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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)DescriptionActionsGraphical viewLength
Metal bindingi183MagnesiumUniRule annotation1
Active sitei185Proton donorBy similarity1
Metal bindingi209MagnesiumUniRule annotation1
Metal bindingi235MagnesiumUniRule annotation1
Sitei258Increases basicity of active site HisUniRule annotation1
Active sitei285Proton acceptorBy similarity1
Sitei310Transition state stabilizerUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

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)DescriptionActionsGraphical viewLength
ChainiPRO_10001403851 – 382D-galactonate dehydrataseAdd BLAST382

Interactioni

Protein-protein interaction databases

STRINGi402626.Rpic_2990.

Structurei

Secondary structure

1382
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi3 – 11Combined sources9
Turni12 – 14Combined sources3
Beta strandi15 – 22Combined sources8
Beta strandi27 – 30Combined sources4
Helixi38 – 48Combined sources11
Helixi49 – 51Combined sources3
Turni52 – 54Combined sources3
Helixi60 – 69Combined sources10
Beta strandi71 – 73Combined sources3
Helixi77 – 98Combined sources22
Helixi102 – 105Combined sources4
Beta strandi114 – 119Combined sources6
Helixi125 – 137Combined sources13
Beta strandi142 – 147Combined sources6
Beta strandi150 – 152Combined sources3
Helixi157 – 172Combined sources16
Helixi175 – 177Combined sources3
Beta strandi178 – 183Combined sources6
Helixi190 – 200Combined sources11
Helixi201 – 203Combined sources3
Helixi218 – 224Combined sources7
Beta strandi231 – 233Combined sources3
Helixi240 – 249Combined sources10
Beta strandi253 – 255Combined sources3
Turni259 – 263Combined sources5
Helixi264 – 276Combined sources13
Turni277 – 279Combined sources3
Helixi290 – 302Combined sources13
Beta strandi309 – 311Combined sources3
Helixi323 – 326Combined sources4
Helixi330 – 333Combined sources4
Beta strandi345 – 347Combined sources3
Helixi354 – 362Combined sources9

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3RR1X-ray1.95A/B2-382[»]
3RRAX-ray2.30A/B2-382[»]
ProteinModelPortaliB2UCA8.
SMRiB2UCA8.
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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3RR1X-ray1.95A/B2-382[»]
3RRAX-ray2.30A/B2-382[»]
ProteinModelPortaliB2UCA8.
SMRiB2UCA8.
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.

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: November 2, 2016
This is version 60 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.