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Protein

Glucarate dehydratase

Gene

gudD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the dehydration of glucarate to 5-keto-4-deoxy-D-glucarate (5-kdGluc). Also acts on L-idarate.

Catalytic activityi

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

Cofactori

Mg2+1 Publication

Kineticsi

  1. KM=16 µM for idarate1 Publication
  2. KM=60 µM for glucarate1 Publication

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei32 – 321Substrate
Binding sitei103 – 1031Substrate
Binding sitei150 – 1501Substrate
Binding sitei205 – 2051Substrate
Active sitei207 – 2071Proton acceptor
Metal bindingi235 – 2351Magnesium
Metal bindingi266 – 2661Magnesium
Metal bindingi289 – 2891Magnesium
Binding sitei289 – 2891Substrate
Active sitei339 – 3391Proton acceptor
Binding sitei368 – 3681Substrate
Binding sitei422 – 4221Substrate

GO - Molecular functioni

  1. glucarate dehydratase activity Source: UniProtKB
  2. magnesium ion binding Source: UniProtKB

GO - Biological processi

  1. D-glucarate catabolic process Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:GLUCARDEHYDRA-MONOMER.
ECOL316407:JW2758-MONOMER.
MetaCyc:GLUCARDEHYDRA-MONOMER.
SABIO-RKP0AES2.
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
Synonyms:ygcX
Ordered Locus Names:b2787, JW2758
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG13167. gudD.

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi150 – 1501Y → F: Reduces activity 100-fold. 1 Publication
Mutagenesisi207 – 2071K → Q: Reduces activity 1000-fold. 1 Publication
Mutagenesisi207 – 2071K → R: Reduces activity 10000-fold. 1 Publication
Mutagenesisi339 – 3391H → A: Loss of activity. 1 Publication
Mutagenesisi339 – 3391H → N: Reduces activity 10000-fold. 1 Publication
Mutagenesisi339 – 3391H → Q: Reduces activity 1000-fold. 1 Publication
Mutagenesisi366 – 3661D → A or N: Reduces activity over 100-fold. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed1 Publication
Chaini2 – 446445Glucarate dehydratasePRO_0000171264Add
BLAST

Proteomic databases

PaxDbiP0AES2.
PRIDEiP0AES2.

Expressioni

Gene expression databases

GenevestigatoriP0AES2.

Interactioni

Subunit structurei

Homodimer.2 Publications

Protein-protein interaction databases

IntActiP0AES2. 3 interactions.
STRINGi511145.b2787.

Structurei

Secondary structure

1
446
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi9 – 2113Combined sources
Beta strandi25 – 273Combined sources
Beta strandi34 – 4512Combined sources
Beta strandi50 – 567Combined sources
Helixi59 – 7214Combined sources
Helixi77 – 793Combined sources
Helixi80 – 9011Combined sources
Helixi92 – 954Combined sources
Turni96 – 994Combined sources
Beta strandi101 – 1044Combined sources
Helixi109 – 12820Combined sources
Beta strandi130 – 1323Combined sources
Helixi133 – 1353Combined sources
Beta strandi143 – 1475Combined sources
Beta strandi149 – 1524Combined sources
Helixi157 – 1593Combined sources
Beta strandi160 – 1623Combined sources
Helixi173 – 1775Combined sources
Helixi185 – 19915Combined sources
Beta strandi202 – 2076Combined sources
Beta strandi209 – 2113Combined sources
Helixi213 – 22614Combined sources
Beta strandi230 – 2356Combined sources
Helixi242 – 25110Combined sources
Turni252 – 2554Combined sources
Beta strandi256 – 2616Combined sources
Helixi271 – 28212Combined sources
Beta strandi286 – 2916Combined sources
Helixi295 – 30410Combined sources
Beta strandi308 – 3114Combined sources
Helixi314 – 3174Combined sources
Helixi319 – 33113Combined sources
Helixi345 – 35612Combined sources
Helixi369 – 3724Combined sources
Turni373 – 3753Combined sources
Beta strandi378 – 3814Combined sources
Beta strandi389 – 3913Combined sources
Beta strandi395 – 3973Combined sources
Helixi404 – 41613Combined sources
Helixi425 – 4295Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1EC7X-ray1.90A/B/C/D1-446[»]
1EC8X-ray1.90A/B/C/D1-446[»]
1EC9X-ray2.00A/B/C/D1-446[»]
1ECQX-ray2.00A/B/C/D1-446[»]
1JCTX-ray2.75A/B1-446[»]
1JDFX-ray2.00A/B/C/D1-446[»]
3PWGX-ray2.00A/B/C/D1-446[»]
3PWIX-ray2.23A/B1-446[»]
4GYPX-ray2.10A/B1-446[»]
ProteinModelPortaliP0AES2.
SMRiP0AES2. Positions 5-446.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0AES2.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni235 – 2373Substrate binding
Regioni339 – 3413Substrate binding

