Top Level Name

  ⌊ Superfamily (core) Enolase

    ⌊ Subgroup mandelate racemase

     ⌊ Family rhamnonate dehydratase

  ⌊ FunctionalDomain rhamnonate dehydratase (ID 9202)

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

References to Other Databases

Genbank

SpeciesGIAccessionProteome
Shigella sonnei Ss046 Taxon ID: 300269 73856246 AAZ88953.1 (Genbank) URP
Shigella sonnei Ss046 Taxon ID: 300269 123616717 URP

Uniprot

Protein NameAccessionEC Number Identifier
L-rhamnonate dehydratase {ECO:0000255|HAMAP-Rule:MF_01288} Q3YZV9 RHMD_SHISS (Swiss-Prot)

Sequence

Length of Enzyme (full-length): 428 | Length of Functional Domain: 395

1       10        20        30        40        50        60

MPAPGIFHVCWDGKVPLTYRPHNNGEHHDPTKNQTGSRLVYWRCDSRKRCWRGDYHDQGA
NHWIDDHIATPMSKYRDYEQSRQSFGINVLGTLIVEVEAENGQTGFAVSTAGEMGCFIVE
KHLNRFIEGKCVSDIKLIHDQMLNATLYYSGSGGLVMNTISCVDLALWDLFGKVVGLPVY
KLLGGAVRDEIQFYATGARPDLAKEMGFIGGKMPTHWGPHDGDAGIRKDAVMVADMREKC
GEDFWLMLDCWMSQDVNYATKLAHACAPYNLKWIEECLPPQQYEGYRELKRNAPVGMMVT
SGEHHGTLQSFRTLSETGIDIMQPDVGWCGGLTTLVEIAAIAKSRGQLVVPHGSSVYSHH
AVITFTNTPFSEFLMTSPDCSTMRPQFDPILLNEPVPVNGRIHKSVLDKPGFGVELNRDC
NLKRPYSH
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
249 Asp (D) side chain metal binding ligand metal ligand -- binding ISS PubMed:8987982
275 Glu (E) side chain metal binding ligand metal ligand -- binding ISS PubMed:8987982
303 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
249 Asp (D) side chain metal binding ligand metal ligand -- binding ICS
275 Glu (E) side chain metal binding ligand metal ligand -- binding ICS
303 Glu (E) side chain metal binding ligand metal ligand -- binding ICS
325 Asp (D) side chain controls pKa of catalytic His perturbates pKa -- spectator IDA
352 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
212 Lys (K) side chain electrophilic catalyst covalent catalysis -- reactant ICS PubMed:18754693
249 Asp (D) side chain metal binding ligand metal ligand -- binding ICS PubMed:18754693
275 Glu (E) side chain metal binding ligand metal ligand -- binding ICS PubMed:18754693
303 Glu (E) side chain metal binding ligand metal ligand -- binding ICS PubMed:18754693
325 Asp (D) side chain controls pKa of catalytic His perturbates pKa -- spectator ICS PubMed:18754693
352 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
372 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
2I5Q Crystal Structure Of Apo L-Rhamnonate Dehydratase From Escherichia Coli L-Rhamnonate Dehydratase 319 2.1 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
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
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
Nov. 3, 2014, 2:48 a.m. update curation agent sbrown setDomainBoundaries.py
EC number assigned by UniProtKB accession ID.