 2569Combined sources
Beta strandi261 – 2666Combined sources
Helixi267 – 2704Combined sources
Helixi273 – 28513Combined sources
Beta strandi290 – 2934Combined sources
Helixi299 – 30911Combined sources
Helixi314 – 3163Combined sources
Beta strandi317 – 3193Combined sources
Helixi324 – 3263Combined sources
Turni333 – 3353Combined sources
Beta strandi343 – 3453Combined sources
Beta strandi349 – 3513Combined sources
Helixi358 – 3603Combined sources
Beta strandi365 – 3684Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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_dom.
IPR001354. MR/MLE/MAL.
[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

        10         20         30         40         50
MKIAEIHVYA HDLPVKDGPY TIASSTVWSL QTTLVKIVAD SGLAGWGETC
60 70 80 90 100
PVGPTYAPSH ALGARAALAE MAPGLIGANP LQPLVLRRRM DGLLCGHNYA
110 120 130 140 150
KAAIDIAAYD LMGKHYGVRV ADLLGGVAAE RVPSYYATGI GQPDEIARIA
160 170 180 190 200
AEKVAEGFPR LQIKIGGRPV EIDIETVRKV WERIRGTGTR LAVDGNRSLP
210 220 230 240 250
SRDALRLSRE CPEIPFVLEQ PCNTLEEIAA IRGRVQHGIY LDESGEDLST
260 270 280 290 300
VIRAAGQGLC DGFGMKLTRI GGLQQMAAFR DICEARALPH SCDDAWGGDI
310 320 330 340 350
IAAACTHIGA TVQPRLNEGV WVAQPYIAQP YDEENGIRIA GGHIDLPKGP
360
GLGITPDESL FGPPVASFS
Length:369
Mass (Da):39,382
Last modified:January 23, 2007 - v1
Checksum:i31E3E18DBDF60A5A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000489 Genomic DNA. Translation: ABL69292.1.
RefSeqiYP_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:
EMBLi
GenBanki
DDBJi
Links Updated
CP000489 Genomic DNA. Translation: ABL69292.1 .
RefSeqi YP_914988.1. NC_008686.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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_dom.
IPR001354. MR/MLE/MAL.
[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: November 26, 2014
This is version 46 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