Top Level Name

  ⌊ Superfamily (core) Enolase

    ⌊ Subgroup mandelate racemase

     ⌊ Family D-tartrate dehydratase

  ⌊ FunctionalDomain D-tartrate dehydratase (ID 2135573)

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 japonicum Taxon ID: 375 654698107 WP_028156255.1 (RefSeq) URP
Bradyrhizobium japonicum Taxon ID: 375 712706714 KGT81782.1 (Genbank) URP

Uniprot

Protein NameAccessionEC Number Identifier
n/a A0A0A3Y4X7 A0A0A3Y4X7_BRAJP (TrEMBL)

Sequence

Length of Enzyme (full-length): 389 | Length of Functional Domain: 387

1       10        20        30        40        50        60

MSVRIVDVREITKPISSPIRNAYIDFTKMTTSLVAVVTDVVRDGKRVVGYGFNSNGRYGQ
GGLIRERFASRILEADPKSLLNAAGDNLDPDKVWAAMMTNEKPGGHGERSVAVGTIDMAV
WDAVAKIAGKPLFRLLAERHGVTANPRVFVYAAGGYYYPGKDLSMLRGEMRGYLDRGYNV
VKMKIGGASIEDDRTRIEAVLKEIGKDAQLAVDANGRFDLETGIAYAKMLRDYPLFWYEE
VGDPLDYALQAALAEFYPGPMATGENLFSHQDARNLIRYGGMRPDRDWLQFDCALSYGLC
EYQRTLEVLKTYGWSPSRCIPHGGHQMSLNIAAGLGLGGNESYPDLFQPYGGFPDGVRVE
NGHITMPDLPGIGFEGKSDLYKEMKALAE
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
213 Asp (D) side chain metal binding ligand metal ligand -- binding ISS PubMed:8987982
239 Glu (E) side chain metal binding ligand metal ligand -- binding ISS PubMed:8987982
265 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
213 Asp (D) side chain metal binding ligand metal ligand -- binding ICS
239 Glu (E) side chain metal binding ligand metal ligand -- binding ICS
265 Glu (E) side chain metal binding ligand metal ligand -- binding ICS
292 Asp (D) side chain controls pKa of catalytic His perturbates pKa -- spectator IDA
322 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
184 Lys (K) side chain abstracts alpha proton from D-tartrate proton relay -- reactant IDA PubMed:17144653
213 Asp (D) side chain metal binding ligand metal ligand -- binding ICS PubMed:17144653
239 Glu (E) side chain metal binding ligand metal ligand -- binding ICS PubMed:17144653
265 Glu (E) side chain metal binding ligand metal ligand -- binding ICS PubMed:17144653
292 Asp (D) side chain Controls pKa of H323 perturbates pKa -- spectator ICS PubMed:17144653
322 His (H) side chain acid catalyst for beta elimination reaction proton relay -- reactant ICS PubMed:17144653
341 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
2DW6 Crystal Structure Of The Mutant K184A Of D-Tartrate Dehydratase From Bradyrhizobium Japonicum Complexed With Mg++ And D-Tartrate Bll6730 Protein 25 2.3 Yes Magnesium Ion
(2 more ⇓) 		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
Aug. 1, 2014, 2:54 a.m. update curation agent updateSuperfamily.py setDomainBoundaries.py
EC number assigned by UniProtKB accession ID.