Top Level Name

  ⌊ Superfamily (core) Enolase

    ⌊ Subgroup mandelate racemase

     ⌊ Family D-tartrate dehydratase

  ⌊ FunctionalDomain D-tartrate dehydratase (ID 2575924)

Superfamily Assignment Evidence Code(s) IEA
Family Assignment Evidence Code IEA
This entry was last updated onNov. 22, 2017

References to Other Databases

Genbank

SpeciesGIAccessionProteome
Bradyrhizobium sp. Ec3.3 Taxon ID: 189753 737692983 WP_035661998.1 (RefSeq)

Sequence

Length of Enzyme (full-length): 388 | Length of Functional Domain: 387

1       10        20        30        40        50        60

MVRIVDVREITKPISSPIRNAYIDFTKMTTSLVAVVTDVVRDGKRVVGYGFNSNGRYGQG
GLIRERFASRILEADPKSLLDAAGDNLDPDKVWTAMMTNEKPGGHGERSVAVGTIDMAVW
DAVAKIAGKPLFRLLAERHGVKANPRVFVYAAGGYYYPGKDLSMLRGEMRGYLDRGYNVV
KMKIGGAPIEEDRTRIEAVLKEIGKDAQLAVDANGRFDLETAIAYAKMLRDYPLFWYEEA
GDPLDYSLQAALAEFYPAAMATGENLFSHQDARNLIRHGGMRPDRDWLQFDCALSYGLCE
YQRTLQVLKTHGWSPSRCIPHGGHQMSLNIAAGLGLGGNESYPDLFQPYGGFPDGVRVEN
GHITMPDLPGIGFEGKSDLYQEMKALAE
This shows the full-length sequence of the enzyme. The region of the functional domain is highlighted in black letters, while the residual residues are shown in grey. The Superfamily domain, when present, is shown using underlining. In many cases the functional domain is the full-length sequence.
Conserved catalytic residues (as determined by automated alignment to family, subgroup, or superfamily HMMs) are shown with teal highlighting . Conserved catalytic residues which do not matched the Conserved Alignment Residue are shown with maroon highlighting . Information regarding their function can be found in the Conserved Residues section below.
FASTA formatted full-length sequence.
BLAST this sequence against SFLD.
Scan SFLD-HMMs with this sequence.

Conserved Residues
Superfamily CAR This EFD conserves 3/3 Superfamily-specific Conserved Alignment Residues.
Position Amino Acid Location Function Role Evidence Code Reference
212 Asp (D) side chain metal binding ligand metal ligand -- binding ISS PubMed:8987982
238 Glu (E) side chain metal binding ligand metal ligand -- binding ISS PubMed:8987982
264 Glu (E) side chain metal binding ligand metal ligand -- binding ISS PubMed:8987982
Subgroup CAR This EFD conserves 5/5 Subgroup-specific Conserved Alignment Residues.
Position Amino Acid Location Function Role Evidence Code Reference
212 Asp (D) side chain metal binding ligand metal ligand -- binding ICS
238 Glu (E) side chain metal binding ligand metal ligand -- binding ICS
264 Glu (E) side chain metal binding ligand metal ligand -- binding ICS
291 Asp (D) side chain controls pKa of catalytic His perturbates pKa -- spectator IDA
321 His (H) side chain proton abstraction (general base) proton relay -- reactant IDA
Family CAR This EFD conserves 7/7 Family-specific Conserved Alignment Residues.
Position Amino Acid Location Function Role Evidence Code Reference
183 Lys (K) side chain abstracts alpha proton from D-tartrate proton relay -- reactant IDA PubMed:17144653
212 Asp (D) side chain metal binding ligand metal ligand -- binding ICS PubMed:17144653
238 Glu (E) side chain metal binding ligand metal ligand -- binding ICS PubMed:17144653
264 Glu (E) side chain metal binding ligand metal ligand -- binding ICS PubMed:17144653
291 Asp (D) side chain Controls pKa of H323 perturbates pKa -- spectator ICS PubMed:17144653
321 His (H) side chain acid catalyst for beta elimination reaction proton relay -- reactant ICS PubMed:17144653
340 Glu (E) side chain stabilizes intermediate electrostatic stabiliser -- spectator ICS PubMed:17144653

Structures

PDB ID Title Molecule Name Number of
EFDs		 Resolution (Å) Mutant? Het group Links
1TZZ Crystal Structure Of The Protein L1841, Unknown Member Of Enolase Superfamily From Bradyrhizobium Japonicum Hypothetical Protein L1841 28 1.86 Magnesium Ion CSA • PDB • PDBSum
2DW7 Crystal Structure Of D-Tartrate Dehydratase From Bradyrhizobium Japonicum Complexed With Mg++ And Meso-Tartrate Bll6730 Protein 28 2.5 Magnesium Ion • S,R Meso-Tartaric Acid CSA • PDB • PDBSum
Percent identity and alignment length from the BLAST match of the Functional Domain sequence to the PDB sequence.
"Yes" indicates that a GI associated with this Functional Domain was mapped to the PDB ID via UniProtKB.

Curation History
Time Change Annotation Old Value New Value
May 8, 2015, 4:18 a.m. update curation agent updateSuperfamily.py setDomainBoundaries.py
EC number assigned by UniProtKB accession ID.