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Protein

D(-)-tartrate dehydratase

Gene

tarD

Organism
Bradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the dehydration of D-tartrate to oxaloacetate.1 Publication

Catalytic activityi

(S,S)-tartrate = oxaloacetate + H2O.1 Publication

Cofactori

Mg2+1 PublicationNote: Binds 1 Mg2+ ion per subunit.1 Publication

Kineticsi

kcat is 7.3 sec(-1) for D-tartrate.

  1. KM=0.086 mM for D-tartrate1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei21 – 211Substrate
Binding sitei55 – 551Substrate
Sitei55 – 551Transition state stabilizer
Binding sitei102 – 1021Substrate
Binding sitei156 – 1561Substrate
Binding sitei182 – 1821Substrate
Sitei182 – 1821Transition state stabilizer
Active sitei184 – 1841acceptor1 Publication
Metal bindingi213 – 2131Magnesium1 Publication
Metal bindingi239 – 2391Magnesium1 Publication
Binding sitei239 – 2391Substrate
Metal bindingi265 – 2651Magnesium1 Publication
Binding sitei265 – 2651Substrate
Sitei292 – 2921Increases basicity of active site His
Active sitei322 – 3221Proton donor/acceptor1 Publication
Binding sitei322 – 3221Substrate
Sitei341 – 3411Transition state stabilizer

GO - Molecular functioni

  1. D(-)-tartrate dehydratase activity Source: UniProtKB
  2. magnesium ion binding Source: UniProtKB

GO - Biological processi

  1. protein homooligomerization Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

BioCyciBJAP224911:GJEJ-6781-MONOMER.
SABIO-RKQ89FH0.

Names & Taxonomyi

Protein namesi
Recommended name:
D(-)-tartrate dehydratase (EC:4.2.1.81)
Gene namesi
Name:tarD
Ordered Locus Names:bll6730
OrganismiBradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110)
Taxonomic identifieri224911 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesBradyrhizobiaceaeBradyrhizobium
ProteomesiUP000002526: Chromosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi102 – 1021K → A or M: Loss of dehydration activity. 1 Publication
Mutagenesisi184 – 1841K → A: Loss of dehydration activity. 1 Publication
Mutagenesisi184 – 1841K → R: Reduced dehydration activity. 1 Publication
Mutagenesisi322 – 3221H → N: Decreased but measurable dehydration activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 389389D(-)-tartrate dehydratasePRO_0000430443Add
BLAST

Interactioni

Subunit structurei

Homooctamer; tetramer of dimers.1 Publication

Protein-protein interaction databases

STRINGi224911.bll6730.

Structurei

Secondary structure

1
389
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi5 – 1410Combined sources
Beta strandi30 – 4112Combined sources
Beta strandi43 – 5210Combined sources
Helixi61 – 666Combined sources
Helixi68 – 736Combined sources
Helixi77 – 793Combined sources
Beta strandi85 – 884Combined sources
Helixi90 – 978Combined sources
Turni98 – 1003Combined sources
Helixi108 – 12821Combined sources
Helixi132 – 1398Combined sources
Beta strandi147 – 1537Combined sources
Helixi163 – 17412Combined sources
Turni175 – 1773Combined sources
Beta strandi179 – 1846Combined sources
Beta strandi186 – 1883Combined sources
Helixi190 – 20415Combined sources
Turni205 – 2073Combined sources
Beta strandi209 – 2135Combined sources
Helixi220 – 23011Combined sources
Beta strandi236 – 2394Combined sources
Helixi247 – 2537Combined sources
Turni254 – 2563Combined sources
Beta strandi261 – 2633Combined sources
Helixi270 – 27910Combined sources
Turni284 – 2863Combined sources
Turni293 – 2975Combined sources
Helixi299 – 31113Combined sources
Helixi316 – 3183Combined sources
Helixi326 – 33510Combined sources
Beta strandi340 – 3423Combined sources
Turni348 – 3503Combined sources
Beta strandi363 – 3653Combined sources
Helixi374 – 3763Combined sources
Helixi378 – 3858Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1TZZX-ray1.86A/B1-389[»]
2DW6X-ray2.30A/B/C/D1-389[»]
2DW7X-ray2.50A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P1-389[»]
ProteinModelPortaliQ89FH0.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ89FH0.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni182 – 1843Substrate binding
Regioni213 – 2153Substrate binding
Regioni341 – 3433Substrate binding

Sequence similaritiesi

Phylogenomic databases

HOGENOMiHOG000257327.
InParanoidiQ89FH0.
OrthoDBiEOG6Q2SGK.
PhylomeDBiQ89FH0.

Family and domain databases

Gene3Di3.20.20.120. 1 hit.
3.30.390.10. 1 hit.
InterProiIPR029065. Enolase_C-like.
IPR029017. Enolase_N_like.
IPR013342. Mandelate_racemase_C.
IPR001354. MR/MLE/MAL.
[Graphical view]
PANTHERiPTHR13794. PTHR13794. 1 hit.
SMARTiSM00922. MR_MLE. 1 hit.
[Graphical view]
SUPFAMiSSF51604. SSF51604. 1 hit.
SSF54826. SSF54826. 1 hit.

