Table 1.
Microbial enzymes with 5'-nucleotidase activity
| Cellular location | Protein family | The catalytic mechanism/initial phosphoryl acceptor | Source | Protein (Accession number) | Substrates | Metal ion requirement | References |
|---|---|---|---|---|---|---|---|
| Membrane-bound / cell wall-anchored, surface-located | N-terminal calcineurin-like phosphoesterase domain (Metallophos; PF00149) and C-terminal 5´-nucleotidase (5'_nucleotid_C; PF02872) domain | Type I / a water molecule | Staphylococcus aureus (G +) | AdsA (UshA) (WP_061821283) | AMP, ADP, ATP, dAMP, GDP, GTP | Mg2+, Mn2+ | Thammavongsa et al. 2011 |
| Streptococcus sanguinis (G +) | Nt5e (AFK32764) | AMP, ADP, ATP | Mg2+, Ca2+ | Fan et al. 2012 | |||
| Streptococcus agalactiae (G +) | NudP (CDN66659) | (d)NMP, (d)NDP, but not (d)NTP | Mn2+ | Firon et al. 2014 | |||
| Streptococcus equi subsp. zooepidemicus (G +) | 5Nuc (AEJ25391) | AMP, ADP, ATP, dAMP | Mg2+, Ca2+ | Ma et al. 2016 | |||
| Streptococcus pyogenes (G +) | S5nA (Q9A0A2) | AMP, ADP, dAMP, CMP, GMP, but not ATP | Mg2+, Mn2+, Ca2+ | Zheng et al. 2015 | |||
| Streptococcus suis (G +) | Ssads (CAR45827) | AMP, ADP, ATP | Mn2+ | Liu et al. 2014 | |||
| Streptococcus iniae (G +) | S5nAi (WP_003099850) | ADP, AMP, dAMP, GMP, CMP, TMP, but not ATP | Mg2+, Mn2+, Ca2+ | Soh et al. 2018 | |||
| Bacillus anthracis (G +) | AdsA (Q6HTQ7) | dAMP | Mn2+ | Thammavongsa et al. 2009 | |||
| Vibrio parahaemolyticus (G −) | NutA (UshA) (P22848) | AMP, ADP, ATP | Cl−, Mg2+, Mn2+, Co2+ | Itami et al. 1989; Sakai et al. 1987 | |||
| Vibrio (Salinivibrio) costicola (G −) | UshA (WP_102505627) | NMP, NDP, NTP | Cl- | Bengis-Garber and Kushner 1981 | |||
| Shewanella violacea (G −) | UshA (WP_041419915) | AMP, ATP, GTP | Mg2+, Mn2+ | Kuribayashi et al. 2017 | |||
| Shewanella amazonensis (G −) | UshA (WP_011760134) | ||||||
| Class C acid phosphatase (cd07534); belong to HAD-like superfamily (IPR036412) | Type II / nucleophilic amino acid residue | Helicobacter pylori (G −) | HppA (Q6UC93) | NMP | Cu2+, Ni2+, Co2+, Mg2+ | Reilly and Calcutt 2004 | |
| Clostridium perfringens (G +) | CppA (ACB11490) | UMP, GMP, AMP, 3′ TMP, ATP, 3′ AMP, FMN, R5P, pyridoxal phosphate, ADP, 2′ AMP, NADP | Cu2+, Co2+, Cr2+ | Reilly et al. 2009 | |||
| Chryseobacterium meningosepticum (Elizabethkingia meningoseptica) (G −) | OlpA (O08351) | NMP, 3′ AMP | Cu2+, Mg2+ | Passariello et al. 2003 | |||
| Haemophilus influenzae (G −) | Lipoprotein Hel [e (P4)] (WP_118891437) | Aryl phosphates | Cu2+ | Reilly et al. 1999 | |||
| Phosphoesterase family (PF04185), consists of two domains: alkaline-phosphatase-like, core domain superfamily (IPR017850) and Phosphoesterase (IPR007312) | Type II / nucleophilic amino acid residue |
