Top Level Name

  ⌊ Superfamily (core) Enolase

    ⌊ Subgroup mandelate racemase

     ⌊ Family rhamnonate dehydratase

  ⌊ FunctionalDomain rhamnonate dehydratase (ID 75)

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 subsp. enterica serovar Typhimurium str. LT2 Taxon ID: 99287 16765618 NP_461233.1 (RefSeq) PRP URP
Salmonella enterica Taxon ID: 28901 446349972 WP_000427827.1 (RefSeq) URP
Salmonella enterica subsp. enterica serovar Typhimurium str. USDA-ARS-USMARC-1909 Taxon ID: 1454642 808189434 AKD08977.1 (Genbank) URP
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Uniprot

Protein NameAccessionEC Number Identifier
L-rhamnonate dehydratase Q8ZNF9 4.2.1.90 RHMD_SALTY (Swiss-Prot)

Sequence

Length of Enzyme (full-length): 405 | Length of Functional Domain: 405

1       10        20        30        40        50        60

MENIMTLPKIKHVRAWFIGGATAEKGAGGGDYHDQGGNHWIDDHIATPMSKYRDYEQSRQ
SFGINVLGTLIVEVEAENRQTGFAVSTAGEMGCFIVEKHLNRFIEGKCVSDIKLIHDQML
GATMYYSGSGGLVMNTISCVDLALWDLFGKVVGLPVYKLLGGAVRDEIQFYATGARPDLA
KEMGFIGGKMPTHWGPHDGDAGIRKDAAMVADMREKCGPDFWLMLDCWMSQDVNYATKLA
HACAPFNLKWIEECLPPQQYEGYRELKRNAPAGMMVTSGEHHGTLQSFRTLAETGIDIMQ
PDVGWCGGLTTLVEIAALAKSRGQLVVPHGSSVYSHHAVITFTNTPFSEFLMTSPDCSTL
RPQFDPILLDEPVPVNGRIHKSVLDKPGFGVELNRDCHLKRPYSH
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
226 Asp (D) side chain metal binding ligand metal ligand -- binding ISS PubMed:8987982
252 Glu (E) side chain metal binding ligand metal ligand -- binding ISS PubMed:8987982
280 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
226 Asp (D) side chain metal binding ligand metal ligand -- binding ICS
252 Glu (E) side chain metal binding ligand metal ligand -- binding ICS
280 Glu (E) side chain metal binding ligand metal ligand -- binding ICS
302 Asp (D) side chain controls pKa of catalytic His perturbates pKa -- spectator IDA
329 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
189 Lys (K) side chain electrophilic catalyst covalent catalysis -- reactant ICS PubMed:18754693
226 Asp (D) side chain metal binding ligand metal ligand -- binding ICS PubMed:18754693
252 Glu (E) side chain metal binding ligand metal ligand -- binding ICS PubMed:18754693
280 Glu (E) side chain metal binding ligand metal ligand -- binding ICS PubMed:18754693
302 Asp (D) side chain controls pKa of catalytic His perturbates pKa -- spectator ICS PubMed:18754693
329 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
349 Glu (E) side chain electrophilic catalyst covalent catalysis -- reactant ICS PubMed:18754693

Catalyzed Reaction

L-rhamnonate dehydratase

+
L-rhamnonate
58118		 2-dehydro-3-deoxy-L-rhamnonate
58371		 water
15377

EC: 4.2.1.90 | IntEnz: 4.2.1.90 | Kegg: 4.2.1.90 | BioCyc: 4.2.1.90 | BRENDA: 4.2.1.90

Structures

PDB ID Title Molecule Name Number of
EFDs		 Resolution (Å) Mutant? Het group Links
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
2GSH Crystal Structure Of L-Rhamnonate Dehydratase From Salmonella Typhimurium L-Rhamnonate Dehydratase 312 2.39 Magnesium Ion • Glycerol 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 stm:STM2291 yfaW; putative galactonate dehydratase SFA Feb. 17, 2006
NR 16420830 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 putative galactonate dehydratase SFA Feb. 17, 2006
NR 16765618 Salmonella typhimurium LT2 putative galactonate dehydratase SFA Feb. 17, 2006
TrEMBL Q8ZNF9_SALTY Salmonella typhimurium Putative galactonate dehydratase SFA Feb. 17, 2006

Curation History
Time Change Annotation Old Value New Value
Nov. 3, 2014, 2:33 a.m. update curation agent sbrown setDomainBoundaries.py
EC number assigned by UniProtKB accession ID.