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Protein

Glucarate dehydratase

Gene

gudD

Organism
Pseudomonas putida (Arthrobacter siderocapsulatus)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the dehydration of glucarate to 5-keto-4-deoxy-D-glucarate (5-kdGluc).

Catalytic activityi

D-glucarate = 5-dehydro-4-deoxy-D-glucarate + H2O.

Cofactori

Mg2+By similarity

Pathwayi: D-glucarate degradation

This protein is involved in step 1 of the subpathway that synthesizes 2,5-dioxopentanoate from D-glucarate.
Proteins known to be involved in the 2 steps of the subpathway in this organism are:
  1. Glucarate dehydratase (gudD)
  2. Probable 5-dehydro-4-deoxyglucarate dehydratase (HA62_06375), Probable 5-dehydro-4-deoxyglucarate dehydratase (DW66_3364), 5-dehydro-4-deoxyglucarate dehydratase, Probable 5-dehydro-4-deoxyglucarate dehydratase (AO269_10510), Probable 5-dehydro-4-deoxyglucarate dehydratase (HB4184_13805), Probable 5-dehydro-4-deoxyglucarate dehydratase (HB13667_24465)
This subpathway is part of the pathway D-glucarate 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 2,5-dioxopentanoate from D-glucarate, the pathway D-glucarate degradation and in Carbohydrate acid metabolism.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei38 – 381SubstrateBy similarity
Binding sitei109 – 1091SubstrateBy similarity
Binding sitei156 – 1561SubstrateBy similarity
Binding sitei211 – 2111SubstrateBy similarity
Active sitei213 – 2131Proton acceptorBy similarity
Metal bindingi241 – 2411MagnesiumBy similarity
Metal bindingi272 – 2721MagnesiumBy similarity
Metal bindingi295 – 2951MagnesiumBy similarity
Binding sitei295 – 2951SubstrateBy similarity
Active sitei345 – 3451Proton acceptorBy similarity
Binding sitei374 – 3741SubstrateBy similarity
Binding sitei427 – 4271SubstrateBy similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-15627.
BRENDAi4.2.1.40. 5092.
SABIO-RKP42206.
UniPathwayiUPA00564; UER00627.

Names & Taxonomyi

Protein namesi
Recommended name:
Glucarate dehydratase (EC:4.2.1.40)
Short name:
GDH
Short name:
GlucD
Gene namesi
Name:gudD
OrganismiPseudomonas putida (Arthrobacter siderocapsulatus)
Taxonomic identifieri303 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 451451Glucarate dehydratasePRO_0000171268Add
BLAST

Interactioni

Subunit structurei

Homotetramer.1 Publication

Structurei

Secondary structure

1
451
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi15 – 2713Combined sources
Beta strandi31 – 333Combined sources
Beta strandi40 – 5112Combined sources
Beta strandi56 – 627Combined sources
Helixi65 – 728Combined sources
Helixi75 – 784Combined sources
Helixi83 – 853Combined sources
Helixi86 – 9611Combined sources
Helixi113 – 13422Combined sources
Helixi138 – 1414Combined sources
Beta strandi149 – 1535Combined sources
Beta strandi155 – 1573Combined sources
Helixi163 – 1653Combined sources
Beta strandi166 – 1683Combined sources
Helixi179 – 1835Combined sources
Helixi191 – 20515Combined sources
Beta strandi208 – 2136Combined sources
Beta strandi215 – 2173Combined sources
Helixi219 – 23214Combined sources
Beta strandi236 – 2416Combined sources
Helixi248 – 2558Combined sources
Turni259 – 2613Combined sources
Beta strandi263 – 2675Combined sources
Helixi277 – 28812Combined sources
Beta strandi292 – 2976Combined sources
Helixi301 – 31010Combined sources
Beta strandi314 – 3174Combined sources
Turni320 – 3223Combined sources
Helixi325 – 33814Combined sources
Helixi351 – 36111Combined sources
Helixi375 – 3773Combined sources
Turni378 – 3803Combined sources
Beta strandi383 – 3864Combined sources
Beta strandi394 – 3963Combined sources
Beta strandi400 – 4023Combined sources
Helixi409 – 42012Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1BQGX-ray2.30A1-451[»]
ProteinModelPortaliP42206.
SMRiP42206. Positions 12-451.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP42206.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni241 – 2433Substrate bindingBy similarity
Regioni345 – 3473Substrate bindingBy similarity

