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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 (A3L25_25870), Probable 5-dehydro-4-deoxyglucarate dehydratase (DW66_3364), Probable 5-dehydro-4-deoxyglucarate dehydratase (AYO08_14130), 5-dehydro-4-deoxyglucarate dehydratase, Probable 5-dehydro-4-deoxyglucarate dehydratase (AB688_15755), Probable 5-dehydro-4-deoxyglucarate dehydratase (AO269_10510), Probable 5-dehydro-4-deoxyglucarate dehydratase (AYO28_18420), Probable 5-dehydro-4-deoxyglucarate dehydratase (A3K88_25680), 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)DescriptionActionsGraphical viewLength
Binding sitei38SubstrateBy similarity1
Binding sitei109SubstrateBy similarity1
Binding sitei156SubstrateBy similarity1
Binding sitei211SubstrateBy similarity1
Active sitei213Proton acceptorBy similarity1
Metal bindingi241MagnesiumBy similarity1
Metal bindingi272MagnesiumBy similarity1
Metal bindingi295MagnesiumBy similarity1
Binding sitei295SubstrateBy similarity1
Active sitei345Proton acceptorBy similarity1
Binding sitei374SubstrateBy similarity1
Binding sitei427SubstrateBy similarity1

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)DescriptionActionsGraphical viewLength
ChainiPRO_00001712681 – 451Glucarate dehydrataseAdd BLAST451

Interactioni

Subunit structurei

Homotetramer.1 Publication

Structurei

Secondary structure

1451
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi15 – 27Combined sources13
Beta strandi31 – 33Combined sources3
Beta strandi40 – 51Combined sources12
Beta strandi56 – 62Combined sources7
Helixi65 – 72Combined sources8
Helixi75 – 78Combined sources4
Helixi83 – 85Combined sources3
Helixi86 – 96Combined sources11
Helixi113 – 134Combined sources22
Helixi138 – 141Combined sources4
Beta strandi149 – 153Combined sources5
Beta strandi155 – 157Combined sources3
Helixi163 – 165Combined sources3
Beta strandi166 – 168Combined sources3
Helixi179 – 183Combined sources5
Helixi191 – 205Combined sources15
Beta strandi208 – 213Combined sources6
Beta strandi215 – 217Combined sources3
Helixi219 – 232Combined sources14
Beta strandi236 – 241Combined sources6
Helixi248 – 255Combined sources8
Turni259 – 261Combined sources3
Beta strandi263 – 267Combined sources5
Helixi277 – 288Combined sources12
Beta strandi292 – 297Combined sources6
Helixi301 – 310Combined sources10
Beta strandi314 – 317Combined sources4
Turni320 – 322Combined sources3
Helixi325 – 338Combined sources14
Helixi351 – 361Combined sources11
Helixi375 – 377Combined sources3
Turni378 – 380Combined sources3
Beta strandi383 – 386Combined sources4
Beta strandi394 – 396Combined sources3
Beta strandi400 – 402Combined sources3
Helixi409 – 420Combined sources12

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiP42206.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni241 – 243Substrate bindingBy similarity3
Regioni345 – 347Substrate bindingBy similarity3

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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1BQGX-ray2.30A1-451[»]
ProteinModelPortaliP42206.
SMRiP42206.
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...

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: November 2, 2016
This is version 85 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.