Sequencei

Sequence statusi: Complete.

Q89FH0-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSVRIVDVRE ITKPISSPIR NAYIDFTKMT TSLVAVVTDV VREGKRVVGY
60 70 80 90 100
GFNSNGRYGQ GGLIRERFAS RILEADPKKL LNEAGDNLDP DKVWAAMMIN
110 120 130 140 150
EKPGGHGERS VAVGTIDMAV WDAVAKIAGK PLFRLLAERH GVKANPRVFV
160 170 180 190 200
YAAGGYYYPG KGLSMLRGEM RGYLDRGYNV VKMKIGGAPI EEDRMRIEAV
210 220 230 240 250
LEEIGKDAQL AVDANGRFNL ETGIAYAKML RDYPLFWYEE VGDPLDYALQ
260 270 280 290 300
AALAEFYPGP MATGENLFSH QDARNLLRYG GMRPDRDWLQ FDCALSYGLC
310 320 330 340 350
EYQRTLEVLK THGWSPSRCI PHGGHQMSLN IAAGLGLGGN ESYPDLFQPY
360 370 380
GGFPDGVRVE NGHITMPDLP GIGFEGKSDL YKEMKALAE
Length:389
Mass (Da):43,058
Last modified:June 1, 2003 - v1
Checksum:i0FE177A59AB2F82C
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000040 Genomic DNA. Translation: BAC51995.1.
RefSeqiNP_773370.1. NC_004463.1.

Genome annotation databases

EnsemblBacteriaiBAC51995; BAC51995; BAC51995.
GeneIDi1050053.
KEGGibja:bll6730.
PATRICi21197324. VBIBraJap65052_6896.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000040 Genomic DNA. Translation: BAC51995.1.
RefSeqiNP_773370.1. NC_004463.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1TZZX-ray1.86A/B1-389[»]
2DW6X-ray2.30A/B/C/D1-389[»]
2DW7X-ray2.50A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P1-389[»]
ProteinModelPortaliQ89FH0.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224911.bll6730.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAC51995; BAC51995; BAC51995.
GeneIDi1050053.
KEGGibja:bll6730.
PATRICi21197324. VBIBraJap65052_6896.

Phylogenomic databases

HOGENOMiHOG000257327.
InParanoidiQ89FH0.
OrthoDBiEOG6Q2SGK.
PhylomeDBiQ89FH0.

Enzyme and pathway databases

BioCyciBJAP224911:GJEJ-6781-MONOMER.
SABIO-RKQ89FH0.

Miscellaneous databases

EvolutionaryTraceiQ89FH0.

Family and domain databases

Gene3Di3.20.20.120. 1 hit.
3.30.390.10. 1 hit.
InterProiIPR029065. Enolase_C-like.
IPR029017. Enolase_N_like.
IPR013342. Mandelate_racemase_C.
IPR001354. MR/MLE/MAL.
[Graphical view]
PANTHERiPTHR13794. PTHR13794. 1 hit.
SMARTiSM00922. MR_MLE. 1 hit.
[Graphical view]
SUPFAMiSSF51604. SSF51604. 1 hit.
SSF54826. SSF54826. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110.
  2. "Finding Sequences for over 270 Orphan Enzymes."
    Shearer A.G., Altman T., Rhee C.D.
    PLoS ONE 9:E97250-E97250(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION.
  3. "Evolution of enzymatic activities in the enolase superfamily: D-tartrate dehydratase from Bradyrhizobium japonicum."
    Yew W.S., Fedorov A.A., Fedorov E.V., Wood B.M., Almo S.C., Gerlt J.A.
    Biochemistry 45:14598-14608(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) OF MUTANT LYS-184 IN COMPLEX WITH D(-)-TARTRATE AND MAGNESIUM, COFACTOR, ACTIVE SITE, FUNCTION, CATALYTIC ACTIVITY, SUBUNIT, BIOPHYSICOCHEMICAL PROPERTIES, REACTION MECHANISM, MUTAGENESIS OF LYS-102; LYS-184 AND HIS-322.

Entry informationi

Entry nameiTARD_BRADU
AccessioniPrimary (citable) accession number: Q89FH0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 2014
Last sequence update: June 1, 2003
Last modified: January 7, 2015
This is version 70 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

Reaction mechanism is a simple extension of the two-step reaction catalyzed by other members of the family: Lys-184 initiates the reaction by abstraction of the alpha-proton to generate a Mg2+-stabilized enediolate intermediate, and the vinylogous beta-elimination of the 3-OH group is general acid-catalyzed by the His-322, accomplishing the anti-elimination of water. The replacement of the leaving group by solvent-derived hydrogen is stereo-random, suggesting that the enol tautomer of oxaloacetate is the product (PubMed:17144653).1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. 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.