Top Level Name

  ⌊ Superfamily (core) Haloacid Dehalogenase

  ⌊ FunctionalDomain uncharacterized haloacid dehalogenase superfamily sequence (ID 470839)

Superfamily Assignment Evidence Code(s) IEA
This entry was last updated onFeb. 13, 2017

References to Other Databases

Genbank

SpeciesGIAccessionProteome
Macaca nemestrina Taxon ID: 9545 795400525 XP_011755509.1 (RefSeq)
Cercocebus torquatus atys Taxon ID: 9531 795399936 XP_011942606.1 (RefSeq)
Macaca fascicularis Taxon ID: 9541 544497411 XP_005583077.1 (RefSeq) URP

Sequence

Length of Enzyme (full-length): 234 | Length of Functional Domain: 201

1       10        20        30        40        50        60

MIQPGGWCARRLCSAAVPAGRRGAAGGQGLAGGRALRVLVDMDGVLADFEGGFLRKFRAR
FPDQPFIALEDRRGFWVSEQYGRLRPGLSEKAISIWESKNFFFELEPLPGAVEAVKEMAN
LQNTDVFICTSPIKMFKYCPYEKYAWVEKHFGPDFLEQIVLTRDKTVVSADLLIDDRPDI
TGKWPAAGAEPTPSWEHVLFTACHNQHLQLQPPRRRLHSWADDWKAILDSKRPC
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
41 Asp (D) side chain nucleophile: forms covalent intermediate covalent catalysis -- reactant ISS

