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Protein

D-galactonate dehydratase

Gene

dgoD

Organism
Ralstonia pickettii (strain 12J)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the dehydration of D-galactonate to 2-keto-3-deoxy-D-galactonate.UniRule annotation

Catalytic activityi

D-galactonate = 2-dehydro-3-deoxy-D-galactonate + H2O.UniRule annotation

Cofactori

Mg2+UniRule annotationNote: Binds 1 Mg2+ ion per subunit.UniRule annotation

Pathwayi: D-galactonate degradation

This protein is involved in step 1 of the subpathway that synthesizes D-glyceraldehyde 3-phosphate and pyruvate from D-galactonate.UniRule annotation
Proteins known to be involved in the 3 steps of the subpathway in this organism are:
  1. D-galactonate dehydratase (dgoD)
  2. no protein annotated in this organism
  3. no protein annotated in this organism
This subpathway is part of the pathway D-galactonate degradation, which is itself part of Carbohydrate acid metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes D-glyceraldehyde 3-phosphate and pyruvate from D-galactonate, the pathway D-galactonate degradation and in Carbohydrate acid metabolism.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi183 – 1831MagnesiumUniRule annotation
Active sitei185 – 1851Proton donorBy similarity
Metal bindingi209 – 2091MagnesiumUniRule annotation
Metal bindingi235 – 2351MagnesiumUniRule annotation
Sitei258 – 2581Increases basicity of active site HisUniRule annotation
Active sitei285 – 2851Proton acceptorBy similarity
Sitei310 – 3101Transition state stabilizerUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

BioCyciRETL1328306-WGS:GSTH-3772-MONOMER.
RPIC402626:GH94-3029-MONOMER.
UniPathwayiUPA00081; UER00518.

Names & Taxonomyi

Protein namesi
Recommended name:
D-galactonate dehydrataseUniRule annotation (EC:4.2.1.6UniRule annotation)
Short name:
GalDUniRule annotation
Gene namesi
Name:dgoDUniRule annotation
Ordered Locus Names:Rpic_2990
OrganismiRalstonia pickettii (strain 12J)
Taxonomic identifieri402626 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesBurkholderiaceaeRalstonia
Proteomesi
  • UP000002566 Componenti: Chromosome 1

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 382382D-galactonate dehydratasePRO_1000140385Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi402626.Rpic_2990.

Structurei

Secondary structure

1
382
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 119Combined sources
Turni12 – 143Combined sources
Beta strandi15 – 228Combined sources
Beta strandi27 – 304Combined sources
Helixi38 – 4811Combined sources
Helixi49 – 513Combined sources
Turni52 – 543Combined sources
Helixi60 – 6910Combined sources
Beta strandi71 – 733Combined sources
Helixi77 – 9822Combined sources
Helixi102 – 1054Combined sources
Beta strandi114 – 1196Combined sources
Helixi125 – 13713Combined sources
Beta strandi142 – 1476Combined sources
Beta strandi150 – 1523Combined sources
Helixi157 – 17216Combined sources
Helixi175 – 1773Combined sources
Beta strandi178 – 1836Combined sources
Helixi190 – 20011Combined sources
Helixi201 – 2033Combined sources
Helixi218 – 2247Combined sources
Beta strandi231 – 2333Combined sources
Helixi240 – 24910Combined sources
Beta strandi253 – 2553Combined sources
Turni259 – 2635Combined sources
Helixi264 – 27613Combined sources
Turni277 – 2793Combined sources
Helixi290 – 30213Combined sources
Beta strandi309 – 3113Combined sources
Helixi323 – 3264Combined sources
Helixi330 – 3334Combined sources
Beta strandi345 – 3473Combined sources
Helixi354 – 3629Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3RR1X-ray1.95A/B2-382[»]
3RRAX-ray2.30A/B2-382[»]
ProteinModelPortaliB2UCA8.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiB2UCA8.

Family & Domainsi

Sequence similaritiesi

Belongs to the mandelate racemase/muconate lactonizing enzyme family. GalD subfamily.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105CXK. Bacteria.
COG4948. LUCA.
HOGENOMiHOG000113756.
KOiK01684.
OMAiLHRPMAK.