Sequence similaritiesi

Family and domain databases

Gene3Di3.20.20.120. 2 hits.
3.30.390.10. 1 hit.
InterProiIPR029065. Enolase_C-like.
IPR029017. Enolase_N-like.
IPR017653. Glucarate_dehydratase.
IPR013342. Mandelate_racemase_C.
IPR013341. Mandelate_racemase_N_dom.
IPR001354. MR/MLE/MAL.
[Graphical view]
PANTHERiPTHR13794. PTHR13794. 2 hits.
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.
TIGRFAMsiTIGR03247. glucar-dehydr. 1 hit.

Sequencei

Sequence statusi: Complete.

P42206-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEALNQSQAA TGAPVITDLK VVPVAGHDSM LLNLSGAHGP LFTRNILILT
60 70 80 90 100
DSSGHVGVGE VPGGEGIRKT LEDARHLLIN QSIGNYQSLL NKVRNAFADR
110 120 130 140 150
DVGGRGLQTF DLRIAVHAVT AVESALLDLL GQHLQVPVAA LLGEGQQRDA
160 170 180 190 200
VEMLGYLFYV GDRNKTDLGY RSEHEADNEW FRLRNKEALT PESVVALAEA
210 220 230 240 250
AYDRYGFKDF KLKGGVLRGE DEIAAVTALS ERFPDARITL DPNGAWSLKE
260 270 280 290 300
AVALCRDQHH VLAYAEDPCG AENGYSGREV MAEFRRSTGL RTATNMIATD
310 320 330 340 350
WRQMGHAIQL QSVDIPLADP HFWTMQGSVR VAQMCNEWGL TWGSHSNNHF
360 370 380 390 400
DISLAMFTHV AAAAPGNITA IDTHWIWQDG QRLTKEPLQI KGGLVEVPKK
410 420 430 440 450
PGLGVELDWD ALMKAHEVYK SMGLGARDDA TAMRYLVSGW EFNNKRPCMV

R
Length:451
Mass (Da):49,572
Last modified:November 1, 1995 - v1
Checksum:i04CCB563BCB1C6EA
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M69160 Genomic DNA. Translation: AAA25868.1.
PIRiS27617.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M69160 Genomic DNA. Translation: AAA25868.1.
PIRiS27617.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1BQGX-ray2.30A1-451[»]
ProteinModelPortaliP42206.
SMRiP42206. Positions 12-451.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Enzyme and pathway databases

UniPathwayiUPA00564; UER00627.
BioCyciMetaCyc:MONOMER-15627.
BRENDAi4.2.1.40. 5092.
SABIO-RKP42206.

Miscellaneous databases

EvolutionaryTraceiP42206.

Family and domain databases

Gene3Di3.20.20.120. 2 hits.
3.30.390.10. 1 hit.
InterProiIPR029065. Enolase_C-like.
IPR029017. Enolase_N-like.
IPR017653. Glucarate_dehydratase.
IPR013342. Mandelate_racemase_C.
IPR013341. Mandelate_racemase_N_dom.
IPR001354. MR/MLE/MAL.
[Graphical view]
PANTHERiPTHR13794. PTHR13794. 2 hits.
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.
TIGRFAMsiTIGR03247. glucar-dehydr. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. "Nucleotide sequence of genes for glucarate dehydratase and 5-keto-4-deoxyglucarate dehydratase from Pseudomonas putida pp3."
    Burlingame R.P., Lauer G.D., Platz J.G., Rudd E.A., Ally A., Ally D., Backman K.C.
    Submitted (JUN-1992) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: pp3.
  2. "Evolution of enzymatic activities in the enolase superfamily: crystal structure of (D)-glucarate dehydratase from Pseudomonas putida."
    Gulick A.M., Palmer D.R., Babbitt P.C., Gerlt J.A., Rayment I.
    Biochemistry 37:14358-14368(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS), SUBUNIT.

Entry informationi

Entry nameiGUDD_PSEPU
AccessioniPrimary (citable) accession number: P42206
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: November 1, 1995
Last modified: January 20, 2016
This is version 83 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

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.