Top Level Name

  ⌊ Superfamily (core) Haloacid Dehalogenase

    ⌊ Subgroup C1.6: Phosphoserine Phosphatase Like

  ⌊ C1.6.2: Deoxy-d-mannose-octulosonate 8-phosphate Phosphatase Like

  ⌊ FunctionalDomain C1.6.2: Deoxy-d-mannose-octulosonate 8-phosphate Phosphatase Like (ID 37789)

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

References to Other Databases

Genbank

SpeciesGIAccessionProteome
Shigella flexneri 2a str. 301 Taxon ID: 198214 24114487 NP_708997.1 (RefSeq)
Taxon ID: 543 445952161 WP_000030016.1 (RefSeq)
Escherichia coli O104:H4 str. 2011C-3493 Taxon ID: 1133852 407480171 YP_006777320.1 (RefSeq) URP
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Uniprot

Protein NameAccessionEC Number Identifier
3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC P67653 3.1.3.45 KDSC_ECOL6 (Swiss-Prot)
3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC P67654 3.1.3.45 KDSC_SHIFL (Swiss-Prot)

Sequence

Length of Enzyme (full-length): 188 | Length of Functional Domain: 163

1       10        20        30        40        50        60

MSKAGASLATCYGPVSADVMAKAENIRLLILDVDGVLSDGLIYMGNNGEELKAFNVRDGY
GIRCALTSDIEVAIITGRKAKLVEDRCATLGITHLYQGQSNKLIAFSDLLEKLAIAPENV
AYVGDDLIDWPVMEKVGLSVAVADAHPLLIPRADYVTRIAGGRGAVREVCDLLLLAQGKL
DEAKGQSI
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 1/2 Superfamily-specific Conserved Alignment Residues.
Position Amino Acid Location Function Role Evidence Code Reference
76 Thr (T) side chain interacts with substrate/intermediate substrate binding -- binding ISS
Subgroup CAR This EFD conserves 6/6 Subgroup-specific Conserved Alignment Residues.
Position Amino Acid Location Function Role Evidence Code Reference
32 Asp (D) side chain Mg2+ ligand, nucleophile: attacks phosphate moiety of substrate to form covalent intermediate covalent catalysis -- reactant,
metal ligand -- binding 		ISS PubMed:11835514
34 Asp (D) side chain Mg2+ ligand, general acid: donates proton to leaving group, general base: activates water metal ligand -- binding,
proton relay -- reactant 		ICS PubMed:11835514
76 Thr (T) side chain binds phosphate moiety of substrate, positions water steric role -- spectator,
substrate binding -- binding 		ICS PubMed:11835514
102 Lys (K) side chain positions nucleophilic Asp, binds phosphate moiety of substrate steric role -- spectator,
substrate binding -- binding 		ICS PubMed:11835514
125 Asp (D) side chain Mg2+ ligand metal ligand -- binding ISS PubMed:11835514
129 Asp (D) side chain positions Lys steric role -- spectator ICS PubMed:11835514

Catalyzed Reaction

3-deoxy-manno-octulosonate-8-phosphatase

+ +
8-phosphonato-3-deoxy-D-manno-oct-2-ulosonate(3-)
58368		 water
15377		 keto-3-deoxy-D-manno-octulosonate
16064		 hydrogenphosphate
43474

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

Structures

PDB ID Title Molecule Name Number of
EFDs		 Resolution (Å) Mutant? Het group Links
2R8X Crystal Structure Of Yrbi Phosphatase From Escherichia Coli 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Phosphatase 41 2.6 Chloride Ion CSA • PDB • PDBSum
2R8Y Crystal Structure Of Yrbi Phosphatase From Escherichia Coli In A Complex With Ca Yrbi From Escherichia Coli 41 1.85 Calcium Ion • Chloride Ion CSA • PDB • PDBSum
2R8Z Crystal Structure Of Yrbi Phosphatase From Escherichia Coli In Complex With A Phosphate And A Calcium Ion 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Phosphatase 41 2.1 Calcium Ion • Phosphate Ion CSA • PDB • PDBSum
2R8E Crystal Structure Of Yrbi From Escherichia Coli In Complex With Mg 3-Deoxy-D-Manno-Octulosonate 8-Phosphatephosphatase 41 1.4 Magnesium Ion • Chloride Ion CSA • PDB • PDBSum
3HYC Crystal Structure Of E. Coli Phosphatase Yrbi, With Mg, Tetragonal Form 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Phosphatase 41 3.06 Magnesium Ion • Chloride Ion CSA • PDB • PDBSum
3I6B Crystal Structure Of Yrbi Lacking The Last 8 Residues, In Complex With Kdo And Inorganic Phosphate 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Phosphatase 41 2.49 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
April 30, 2014, 6:08 a.m. update curation agent sbrown setDomainBoundaries.py
update domain end position 188 182
update domain start position 1 20
EC number assigned by UniProtKB accession ID.