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG4948.
HOGENOMiHOG000238021.
InParanoidiP0AES2.
KOiK01706.
OMAiMQYLIPN.
OrthoDBiEOG6V7BH9.
PhylomeDBiP0AES2.

Family and domain databases

Gene3Di3.20.20.120. 1 hit.
3.30.390.10. 1 hit.
InterProiIPR029065. Enolase_C-like.
IPR029017. Enolase_N_like.
IPR017653. Glucarate_dehydratase.
IPR013342. Mandelate_racemase_C.
IPR001354. MR/MLE/MAL.
[Graphical view]
PANTHERiPTHR13794. PTHR13794. 1 hit.
PfamiPF01188. MR_MLE. 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.

Sequence processingi: The displayed sequence is further processed into a mature form.

P0AES2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSSQFTTPVV TEMQVIPVAG HDSMLMNLSG AHAPFFTRNI VIIKDNSGHT
60 70 80 90 100
GVGEIPGGEK IRKTLEDAIP LVVGKTLGEY KNVLTLVRNT FADRDAGGRG
110 120 130 140 150
LQTFDLRTTI HVVTGIEAAM LDLLGQHLGV NVASLLGDGQ QRSEVEMLGY
160 170 180 190 200
LFFVGNRKAT PLPYQSQPDD SCDWYRLRHE EAMTPDAVVR LAEAAYEKYG
210 220 230 240 250
FNDFKLKGGV LAGEEEAESI VALAQRFPQA RITLDPNGAW SLNEAIKIGK
260 270 280 290 300
YLKGSLAYAE DPCGAEQGFS GREVMAEFRR ATGLPTATNM IATDWRQMGH
310 320 330 340 350
TLSLQSVDIP LADPHFWTMQ GSVRVAQMCH EFGLTWGSHS NNHFDISLAM
360 370 380 390 400
FTHVAAAAPG KITAIDTHWI WQEGNQRLTK EPFEIKGGLV QVPEKPGLGV
410 420 430 440
EIDMDQVMKA HELYQKHGLG ARDDAMGMQY LIPGWTFDNK RPCMVR
Length:446
Mass (Da):49,141
Last modified:January 23, 2007 - v2
Checksum:iDFB07C9CA33F542C
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti310 – 3134PLAD → RWRI in AAB40437 (PubMed:9278503).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC75829.1.
U29581 Genomic DNA. Translation: AAB40437.1.
AP009048 Genomic DNA. Translation: BAA16572.2.
PIRiG65060.
RefSeqiNP_417267.1. NC_000913.3.
YP_490995.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC75829; AAC75829; b2787.
BAA16572; BAA16572; BAA16572.
GeneIDi12933293.
947258.
KEGGiecj:Y75_p2724.
eco:b2787.
PATRICi32120990. VBIEscCol129921_2887.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC75829.1.
U29581 Genomic DNA. Translation: AAB40437.1.
AP009048 Genomic DNA. Translation: BAA16572.2.
PIRiG65060.
RefSeqiNP_417267.1. NC_000913.3.
YP_490995.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1EC7X-ray1.90A/B/C/D1-446[»]
1EC8X-ray1.90A/B/C/D1-446[»]
1EC9X-ray2.00A/B/C/D1-446[»]
1ECQX-ray2.00A/B/C/D1-446[»]
1JCTX-ray2.75A/B1-446[»]
1JDFX-ray2.00A/B/C/D1-446[»]
3PWGX-ray2.00A/B/C/D1-446[»]
3PWIX-ray2.23A/B1-446[»]
4GYPX-ray2.10A/B1-446[»]
ProteinModelPortaliP0AES2.
SMRiP0AES2. Positions 5-446.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiP0AES2. 3 interactions.
STRINGi511145.b2787.

