Top Level Name

  ⌊ Superfamily (core) Enolase

    ⌊ Subgroup mannonate dehydratase

  ⌊ FunctionalDomain uncharacterized mannonate dehydratase subgroup sequence, enolase superfamily (ID 371)

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

References to Other Databases

Genbank

SpeciesGIAccessionProteome
Chromohalobacter salexigens Taxon ID: 158080 499827531 WP_011508265.1 (RefSeq)
Chromohalobacter salexigens DSM 3043 Taxon ID: 290398 91798180 ABE60319.1 (Genbank) URP
Chromohalobacter salexigens DSM 3043 Taxon ID: 290398 122419197 URP

Uniprot

Protein NameAccessionEC Number Identifier
D-galactonate dehydratase family member ManD Q1QT89 4.2.1.- DMGD_CHRSD (Swiss-Prot)

Sequence

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

1       10        20        30        40        50        60

MKIRDAYTIVTCPGRNFVTLKIVTESGTHGIGDATLNGREMAVAAYLDEHVVPALIGRDA
GRIEDTWQYLYRGAYWRRGPVTMTAIAAVDMALWDIKAKAAGMPLYQLLGGKSRERVMTY
AHCTGQTIEDCLGEVARHVELGYRAVRVQSGVPGIETTYGVAKTPGERYEPADSSLPAEH
VWSTEKYLNHAPKLFAAVRERFGDDLHVLHDVHHRLTPIEAARLGKAVEPYHLFWLEDCV
PAENQESLRLIREHTTTPLAIGEVFNSIHDCRELIQNQWIDYIRMPLTHGGGITAMRRVA
DLASLYHVRTGFHGPTDLSPVCLGAAIHFDTWVPNFGIQEHMPHTDETDAVFPHDYRFED
GHFLAGESPGHGVDIDEELAAKYPYERASLPVNRLEDGTLWHW
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
211 Asp (D) side chain metal binding ligand metal ligand -- binding ISS PubMed:8987982
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
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
211 Asp (D) side chain metal binding ligand metal ligand -- binding ICS PubMed:17944491
213 His (H) side chain may facilitate departure of 3-OH leaving group increase electrophilicity -- spectator ICS PubMed:17944491
237 Glu (E) side chain metal binding ligand metal ligand -- binding ICS PubMed:17944491
263 Glu (E) side chain metal binding ligand metal ligand -- binding ICS PubMed:17944491
284 Arg (R) side chain electrophilic catalyst, stabilizes enolate anion intermediate covalent catalysis -- reactant,
electrostatic stabiliser -- spectator 		ICS PubMed:17944491
340 Glu (E) side chain electrophilic catalyst, stabilizes enolate anion intermediate covalent catalysis -- reactant,
electrostatic stabiliser -- 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
4F4R Crystal Structure Of D-Mannonate Dehydratase Homolog From Chromohalobacter Salexigens (Target Efi-502114), With Bound Na, Ordered Loop D-Mannonate Dehydratase 7 1.8 Sodium Ion
(2 more ⇓) 		CSA • PDB • PDBSum
3QKE Crystal Structure Of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed With Mg And D-Gluconate Mandelate Racemase/Muconate Lactonizing Enzyme 7 1.55 Gluconic Acid • Magnesium Ion CSA • PDB • PDBSum
3P93 Crystal Structure Of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed With Mg,D-Mannonate And 2-Keto-3-Deoxy-D-Gluconate Mandelate Racemase/Muconate Lactonizing Enzyme 7 1.8 Magnesium Ion
(2 more ⇓) 		CSA • PDB • PDBSum
3OW1 Crystal Structure Of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed With Mg Mandelate Racemase/Muconate Lactonizing Enzyme 7 1.8 Magnesium Ion
(2 more ⇓) 		CSA • PDB • PDBSum
3PK7 Crystal Structure Of D-Mannonate Dehydratase From Chromohalobacter Salexigens With Mg And Glycerol Bound In The Active Site Mandelate Racemase/Muconate Lactonizing Enzyme 7 1.64 Magnesium Ion • Glycerol CSA • PDB • PDBSum
3RGT Crystal Structure Of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed With D-Arabinohydroxamate D-Mannonate Dehydratase 7 1.9 Cobalt (Ii) Ion • (2S,3R,4R)-2,3,4,5-Tetrahydroxy-N-Oxo-Pentanamide CSA • PDB • PDBSum
3BSM Crystal Structure Of D-Mannonate Dehydratase From Chromohalobacter Salexigens Mandelate Racemase/Muconate Lactonizing Enzyme 7 2.2 CSA • PDB • PDBSum
4KWS Crystal Structure Of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed With Mg And Glycerol D-Mannonate Dehydratase 7 1.64 Magnesium Ion
(2 more ⇓) 		CSA • PDB • PDBSum
4KT2 Crystal Structure Of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed With Mg And Glycerol D-Mannonate Dehydratase 7 1.8 Chloride Ion
(3 more ⇓) 		CSA • PDB • PDBSum
4KPL Crystal Structure Of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed With Mg,D-Mannonate And 2-Keto-3-Deoxy-D-Gluconate D-Mannonate Dehydratase 7 2.0 D-Mannonic Acid
(4 more ⇓) 		CSA • PDB • PDBSum
4K2S Crystal Structure Of The Mutant P317A Of D-Mannonate Dehydratase From Chromohalobacter Salexigens Complexed With Mg And D-Gluconate D-Mannonate Dehydratase 6 1.7 Yes Gluconic Acid
(3 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
Nov. 3, 2014, 2:33 a.m. update curation agent updateSFLDGIs.py setDomainBoundaries.py
June 8, 2015, 3:04 a.m. update curation agent setDomainBoundaries.py sbrown
update curation agent sbrown setDomainBoundaries.py
remove family assignment evidence code ISS -
remove family mannonate dehydratase -
update name mannonate dehydratase uncharacterized mannonate dehydratase subgroup sequence, enolase superfamily
update superfamily assignment evidence code ISS IEA
EC number assigned by UniProtKB accession ID.