Top Level Name

  ⌊ Superfamily (core) Enolase

    ⌊ Subgroup mandelate racemase

     ⌊ Family L-lyxonate dehydratase

  ⌊ FunctionalDomain L-lyxonate dehydratase (ID 277983)

Superfamily Assignment Evidence Code(s) ISS
Family Assignment Evidence Code IES PubMed:24831290
This entry was last updated onNov. 21, 2017

References to Other Databases

Genbank

SpeciesGIAccessionProteome
Dinoroseobacter shibae DFL 12 Taxon ID: 398580 345101064 URP

Sequence

Length of Enzyme (full-length): 413 | Length of Functional Domain: 390

1       10        20        30        40        50        60

MHHHHHHSSGVDLGTENLYFQSMTKIKSVRTRVWNWTGPTVPPQGNFCTNASDALWIQGD
AMASFRFHQWLTCEVETEDGTIGIGNAALAPNVVKQAIDEWYAPLVIGEDPFDYAYLWEK
MYRRTHAWGRKGIGMTAISAIDIAIWDLMGKLVGKPVFKLLGGRTKEKIPVYYSKLYADS
IPAMQAEAEEAQKHGYQGYKTRFGYGPKDGPAGMRENLKRVEALREVLGYDVDLMLECYM
GWNLDYTKRMLPKLERFEPRWLEEPVIADDVAGYAELNAMGIVPISGGEHEFSVMGCAEL
INRKAVSVLQYDTNRVGGITAAQKINAIAEAAQIIVIPHAGQMHNYHLTMANMNCPISEY
FPVFDVEVGNELFYYIFDGDPEAVDGYLQLDDDTPGLGITISDAHLKHFEITE
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
237 Glu (E) side chain metal binding ligand metal ligand -- binding ISS PubMed:8987982
263 Glu (E) side chain metal binding ligand metal ligand -- binding ISS PubMed:8987982
289 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
237 Glu (E) side chain metal binding ligand metal ligand -- binding ICS
263 Glu (E) side chain metal binding ligand metal ligand -- binding ICS
289 Glu (E) side chain metal binding ligand metal ligand -- binding ICS
312 Asp (D) side chain controls pKa of catalytic His perturbates pKa -- spectator IDA
339 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
200 Lys (K) side chain Electrophile electrophile -- reactant ISS PubMed:24831290
202 Arg (R) side chain None -- IME PubMed:24831290
237 Glu (E) side chain metal binding ligand metal ligand -- binding ICS PubMed:24831290
263 Glu (E) side chain metal binding ligand metal ligand -- binding ICS PubMed:24831290
289 Glu (E) side chain metal binding ligand metal ligand -- binding ICS PubMed:24831290
312 Asp (D) side chain General base proton relay -- reactant ISS PubMed:24831290
339 His (H) side chain Forms hydrogen bond dyad with Asp general base activation -- spectator IME PubMed:24831290

Catalyzed Reaction

L-lyxonate dehydratase

+
L-Lyxonate
6268		 2-dehydro-3-deoxy-L-arabinonic acid
17647		 water
15377

EC: 4.2.1.- | IntEnz: 4.2.1.- | Kegg: 4.2.1.- | BioCyc: 4.2.1.- | BRENDA: 4.2.1.- |

Structures

PDB ID Title Molecule Name Number of
EFDs		 Resolution (Å) Mutant? Het group Links
3SQS Crystal Structure Of A Putative Mandelate Racemase/Muconate Lactonizing Protein From Dinoroseobacter Shibae Dfl 12 Mandelate Racemase/Muconate Lactonizing Protein 2 1.9 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, 2:37 a.m. update curation agent updateSuperfamily.py setDomainBoundaries.py
July 9, 2015, 3:10 a.m. update curation agent setDomainBoundaries.py sbrown
update curation agent sbrown setDomainBoundaries.py
update name uncharacterized mandelate racemase subgroup sequence L-lyxonate dehydratase
update domain start position 23 24
update superfamily assignment evidence code IEA ISS
EC number assigned by UniProtKB accession ID.