Structures

PDB ID Title Molecule Name Number of
EFDs		 Resolution (Å) Mutant? Het group Links
4MUM Crystal Structure Of Mitochondrial 5'(3')-Deoxy Ribonucleotidase Alternative Spliced Variant Mitochondrial 5' Nucleotidase 10 1.27 Magnesium Ion
(6 more ⇓) 		CSA • PDB • PDBSum
1Q91 Crystal Structure Of Human Mitochondrial Deoxyribonucleotidase In Complex With The Inhibitor Dpb-T 5(3)-Deoxyribonucleotidase 10 1.6 Phosphate Ion
(2 more ⇓) 		CSA • PDB • PDBSum
1MH9 Crystal Structure Analysis Of Deoxyribonucleotidase Deoxyribonucleotidase 10 1.8 Phosphate Ion • Magnesium Ion CSA • PDB • PDBSum
1Q92 Crystal Structure Of Human Mitochondrial Deoxyribonucleotidase In Complex With The Inhibitor Pmcp-U 5(3)-Deoxyribonucleotidase 10 1.4 Magnesium Ion
(2 more ⇓) 		CSA • PDB • PDBSum
1Z4I Structure Of The D41N Variant Of The Human Mitochondrial Deoxyribonucleotidase In Complex With Deoxyribouridine 5'-Monophosphate 5'(3')-Deoxyribonucleotidase 10 1.98 Yes Magnesium Ion
(2 more ⇓) 		CSA • PDB • PDBSum
1Z4K Structure Of The D41N Variant Of The Human Mitochondrial Deoxyribonucleotidase In Complex With Thymidine 3'-Monophosphate 5'(3')-Deoxyribonucleotidase 10 1.75 Yes Magnesium Ion • Thymidine-3'-Phosphate CSA • PDB • PDBSum
1Z4J Structure Of The D41N Variant Of The Human Mitochondrial Deoxyribonucleotidase In Complex With Uridine 2'-Monophosphate 5'(3')-Deoxyribonucleotidase 10 1.8 Yes Magnesium Ion
(2 more ⇓) 		CSA • PDB • PDBSum
1Z4M Structure Of The D41N Variant Of The Human Mitochondrial Deoxyribonucleotidase In Complex With Uridine 5'-Monophosphate 5'(3')-Deoxyribonucleotidase 10 1.7 Yes Magnesium Ion
(2 more ⇓) 		CSA • PDB • PDBSum
1Z4L Structure Of The D41N Variant Of The Human Mitochondrial Deoxyribonucleotidase In Complex With Thymidine 5'-Monophosphate 5'(3')-Deoxyribonucleotidase 10 1.8 Yes Magnesium Ion • Thymidine-5'-Phosphate CSA • PDB • PDBSum
2JAW Crystal Structure Of D41N Variant Of Human Mitochondrial 5' (3')-Deoxyribonucleotidase (Mdn) In Complex With 5-Bromovinyldeoxyuridine 5'-Monophosphate 5'(3')-Deoxyribonucleotidase 10 1.95 Yes (E)-5-(2-Bromovinyl)-2'-Deoxyuridine-5'-Monophosphate • Magnesium Ion CSA • PDB • PDBSum
2JAU Crystal Structure Of D41N Variant Of Human Mitochondrial 5' (3')-Deoxyribonucleotidase (Mdn) In Complex With 3'-Azidothymidine 5'-Monophosphate 5'(3')-Deoxyribonucleotidase 10 1.8 Yes Phosphate Ion
(2 more ⇓) 		CSA • PDB • PDBSum
1Z4Q Structure Of The D41N Variant Of The Human Mitochondrial Deoxyribonucleotidase In Complex With 2',3'-Dideoxy-2',3-Didehydrothymidine 5'-Monophosphate (D4T-Mp) 5'(3')-Deoxyribonucleotidase 10 2.05 Yes Magnesium Ion • [(5R)-5-(5-Methyl-2,4-Dioxo-3,4-Dihydropyrimidin-1(2H)-Yl)-2,5-Dihydrofuran-2-Yl]Methyl Dihydrogen Phosphate CSA • PDB • PDBSum
1Z4P Structure Of The D41N Variant Of The Human Mitochondrial Deoxyribonucleotidase In Complex With Deoxyriboguanosine 5'-Monophosphate 5'(3')-Deoxyribonucleotidase 10 2.0 Yes Magnesium Ion • 2'-Deoxyguanosine-5'-Monophosphate CSA • PDB • PDBSum
4L6A Structure Of Human Mitochondrial 5'(3')-Deoxyribonucleotidase 5'(3')-Deoxyribonucleotidase, Mitochondrial 10 1.4 Magnesium Ion
(4 more ⇓) 		CSA • PDB • PDBSum
4NFL Crystal Structure Of Human Mitochondrial 5'(3')-Deoxyribonucleotidase In Complex With The Inhibitor Npb-T 5'(3')-Deoxyribonucleotidase, Mitochondrial 10 1.38 Magnesium Ion
(5 more ⇓) 		CSA • PDB • PDBSum
4MWO Crystal Structure Of Human Mitochondrial 5'(3')-Deoxyribonucleotidase In Complex With The Inhibitor Cpb-T 5'(3')-Deoxyribonucleotidase, Mitochondrial 10 1.67 1-{3,5-O-[(4-Carboxyphenyl)(Phosphono)Methylidene]-2-Deoxy-Beta-D-Threo-Pentofuranosyl}-5-Methylpyrimidine-2,4(1H,3H)-Dione
(3 more ⇓) 		CSA • PDB • PDBSum
4L6C Crystal Structure Of Human Mitochondrial Deoxyribonucleotidase In Complex With The Inhibitor Pib-T 5'(3')-Deoxyribonucleotidase, Mitochondrial 10 1.8 Magnesium Ion
(4 more ⇓) 		CSA • PDB • PDBSum
4YIK Crystal Structure Of Human Cytosolic 5'(3')-Deoxyribonucleotidase In Complex With The Inhibitor Pb-Pvu 5'(3')-Deoxyribonucleotidase, Mitochondrial 5 1.48 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, 3:02 p.m. update curation agent updateSuperfamily.py setDomainBoundaries.py
EC number assigned by UniProtKB accession ID.