Francisella tularensis (G −) |
AcpA (WP_003027314) | NMP, NTP, NDP, FMN, NMN, NADP etc | Me2+ | Mohapatra et al. 2007; Reilly et al. 2006 | |
| Periplasmic | N-terminal calcineurin-like phosphoesterase domain (Metallophos; PF00149) and C-terminal 5´-nucleotidase (5'_nucleotid_C; PF02872) domain | Type I / a water molecule | Escherichia coli (G −) | UshA (P07024) | (d)NTP, bis(5'-nucleosidyl)polyphosphates, UDP sugars, CDP-alcohols, NAD(H) | Zn2+, Co2+or Mg2+, depending on type of hydrolase activity | Alves-Pereira et al. 2008; Ruiz 1989; Glaser et al. 1967; Neu 1967; Wang et al. 2014 |
| Vibrio cholerae (G −) | UshA (Q9KQ30) | dNTP | - | McDonough et al. 2016 | |||
| Yersinia intermedia (G −) | UshA (A4URQ8) | (d)NTP, bis(5'-nucleosidyl)polyphosphates, UDP sugars, CDP-alcohols | Co2+ or Mg2+, depending on the type of hydrolase activity | Alves-Pereira et al. 2008; Neu 1967 | |||
| Shewanella oneidensis (G −) | UshA (Q8EFH1) | FAD, AMP | - | Covington et al. 2010 | |||
| Haemophilus influenzae (G −) | NadN (P44569) | AMP, NAD + , UDP sugars | Zn2 + | Garavaglia et al. 2011 | |||
| Klebsiella aerogenes (Enterobacter aerogenes) (G −) | UshA (A0A0H3FPS2) | UDP sugars | - | Lee et al. 2000 | |||
| Class A acid phosphatase (IPR001011) | Type II / nucleophilic amino acid residue | Morganella morganii (Proteus morganii) (G −) | PhoC (P28581) | UMP, AMP, 3’-UMP, 3’-AMP | - | Thaller et al. 1994 | |
| Acid phosphatase class B-like (IPR005519) or HAD superfamily, subfamily IIIB (acid phosphatase) (PF03767) | Morganella morganii (Proteus morganii) (G −) | NapA (AphA) (Q59544) | NMP, 3’ NMP, aryl phosphates, β-glycerophosphate, sugar phosphates, but not on diesters | Mg2+, Co2+, Zn2+ | Thaller et al. 1995 | ||
| Salmonella enterica (G −) | AphA (QQL85243) | UMP, 3' -UMP, pNPP and a-naphthyl phosphate, but not diesters | Mg2+, Co2+, Zn2+ | Uerkvitz and Beck 1981 | |||
| Escherichia coli (G −) | AphA (P0AE22) | 3'-(d)NMP, (d)NMP | Mg2+ | Thaller et al. 1997 | |||
| Alkaline phosphatase (PF00245) | Escherichia coli (G −) | PhoA (P00634) | Wide variety of phosphate monoesters, including 5´-ribo- and 5´-deoxyribonucleotides | Mg2+, Zn2+ | Garen and Levinthal 1960 | ||
| Extracellular | N-terminal calcineurin-like phosphoesterase domain (Metallophos; PF00149) and C-terminal 5´-nucleotidase (5'_nucleotid_C; PF02872) domain | Type I / a water molecule | Corynebacterium glutamicum (G +) | UshA (WP_011896359) | GMP, IMP, XMP, AMP, UMP, CMP, ADP, ATP, dATP | Co2+, Ca2+, Mg2+, depending on the type of hydrolase activity | Rittmann et al. 2005 |
