Top Level Name

  ⌊ Superfamily (core) Enolase

    ⌊ Subgroup mandelate racemase

     ⌊ Family rhamnonate dehydratase

  ⌊ FunctionalDomain rhamnonate dehydratase (ID 5820)

Superfamily Assignment Evidence Code(s) ISS
Family Assignment Evidence Code ISS
This entry was last updated onNov. 21, 2017

References to Other Databases

Genbank

SpeciesGIAccessionProteome
Salmonella enterica Taxon ID: 28901 486167283 WP_001530644.1 (RefSeq) URP
Salmonella enterica subsp. enterica serovar Derby Taxon ID: 28144 852270516 KMM41608.1 (Genbank) URP
Salmonella enterica subsp. enterica serovar Thompson str. ATCC 8391 Taxon ID: 935705 820767193 AKG84062.1 (Genbank) URP
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Uniprot

Protein NameAccessionEC Number Identifier
L-rhamnonate dehydratase {ECO:0000255|HAMAP-Rule:MF_01288} B5EZH0 RHMD_SALA4 (Swiss-Prot)
L-rhamnonate dehydratase {ECO:0000255|HAMAP-Rule:MF_01288} Q57M62 RHMD_SALCH (Swiss-Prot)
L-rhamnonate dehydratase {ECO:0000255|HAMAP-Rule:MF_01288} B5FNT1 RHMD_SALDC (Swiss-Prot)
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Sequence

Length of Enzyme (full-length): 401 | Length of Functional Domain: 401

1       10        20        30        40        50        60

MTLPKIKHVRAWFIGGATAEKGAGGGDYHDQGGNHWIDDHIATPMSKYRDYEQSRQSFGI
NVLGTLIVEVEAENGQTGFAVSTAGEMGCFIVEKHLNRFIEGKCVSDIKLIHDQMLGATM
YYSGSGGLVMNTISCVDLALWDLFGKVVGLPVYKLLGGAVRDEIQFYATGARPDLAKEMG
FIGGKMPTHWGPHDGDAGIRKDAAMVADMREKCGPDFWLMLDCWMSQDVNYATKLAHACA
PFNLKWIEECLPPQQYEGYRELKRNAPAGMMVTSGEHHGTLQSFRTLAETGIDIMQPDVG
WCGGLTTLVEIAALAKSRGQLVVPHGSSVYSHHAVITFTNTPFSEFLMTSPDCSTLRPQF
DPILLDEPVPVNGRIHKSVLDKPGFGVELNRDCHLKRPYSH
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
222 Asp (D) side chain metal binding ligand metal ligand -- binding ISS PubMed:8987982
248 Glu (E) side chain metal binding ligand metal ligand -- binding ISS PubMed:8987982
276 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
222 Asp (D) side chain metal binding ligand metal ligand -- binding ICS
248 Glu (E) side chain metal binding ligand metal ligand -- binding ICS
276 Glu (E) side chain metal binding ligand metal ligand -- binding ICS
298 Asp (D) side chain controls pKa of catalytic His perturbates pKa -- spectator IDA
325 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
185 Lys (K) side chain electrophilic catalyst covalent catalysis -- reactant ICS PubMed:18754693
222 Asp (D) side chain metal binding ligand metal ligand -- binding ICS PubMed:18754693
248 Glu (E) side chain metal binding ligand metal ligand -- binding ICS PubMed:18754693
276 Glu (E) side chain metal binding ligand metal ligand -- binding ICS PubMed:18754693
298 Asp (D) side chain controls pKa of catalytic His perturbates pKa -- spectator ICS PubMed:18754693
325 His (H) side chain abstracts proton from C2 of substrate; acid catalyst for vinylogous departure of 2-OH group; protonates C-3 to replace 3-OH group with a solvent-derived hydrogen proton relay -- reactant ICS PubMed:18754693
345 Glu (E) side chain electrophilic catalyst covalent catalysis -- reactant ICS PubMed:18754693

Structures

PDB ID Title Molecule Name Number of
EFDs		 Resolution (Å) Mutant? Het group Links
2GSH Crystal Structure Of L-Rhamnonate Dehydratase From Salmonella Typhimurium L-Rhamnonate Dehydratase 312 2.39 Magnesium Ion • Glycerol CSA • PDB • PDBSum
3D47 Crystal Structure Of L-Rhamnonate Dehydratase From Salmonella Typhimurium Complexed With Mg And D-Malate Putative Galactonate Dehydratase 312 1.8 Magnesium Ion • Malate Ion CSA • PDB • PDBSum
3D46 Crystal Structure Of L-Rhamnonate Dehydratase From Salmonella Typhimurium Complexed With Mg And L-Tartrate Putative Galactonate Dehydratase 312 1.9 Magnesium Ion • L(+)-Tartaric Acid CSA • PDB • PDBSum
3CXO Crystal Structure Of L-Rhamnonate Dehydratase From Salmonella Typhimurium Complexed With Mg And 3-Deoxy-L-Rhamnonate Putative Galactonate Dehydratase 312 2.0 3,6-Dideoxy-L-Arabino-Hexonic Acid
(2 more ⇓) 		CSA • PDB • PDBSum
2P3Z Crystal Structure Of L-Rhamnonate Dehydratase From Salmonella Typhimurium L-Rhamnonate Dehydratase 312 1.8 Sodium Ion CSA • PDB • PDBSum
3BOX Crystal Structure Of L-Rhamnonate Dehydratase From Salmonella Typhimurium Complexed With Mg L-Rhamnonate Dehydratase 312 1.8 Magnesium Ion CSA • PDB • PDBSum
2I5Q Crystal Structure Of Apo L-Rhamnonate Dehydratase From Escherichia Coli L-Rhamnonate Dehydratase 319 2.1 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.

Identical Sequences with Suspect Annotations in Other Databases (Schnoes et.al. 2009)

Genbank

Source DB Accession Species Source Annotation Misannot. Evid. Code Source Date
KEGG sec:SC2294 Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67 yfaW; paral putative galactonate dehydratase SFA Feb. 17, 2006
NR 62128497 Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67 paral putative galactonate dehydratase SFA Feb. 17, 2006
NR 62180864 Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67 paral putative galactonate dehydratase SFA Feb. 17, 2006
TrEMBL Q57M62_SALCH Salmonella choleraesuis Paral putative galactonate dehydratase SFA Feb. 17, 2006

Curation History
Time Change Annotation Old Value New Value
Nov. 3, 2014, 2:34 a.m. update curation agent sbrown setDomainBoundaries.py
EC number assigned by UniProtKB accession ID.