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C6CBG9 (DMGD_DICDC) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 30. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
D-galactonate dehydratase family member Dd703_0947

EC=4.2.1.-
Alternative name(s):
D-gluconate dehydratase
EC=4.2.1.39
D-mannonate dehydratase
EC=4.2.1.8
Gene names
Ordered Locus Names:Dd703_0947
OrganismDickeya dadantii (strain Ech703) [Complete proteome] [HAMAP]
Taxonomic identifier579405 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeDickeya

Protein attributes

Sequence length417 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Has low dehydratase activity with D-mannonate and D-gluconate, suggesting that these are not physiological substrates and that it has no significant role in the in vivo degradation of these compounds. Has no detectable activity with a panel of 70 other acid sugars (in vitro). Ref.2

Catalytic activity

D-mannonate = 2-dehydro-3-deoxy-D-gluconate + H2O. Ref.2

D-gluconate = 2-dehydro-3-deoxy-D-gluconate + H2O. Ref.2

Cofactor

Binds 1 Mg2+ ion per subunit. Ref.2

Sequence similarities

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

Biophysicochemical properties

Kinetic parameters:

kcat is 0.04 sec(-1) with D-mannonate. kcat is 0.03 sec(-1) with D-gluconate. Ref.2

Ontologies

Keywords
   LigandMagnesium
Metal-binding
   Molecular functionLyase
   Technical term3D-structure
Complete proteome
Gene Ontology (GO)
   Biological_processcellular amino acid catabolic process

Inferred from electronic annotation. Source: InterPro

   Molecular_functioncatalytic activity

Inferred from electronic annotation. Source: InterPro

metal ion binding

Inferred from electronic annotation. Source: UniProtKB-KW

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 417417D-galactonate dehydratase family member Dd703_0947
PRO_0000429883

Sites

Active site1581Proton donor/acceptor By similarity
Active site2251Proton donor/acceptor By similarity
Metal binding2231Magnesium
Metal binding2491Magnesium
Metal binding2751Magnesium
Binding site1271Substrate By similarity
Binding site2751Substrate By similarity
Binding site2961Substrate By similarity
Binding site3251Substrate By similarity
Binding site3291Substrate By similarity
Binding site3521Substrate By similarity
Site3271Important for activity and substrate specificity; Pro is observed in family members with low D-mannonate dehydratase activity By similarity

Sequences

Sequence LengthMass (Da)Tools
C6CBG9 [UniParc].

Last modified September 1, 2009. Version 1.
Checksum: 4FF2BB5D58CFEB69

FASTA41746,153
        10         20         30         40         50         60 
MSKLKITNVK TILTAPGGID LAVVKVETNE PGLYGLGCAT FTQRIFAVKS AIDEYMAPFL 

        70         80         90        100        110        120 
IGKDPTRIED IWQSAAVSGY WRNGPIMNNA LSGVDMALWD IKGKLAGMPV YELLGGKCRD 

       130        140        150        160        170        180 
GIPLYCHTDG GDEVEVEDNI RARMEEGYQY VRCQMGMYGG AGTDDLKLIA TQLARAKNIQ 

       190        200        210        220        230        240 
PKRSPRSKTP GIYFDPEAYA KSVPRLFEHL RNKLGFGIEF IHDVHERVTP VTAIQLAKTL 

       250        260        270        280        290        300 
EPYQLFYLED PVAPENIDWL RMLRQQSSTP ISMGELFVNI NEWKPLIDNK LIDYIRCHVS 

       310        320        330        340        350        360 
TIGGITPAKK LAVYSELNGV RTAWHGPGDI SPVGVCANMH LDMSSPNFGI QEYTPMNDAL 

       370        380        390        400        410 
REVFPGCPEI DQGYAYVNDK PGLGIDINET LAEKYPCDGG IPSWTMARTP DGTASRP 

« Hide

References

« Hide 'large scale' references
[1]"Complete sequence of Dickeya dadantii Ech703."
US DOE Joint Genome Institute
Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H., Bruce D., Goodwin L., Pitluck S., Chertkov O., Brettin T., Detter J.C., Han C., Larimer F., Land M., Hauser L., Kyrpides N., Mikhailova N. expand/collapse author list , Balakrishnan V., Glasner J., Perna N.T.
Submitted (JUN-2009) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: Ech703.
[2]"Discovery of function in the enolase superfamily: D-mannonate and D-gluconate dehydratases in the D-mannonate dehydratase subgroup."
Wichelecki D.J., Balthazor B.M., Chau A.C., Vetting M.W., Fedorov A.A., Fedorov E.V., Lukk T., Patskovsky Y.V., Stead M.B., Hillerich B.S., Seidel R.D., Almo S.C., Gerlt J.A.
Biochemistry 53:2722-2731(2014) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) IN COMPLEX WITH MAGNESIUM, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
CP001654 Genomic DNA. Translation: ACS84754.1.
RefSeqYP_002986576.1. NC_012880.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
4IHCX-ray2.00A/B/C/D/E/F/G/H1-417[»]
ProteinModelPortalC6CBG9.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING579405.Dd703_0947.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaACS84754; ACS84754; Dd703_0947.
GeneID8090089.
KEGGdda:Dd703_0947.
PATRIC21789142. VBIDicDad95084_1016.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG4948.
HOGENOMHOG000113758.
KOK08323.
OMAGIQEYTP.
OrthoDBEOG6SBSZM.

Enzyme and pathway databases

BioCycDDAD579405:GHJU-966-MONOMER.

Family and domain databases

Gene3D3.20.20.120. 1 hit.
3.30.390.10. 1 hit.
InterProIPR029065. Enolase_C-like.
IPR029017. Enolase_N_like.
IPR018110. Mandel_Rmase/mucon_lact_enz_CS.
IPR013342. Mandelate_racemase_C.
IPR013341. Mandelate_racemase_N.
IPR001354. MR_MLE.
[Graphical view]
PANTHERPTHR13794. PTHR13794. 1 hit.
PfamPF01188. MR_MLE. 1 hit.
PF02746. MR_MLE_N. 1 hit.
[Graphical view]
SMARTSM00922. MR_MLE. 1 hit.
[Graphical view]
SUPFAMSSF51604. SSF51604. 1 hit.
SSF54826. SSF54826. 1 hit.
PROSITEPS00908. MR_MLE_1. 1 hit.
PS00909. MR_MLE_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameDMGD_DICDC
AccessionPrimary (citable) accession number: C6CBG9
Entry history
Integrated into UniProtKB/Swiss-Prot: July 9, 2014
Last sequence update: September 1, 2009
Last modified: July 9, 2014
This is version 30 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references