| PRK09419 Superfamily (multifunctional 2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase/5'-nucleotidase), contains N-terminal calcineurin-like phosphoesterase domain (Metallophos; PF00149) and C-terminal 5´-nucleotidase (5'_nucleotid_C; PF02872) domain | Bacillus subtilis (G +) | YfkN (BAA23404.1) | 3´-nucleotides, 2′3'-cyclic-nucleotides and 5'-nucleotides | - | Chambert et al. 2003 | ||
| Intracellular | HAD-superfamily hydrolase, subfamily IIA (IPR006357) | Type II / nucleophilic amino acid residue | Escherichia coli (G −) | YigB (P0ADP0) | 5-amino-6-(5-phospho-D-ribitylamino)uracil, FMN | Mg2+ | Haase et al. 2013; Kuznetsova et al. 2006 |
| Bacillus subtilis (G +) | YutF (NucF) (WP_003243196) | R5P, XMP, PRPP, IMP, GMP, dGMP, dIMP | Mg2+ | Zakataeva et al. 2016 | |||
| Escherichia coli (G −) | UmpH (NagD) (C3TJ42) | UMP, GMP, (d)NTP, G1P | Mg2+ | Kuznetsova et al. 2006; Tremblay et al. 2006 | |||
| HAD-superfamily hydrolase, subfamily IA (IPR006439) | Escherichia coli (G −) | YjjG (P0A8Y1) | dTMP, dUMP, UMP, non-canonical pyrimidine derivatives (5-fluoro-2′-deoxyuridine, 5-fluorouridine, 5-fluoroorotic acid, 5-fluorouracil etc.) | Mn2+, Mg2+ | Kuznetsova et al., 2006; Proudfoot et al. 2004; Titz et al. 2007 | ||
| Bacillus subtilis (G +) | YitU (P70947) | FMN, ARPP, (d)NMP (dAMP, GMP, dGMP, CMP, AMP, XMP, IMP), AICAR-P | Mg2+ | Sarge et al. 2015; Yusupova et al. 2020 | |||
| HAD-superfamily hydrolase, subfamily IIB (IPR006379) | Bacillus subtilis (G +) | YcsE (P42962) | ARPP, FMN, IMP, AMP, GMP, CMP, UMP, G6P | Mg2+ | Sarge et al. 2015; Terakawa 2016 | ||
| HAD-superfamily hydrolase, subfamily IG, 5'-nucleotidase (IPR008380) | Legionella pneumophila (G −) | cN-II (Q5ZZB6) | GMP, dGMP, IMP, pNPP | Mg2+ | Srinivasan et al. 2014 | ||
| HD-domain phosphohydrolases (PF01966) | Type I / a water molecule | Escherichia coli (G −) | YfbR (P76491) | dNMP | Co2+, Mn2+, Cu2+ | Proudfoot et al. 2004; Zimmerman et al. 2008 | |
| SurE family (PF01975) or survival protein SurE (IPR030048) | Type I / a water molecule | Escherichia coli (G −) | UmpG (SurE) (P0A840) | (d) NMP, 3′-AMP, polyphosphates with the preference for short-chain-length substrates (P20–25) | Mn2+, Co2+, Ni2+, Mg2+ | Proudfoot et al. 2004 |
The abbreviations used are NMN, nicotinamide mononucleotide; FMN, flavin mononucleotide, NADP, nicotinamide adenine dinucleotide phosphate; FAD, flavin adenine dinucleotide; AICAR-P, 5-aminoimidazole-4-carboxamide-1-β-D-ribofuranosyl 5′-monophosphate; ARPP, 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione 5'-phosphate; G1P, glucose 1-phosphate; G6P, glucose 6-phosphate; R5P, ribose 5-phosphate; PRPP, 5-phosphoribosyl 1-pyrophosphate; pNPP, p-nitrophenyl phosphate; (d)NMP/(d)NDP/(d)NTP, ribonucleoside or deoxyribonucleoside mono-, di- and triphosphates. The accession numbers correspond to the UniProt or NCBI databases; (G −) and (G +)—gram-negative and gram-positive bacteria; –—not found