Top Level Name

  ⌊ Superfamily (core) Haloacid Dehalogenase

    ⌊ Subgroup C1.2: Nucleotidase Like

  ⌊ C1.2.1

     ⌊ Family 5'-nucleotidase

  ⌊ FunctionalDomain 5'-nucleotidase (ID 2321)

Superfamily Assignment Evidence Code(s) ISS
Family Assignment Evidence Code CFM PubMed:12352955
This entry was last updated onNov. 22, 2017

References to Other Databases

Genbank

SpeciesGIAccessionProteome
Homo sapiens Taxon ID: 9606 48425255 PRP URP
Homo sapiens Taxon ID: 9606 48425254 PRP URP
Homo sapiens Taxon ID: 9606 24987754 PRP URP

Uniprot

Protein NameAccessionEC Number Identifier
5'(3')-deoxyribonucleotidase, mitochondrial Q9NPB1 3.1.3.- NT5M_HUMAN (Swiss-Prot)

Sequence

Length of Enzyme (full-length): 197 | Length of Functional Domain: 195

1       10        20        30        40        50        60

GGRALRVLVDMDGVLADFEGGFLRKFRARFPDQPFIALEDRRGFWVSEQYGRLRPGLSEK
AISIWESKNFFFELEPLPGAVEAVKEMASLQNTDVFICTSPIKMFKYCPYEKYAWVEKYF
GPDFLEQIVLTRDKTVVSADLLIDDRPDITGAEPTPSWEHVLFTACHNQHLQLQPPRRRL
HSWADDWKAILDSKRPC
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
10 Asp (D) side chain nucleophile: forms covalent intermediate covalent catalysis -- reactant ISS
Subgroup CAR This EFD conserves 6/6 Subgroup-specific Conserved Alignment Residues.
Position Amino Acid Location Function Role Evidence Code Reference
10 Asp (D) side chain Mg2+ ligand, nucleophile: attacks phosphate moiety of substrate to form covalent intermediate covalent catalysis -- reactant,
metal ligand -- binding 		ICS PubMed:12352955
12 Asp (D) side chain general acid: donates proton to leaving group, general base: activates water proton relay -- reactant ICS PubMed:12352955
99 Thr (T) side chain binds phosphate moiety of substrate, activates water activation -- spectator,
substrate binding -- binding 		ICS PubMed:12352955
134 Lys (K) side chain positions nucleophilic Asp, coordinates anionic groups of substrate steric role -- spectator,
substrate binding -- binding 		ICS PubMed:12352955
144 Asp (D) side chain positions Lys steric role -- spectator ICS PubMed:12352955
145 Asp (D) side chain Mg2+ ligand metal ligand -- binding ICS PubMed:12352955

Structures

PDB ID Title Molecule Name Number of
EFDs		 Resolution (Å) Mutant? Het group Links
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
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
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
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
4E88 Crystal Structure Of De Novo Designed Cysteine Esterase Ech13, Northeast Structural Genomics Consortium Target Or51 De Novo Designed Cysteine Esterase Ech13 4 2.0 Selenomethionine
(2 more ⇓) 		CSA • PDB • PDBSum
3U19 Crystal Structure Of Acylenzyme Intermediate Of De Novo Designed Cysteine Esterase Ech13, Northeast Structural Genomics Consortium Target Or51 Artificial Protein Or51 4 2.0 Selenomethionine
(2 more ⇓) 		CSA • PDB • PDBSum
3U13 Crystal Structure Of De Novo Design Of Cystein Esterase Ech13 At The Resolution 1.6A, Northeast Structural Genomics Consortium Target Or51 Artificial Protein Or51 4 1.6 Selenomethionine
(4 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, 5:15 a.m. update curation agent sbrown setDomainBoundaries.py
update domain end position 197 196
update domain start position 1 2
EC number assigned by UniProtKB accession ID.