Family and domain databases

Gene3Di3.20.20.120. 1 hit.
3.30.390.10. 1 hit.
HAMAPiMF_01289. Galacton_dehydrat. 1 hit.
InterProiIPR029065. Enolase_C-like.
IPR029017. Enolase_N-like.
IPR023592. Galactonate_deHydtase.
IPR018110. Mandel_Rmase/mucon_lact_enz_CS.
IPR013342. Mandelate_racemase_C.
IPR013341. Mandelate_racemase_N_dom.
IPR001354. MR/MLE/MAL.
[Graphical view]
PANTHERiPTHR13794. PTHR13794. 1 hit.
PfamiPF13378. MR_MLE_C. 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.
PROSITEiPS00908. MR_MLE_1. 1 hit.
PS00909. MR_MLE_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

B2UCA8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKITRLTTYR LPPRWMFLKV ETDEGVTGWG EPVIEGRART VEAAVHELSD
60 70 80 90 100
YLIGQDPSRI NDLWQTMYRA GFYRGGPILM SAIAGIDQAL WDIKGKVLGV
110 120 130 140 150
PVYELLGGLV RDKMRTYSWV GGDRPADVIA GMKALQAGGF DHFKLNGCEE
160 170 180 190 200
MGIIDTSRAV DAAVARVAEI RSAFGNTVEF GLDFHGRVSA PMAKVLIKEL
210 220 230 240 250
EPYRPLFIEE PVLAEQAETY ARLAAHTHLP IAAGERMFSR FDFKRVLEAG
260 270 280 290 300
GVSILQPDLS HAGGITECVK IAAMAEAYDV ALAPHCPLGP IALAACLHVD
310 320 330 340 350
FVSWNATLQE QSMGIHYNKG AELLDYVRNK ADFALEGGYI RPPRLPGLGV
360 370 380
DIDEALVIER SKEAPDWRNP VWRHADGSVA EW
Length:382
Mass (Da):42,098
Last modified:July 1, 2008 - v1
Checksum:i198F1A16BC5819F0
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001068 Genomic DNA. Translation: ACD28113.1.
RefSeqiWP_012436402.1. NC_010682.1.

Genome annotation databases

EnsemblBacteriaiACD28113; ACD28113; Rpic_2990.
GeneIDi6288930.
KEGGirpi:Rpic_2990.
PATRICi20256787. VBIRalPic63053_4126.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001068 Genomic DNA. Translation: ACD28113.1.
RefSeqiWP_012436402.1. NC_010682.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3RR1X-ray1.95A/B2-382[»]
3RRAX-ray2.30A/B2-382[»]
ProteinModelPortaliB2UCA8.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi402626.Rpic_2990.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACD28113; ACD28113; Rpic_2990.
GeneIDi6288930.
KEGGirpi:Rpic_2990.
PATRICi20256787. VBIRalPic63053_4126.

Phylogenomic databases

eggNOGiENOG4105CXK. Bacteria.
COG4948. LUCA.
HOGENOMiHOG000113756.
KOiK01684.
OMAiLHRPMAK.

Enzyme and pathway databases

UniPathwayiUPA00081; UER00518.
BioCyciRETL1328306-WGS:GSTH-3772-MONOMER.
RPIC402626:GH94-3029-MONOMER.

Miscellaneous databases

EvolutionaryTraceiB2UCA8.

Family and domain databases

Gene3Di3.20.20.120. 1 hit.
3.30.390.10. 1 hit.
HAMAPiMF_01289. Galacton_dehydrat. 1 hit.
InterProiIPR029065. Enolase_C-like.
IPR029017. Enolase_N-like.
IPR023592. Galactonate_deHydtase.
IPR018110. Mandel_Rmase/mucon_lact_enz_CS.
IPR013342. Mandelate_racemase_C.
IPR013341. Mandelate_racemase_N_dom.
IPR001354. MR/MLE/MAL.
[Graphical view]
PANTHERiPTHR13794. PTHR13794. 1 hit.
PfamiPF13378. MR_MLE_C. 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.
PROSITEiPS00908. MR_MLE_1. 1 hit.
PS00909. MR_MLE_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiDGOD_RALPJ
AccessioniPrimary (citable) accession number: B2UCA8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 14, 2009
Last sequence update: July 1, 2008
Last modified: September 7, 2016
This is version 59 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

Reaction proceeds via an anti dehydration.UniRule annotation

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.