Top Level Name

  ⌊ Superfamily (core) Enolase

    ⌊ Subgroup mannonate dehydratase

     ⌊ Family mannonate dehydratase

  ⌊ FunctionalDomain mannonate dehydratase (ID 1398205)

Superfamily Assignment Evidence Code(s) ISS PubMed:24947666
Family Assignment Evidence Code ISS PubMed:24947666
This entry was last updated onNov. 22, 2017

References to Other Databases

Genbank

SpeciesGIAccessionProteome
Novosphingobium aromaticivorans DSM 12444 Taxon ID: 279238 507043448 URP

Uniprot

Protein NameAccessionEC Number Identifier
D-mannonate dehydratase A4XF23 4.2.1.8 MAND_NOVAD (Swiss-Prot)

Sequence

Length of Enzyme (full-length): 422 | Length of Functional Domain: 403

1       10        20        30        40        50        60

MGSSHHHHHHSSGLVPRGSHMKITAARVIITCPGRNFVTLKIETDQGVYGIGDATLNGRE
LSVVAYLQEHVAPCLIGMDPRRIEDIWQYVYRGAYWRRGPVTMRAIAAVDMALWDIKAKM
AGMPLYQLLGGRSRDGIMVYGHANGSDIAETVEAVGHYIDMGYKAIRAQTGVPGIKDAYG
AGAGGAGAGPADASLPSVTGWDTRKALNYVPKLFEELRKTYGFDHHLLHDGHHRYTPQEA
ANLGKMLEPYQLFWLEDCTPAENQEAFRLVRQHTVTPLAVGEIFNTIWDAKDLIQNQLID
YIRATVVGAGGLTHLRRIADLASLYQVRTGCHGATDLSPVTMGCALHFDTWVPNFGIQEY
MRHTEETDAVFPHDYWFEKGELFVGETPGHGVDIDEELAAKYPYKPAYLPVARLEDGTMW
NW
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
230 Asp (D) side chain metal binding ligand metal ligand -- binding ISS PubMed:8987982
256 Glu (E) side chain metal binding ligand metal ligand -- binding ISS PubMed:8987982
282 Glu (E) side chain metal binding ligand metal ligand -- binding ISS PubMed:8987982
Subgroup CAR This EFD conserves 8/8 Subgroup-specific Conserved Alignment Residues.
Position Amino Acid Location Function Role Evidence Code Reference
167 Arg (R) side chain controls pKa of catalytic Tyr perturbates pKa -- spectator ICS PubMed:17944491
179 Tyr (Y) side chain abstracts proton from C2 of substrate; may facilitate departure of 3-OH leaving group proton relay -- reactant ICS PubMed:17944491
230 Asp (D) side chain metal binding ligand metal ligand -- binding ICS PubMed:17944491
232 His (H) side chain may facilitate departure of 3-OH leaving group increase electrophilicity -- spectator ICS PubMed:17944491
256 Glu (E) side chain metal binding ligand metal ligand -- binding ICS PubMed:17944491
282 Glu (E) side chain metal binding ligand metal ligand -- binding ICS PubMed:17944491
303 Arg (R) side chain electrophilic catalyst, stabilizes enolate anion intermediate covalent catalysis -- reactant,
electrostatic stabiliser -- spectator 		ICS PubMed:17944491
359 Glu (E) side chain electrophilic catalyst, stabilizes enolate anion intermediate covalent catalysis -- reactant,
electrostatic stabiliser -- spectator 		ICS PubMed:17944491
Family CAR This EFD conserves 10/10 Family-specific Conserved Alignment Residues.
Position Amino Acid Location Function Role Evidence Code Reference
167 Arg (R) side chain controls pKa of catalytic Tyr perturbates pKa -- spectator ICS PubMed:17944491
179 Tyr (Y) side chain abstracts proton from C2 of substrate; may facilitate departure of 3-OH leaving group proton relay -- reactant ICS PubMed:17944491
230 Asp (D) side chain metal binding ligand metal ligand -- binding ICS PubMed:17944491
232 His (H) side chain may facilitate departure of 3-OH leaving group increase electrophilicity -- spectator ICS PubMed:17944491
256 Glu (E) side chain metal binding ligand metal ligand -- binding ICS PubMed:17944491
282 Glu (E) side chain metal binding ligand metal ligand -- binding ICS PubMed:17944491
303 Arg (R) side chain electrophilic catalyst, stabilizes enolate anion intermediate covalent catalysis -- reactant,
electrostatic stabiliser -- spectator 		ICS PubMed:17944491
334 Ala (A) side chain Favors dehydration of D-mannonate and disfavors dehydration of D-gluconate steric role -- spectator IME PubMed:24697546
359 Glu (E) side chain electrophilic catalyst, stabilizes enolate anion intermediate covalent catalysis -- reactant,
electrostatic stabiliser -- spectator 		ICS PubMed:17944491
422 Trp (W) side chain controls pKa of catalytic His? perturbates pKa -- spectator ICS PubMed:17944491

Structures

PDB ID Title Molecule Name Number of
EFDs		 Resolution (Å) Mutant? Het group Links
4K8G Crystal Structure Of D-Mannonate Dehydratase From Novosphingobium Aromaticivorans Mutant (V161A, R163A, K165G, L166A, Y167G, Y168A, E169G) Mandelate Racemase/Muconate Lactonizing Enzyme, N-Terminaldomain Protein 4 1.25 Yes Glycerol • Magnesium Ion CSA • PDB • PDBSum
2QJN Crystal Structure Of D-Mannonate Dehydratase From Novosphingobium Aromaticivorans Complexed With Mg And 2-Keto-3-Deoxy-D-Gluconate Mandelate Racemase/Muconate Lactonizing Enzyme 7 2.0 Magnesium Ion • 2-Keto-3-Deoxygluconate CSA • PDB • PDBSum
2QJJ Crystal Structure Of D-Mannonate Dehydratase From Novosphingobium Aromaticivorans Mandelate Racemase/Muconate Lactonizing Enzyme 7 1.8 Magnesium Ion CSA • PDB • PDBSum
2QJM Crystal Structure Of The K271E Mutant Of Mannonate Dehydratase From Novosphingobium Aromaticivorans Complexed With Mg And D-Mannonate Mandelate Racemase/Muconate Lactonizing Enzyme 7 2.2 Yes Magnesium Ion • D-Mannonic Acid CSA • PDB • PDBSum
4K1W Crystal Structure Of The A314P Mutant Of Mannonate Dehydratase From Novosphingobium Aromaticivorans Complexed With Mg And D-Mannonate Mandelate Racemase/Muconate Lactonizing Enzyme, N-Terminaldomain Protein 7 1.65 Yes Magnesium Ion
(5 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, 3:09 a.m. update curation agent updateSuperfamily.py setDomainBoundaries.py
June 8, 2015, 3:30 a.m. update curation agent setDomainBoundaries.py sbrown
update curation agent sbrown setDomainBoundaries.py
update family assignment evidence code IEA ISS
update superfamily assignment evidence code IEA ISS
July 9, 2015, 3:28 a.m. update domain start position 21 20
EC number assigned by UniProtKB accession ID.