Proteomic databases

PaxDbiP0AES2.
PRIDEiP0AES2.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75829; AAC75829; b2787.
BAA16572; BAA16572; BAA16572.
GeneIDi12933293.
947258.
KEGGiecj:Y75_p2724.
eco:b2787.
PATRICi32120990. VBIEscCol129921_2887.

Organism-specific databases

EchoBASEiEB2959.
EcoGeneiEG13167. gudD.

Phylogenomic databases

eggNOGiCOG4948.
HOGENOMiHOG000238021.
InParanoidiP0AES2.
KOiK01706.
OMAiMQYLIPN.
OrthoDBiEOG6V7BH9.
PhylomeDBiP0AES2.

Enzyme and pathway databases

UniPathwayiUPA00564; UER00627.
BioCyciEcoCyc:GLUCARDEHYDRA-MONOMER.
ECOL316407:JW2758-MONOMER.
MetaCyc:GLUCARDEHYDRA-MONOMER.
SABIO-RKP0AES2.

Miscellaneous databases

EvolutionaryTraceiP0AES2.
PROiP0AES2.

Gene expression databases

GenevestigatoriP0AES2.

Family and domain databases

Gene3Di3.20.20.120. 1 hit.
3.30.390.10. 1 hit.
InterProiIPR029065. Enolase_C-like.
IPR029017. Enolase_N_like.
IPR017653. Glucarate_dehydratase.
IPR013342. Mandelate_racemase_C.
IPR001354. MR/MLE/MAL.
[Graphical view]
PANTHERiPTHR13794. PTHR13794. 1 hit.
PfamiPF01188. MR_MLE. 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

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  2. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  3. "Construction of a contiguous 874-kb sequence of the Escherichia coli-K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features."
    Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T., Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K., Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T.
    , Oyama S., Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H., Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.
    DNA Res. 4:91-113(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA] OF 315-446.
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  4. "Evolution of enzymatic activities in the enolase superfamily: characterization of the (D)-glucarate/galactarate catabolic pathway in Escherichia coli."
    Hubbard B.K., Koch M., Palmer D.R., Babbitt P.C., Gerlt J.A.
    Biochemistry 37:14369-14375(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 2-15, BIOPHYSICOCHEMICAL PROPERTIES.
  5. "Evolution of enzymatic activities in the enolase superfamily: crystallographic and mutagenesis studies of the reaction catalyzed by D-glucarate dehydratase from Escherichia coli."
    Gulick A.M., Hubbard B.K., Gerlt J.A., Rayment I.
    Biochemistry 39:4590-4602(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS AND MAGNESIUM IONS, MUTAGENESIS OF TYR-150; LYS-207; HIS-339 AND ASP-366, COFACTOR, SUBUNIT.
  6. "Evolution of enzymatic activities in the enolase superfamily: identification of the general acid catalyst in the active site of D-glucarate dehydratase from Escherichia coli."
    Gulick A.M., Hubbard B.K., Gerlt J.A., Rayment I.
    Biochemistry 40:10054-10062(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.75 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS AND MAGNESIUM IONS, SUBUNIT.

Entry informationi

Entry nameiGUDD_ECOLI
AccessioniPrimary (citable) accession number: P0AES2
Secondary accession number(s): P76637, P78217, Q46914
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 20, 2005
Last sequence update: January 23, 2007
Last modified: January 7, 2015
This is version 82 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.