Top Level Name

  ⌊ Superfamily (core) Haloacid Dehalogenase

    ⌊ Subgroup C1.2: Nucleotidase Like

  ⌊ C1.2.2

  ⌊ FunctionalDomain C1.2.2 (ID 277145)

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

References to Other Databases

Genbank

SpeciesGIAccessionProteome
Taxon ID: 1279 487750793 WP_001832599.1 (RefSeq)
Staphylococcus epidermidis Taxon ID: 1282 760489468 AJP24135.1 (Genbank) URP
Staphylococcus epidermidis Taxon ID: 1282 721492278 KGY35836.1 (Genbank) URP
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Uniprot

Protein NameAccessionEC Number Identifier
Putative 5'(3')-deoxyribonucleotidase Q5HR07 3.1.3.- 53DR_STAEQ (Swiss-Prot)

Sequence

Length of Enzyme (full-length): 179 | Length of Functional Domain: 179

1       10        20        30        40        50        60

MTRQRIAIDMDEVLADTLGAVVKAVNERADLNIKMESLNGKKLKHMIPEHEGLVMDILKE
PGFFRNLDVMPHAQEVVKQLNEHYDIYIATAAMDVPTSFHDKYEWLLEYFPFLDPQHFVF
CGRKNIILADYLIDDNPKQLEIFEGKSIMFTASHNVNEHRFERVSGWRDVKNYFNSIEK
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

Subgroup CAR This EFD conserves 6/6 Subgroup-specific Conserved Alignment Residues.
Position Amino Acid Location Function Role Evidence Code Reference
9 Asp (D) side chain Mg2+ ligand, nucleophile: attacks phosphate moiety of substrate to form covalent intermediate covalent catalysis -- reactant,
metal ligand -- binding 		ISS
11 Asp (D) side chain Mg2+ ligand, general acid: donates proton to leaving group, general base: activates water metal ligand -- binding,
proton relay -- reactant 		ISS
90 Thr (T) side chain binds phosphate moiety of substrate, activates water activation -- spectator,
substrate binding -- binding 		ISS
124 Lys (K) side chain positions nucleophilic Asp, coordinates anionic groups of substrate steric role -- spectator,
substrate binding -- binding 		ISS
134 Asp (D) side chain positions Lys steric role -- spectator ISS
135 Asp (D) side chain Mg2+ ligand metal ligand -- binding ICS

Structures

PDB ID Title Molecule Name Number of
EFDs		 Resolution (Å) Mutant? Het group Links
3BWV Crystal Structure Of Deoxyribonucleotidase-Like Protein (Np_764060.1) From Staphylococcus Epidermidis Atcc 12228 At 1.55 A Resolution Putative 5'(3')-Deoxyribonucleotidase 3 1.55 Selenomethionine
(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, 5:33 a.m. update curation agent sbrown setDomainBoundaries.py
update domain start position 2 1
EC number assigned by UniProtKB accession ID.