Top Level Name

  ⌊ Superfamily (core) Enolase

    ⌊ Subgroup mannonate dehydratase

     ⌊ Family mannonate dehydratase

  ⌊ FunctionalDomain mannonate dehydratase (ID 4878)

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

References to Other Databases

Genbank

SpeciesGIAccessionProteome
Novosphingobium aromaticivorans Taxon ID: 48935 500246567 WP_011906920.1 (RefSeq)
Novosphingobium aromaticivorans DSM 12444 Taxon ID: 279238 145322591 ABP64534.1 (Genbank) URP
Novosphingobium aromaticivorans DSM 12444 Taxon ID: 279238 667467078 URP
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Uniprot

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

Sequence

Length of Enzyme (full-length): 402 | Length of Functional Domain: 402

1       10        20        30        40        50        60

MKITAARVIITCPGRNFVTLKIETDQGVYGIGDATLNGRELSVVAYLQEHVAPCLIGMDP
RRIEDIWQYVYRGAYWRRGPVTMRAIAAVDMALWDIKAKMAGMPLYQLLGGRSRDGIMVY
GHANGSDIAETVEAVGHYIDMGYKAIRAQTGVPGIKDAYGVGRGKLYYEPADASLPSVTG
WDTRKALNYVPKLFEELRKTYGFDHHLLHDGHHRYTPQEAANLGKMLEPYQLFWLEDCTP
AENQEAFRLVRQHTVTPLAVGEIFNTIWDAKDLIQNQLIDYIRATVVGAGGLTHLRRIAD
LASLYQVRTGCHGATDLSPVTMGCALHFDTWVPNFGIQEYMRHTEETDAVFPHDYWFEKG
ELFVGETPGHGVDIDEELAAKYPYKPAYLPVARLEDGTMWNW
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
210 Asp (D) side chain metal binding ligand metal ligand -- binding ISS PubMed:8987982
236 Glu (E) side chain metal binding ligand metal ligand -- binding ISS PubMed:8987982
262 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
147 Arg (R) side chain controls pKa of catalytic Tyr perturbates pKa -- spectator ICS PubMed:17944491
159 Tyr (Y) side chain abstracts proton from C2 of substrate; may facilitate departure of 3-OH leaving group proton relay -- reactant ICS PubMed:17944491
210 Asp (D) side chain metal binding ligand metal ligand -- binding ICS PubMed:17944491
212 His (H) side chain may facilitate departure of 3-OH leaving group increase electrophilicity -- spectator ICS PubMed:17944491
236 Glu (E) side chain metal binding ligand metal ligand -- binding ICS PubMed:17944491
262 Glu (E) side chain metal binding ligand metal ligand -- binding ICS PubMed:17944491
283 Arg (R) side chain electrophilic catalyst, stabilizes enolate anion intermediate covalent catalysis -- reactant,
electrostatic stabiliser -- spectator 		ICS PubMed:17944491
339 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
147 Arg (R) side chain controls pKa of catalytic Tyr perturbates pKa -- spectator ICS PubMed:17944491
159 Tyr (Y) side chain abstracts proton from C2 of substrate; may facilitate departure of 3-OH leaving group proton relay -- reactant ICS PubMed:17944491
210 Asp (D) side chain metal binding ligand metal ligand -- binding ICS PubMed:17944491
212 His (H) side chain may facilitate departure of 3-OH leaving group increase electrophilicity -- spectator ICS PubMed:17944491
236 Glu (E) side chain metal binding ligand metal ligand -- binding ICS PubMed:17944491
262 Glu (E) side chain metal binding ligand metal ligand -- binding ICS PubMed:17944491
283 Arg (R) side chain electrophilic catalyst, stabilizes enolate anion intermediate covalent catalysis -- reactant,
electrostatic stabiliser -- spectator 		ICS PubMed:17944491
314 Ala (A) side chain Favors dehydration of D-mannonate and disfavors dehydration of D-gluconate steric role -- spectator IME PubMed:24697546
339 Glu (E) side chain electrophilic catalyst, stabilizes enolate anion intermediate covalent catalysis -- reactant,
electrostatic stabiliser -- spectator 		ICS PubMed:17944491
402 Trp (W) side chain controls pKa of catalytic His? perturbates pKa -- spectator ICS PubMed:17944491

Catalyzed Reaction

mannonate dehydratase

+
D-mannonate
17767		 2-dehydro-3-deoxy-D-gluconate
57990		 water
15377

EC: 4.2.1.8 | IntEnz: 4.2.1.8 | Kegg: 4.2.1.8 | BioCyc: 4.2.1.8 | BRENDA: 4.2.1.8

Structures

PDB ID Title Molecule Name Number of
EFDs		 Resolution (Å) Mutant? Het group Links
2QJJ Crystal Structure Of D-Mannonate Dehydratase From Novosphingobium Aromaticivorans Mandelate Racemase/Muconate Lactonizing Enzyme 7 1.8 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
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
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
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, 2:34 a.m. update curation agent updateSFLDGIs.py setDomainBoundaries.py
EC number assigned by UniProtKB accession ID.