PHNZ_UNCHF
ID PHNZ_UNCHF Reviewed; 190 AA.
AC D0E8I5;
DT 10-OCT-2018, integrated into UniProtKB/Swiss-Prot.
DT 24-NOV-2009, sequence version 1.
DT 03-AUG-2022, entry version 47.
DE RecName: Full=2-amino-1-hydroxyethylphosphonate dioxygenase (glycine-forming) {ECO:0000303|PubMed:22564006};
DE EC=1.13.11.78 {ECO:0000269|PubMed:22564006, ECO:0000269|PubMed:24198335, ECO:0000269|PubMed:24706911};
DE AltName: Full=Di-iron oxygenase {ECO:0000303|PubMed:24706911};
DE AltName: Full=Nonheme iron-dependent oxygenase {ECO:0000303|PubMed:24706911};
GN Name=phnZ {ECO:0000303|PubMed:19788654};
GN ORFNames=ALOHA_HF130_AEPn_1_06c {ECO:0000312|EMBL:ACU83550.1};
OS Uncultured bacterium HF130_AEPn_1.
OC Bacteria; environmental samples.
OX NCBI_TaxID=663362;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND FUNCTION.
RX PubMed=19788654; DOI=10.1111/j.1462-2920.2009.02062.x;
RA Martinez A., Tyson G.W., DeLong E.F.;
RT "Widespread known and novel phosphonate utilization pathways in marine
RT bacteria revealed by functional screening and metagenomic analyses.";
RL Environ. Microbiol. 12:222-238(2010).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, ACTIVITY REGULATION, AND REACTION
RP MECHANISM.
RX PubMed=22564006; DOI=10.1021/ja302072f;
RA McSorley F.R., Wyatt P.B., Martinez A., DeLong E.F., Hove-Jensen B.,
RA Zechel D.L.;
RT "PhnY and PhnZ comprise a new oxidative pathway for enzymatic cleavage of a
RT carbon-phosphorus bond.";
RL J. Am. Chem. Soc. 134:8364-8367(2012).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS) IN COMPLEX WITH IRON IONS AND
RP SUBSTRATE, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, SUBUNIT, AND REACTION
RP MECHANISM.
RX PubMed=24198335; DOI=10.1073/pnas.1315927110;
RA Worsdorfer B., Lingaraju M., Yennawar N.H., Boal A.K., Krebs C.,
RA Bollinger J.M., Pandelia M.E.;
RT "Organophosphonate-degrading PhnZ reveals an emerging family of HD domain
RT mixed-valent diiron oxygenases.";
RL Proc. Natl. Acad. Sci. U.S.A. 110:18874-18879(2013).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) IN COMPLEX WITH IRON IONS AND
RP SUBSTRATE, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES,
RP MUTAGENESIS OF TYR-24; GLU-27; HIS-34; HIS-58; ASP-59; HIS-62; HIS-80;
RP HIS-104 AND ASP-161, COFACTOR, SUBUNIT, SUBSTRATE SPECIFICITY, AND REACTION
RP MECHANISM.
RX PubMed=24706911; DOI=10.1073/pnas.1320039111;
RA van Staalduinen L.M., McSorley F.R., Schiessl K., Seguin J., Wyatt P.B.,
RA Hammerschmidt F., Zechel D.L., Jia Z.;
RT "Crystal structure of PhnZ in complex with substrate reveals a di-iron
RT oxygenase mechanism for catabolism of organophosphonates.";
RL Proc. Natl. Acad. Sci. U.S.A. 111:5171-5176(2014).
CC -!- FUNCTION: Involved in the degradation of the organophosphonate 2-
CC aminoethylphosphonic acid (2-AEP) (Probable). Catalyzes the cleavage of
CC the carbon-phosphorus bond of (2-amino-1-hydroxyethyl)phosphonic acid
CC to yield glycine and phosphate through an oxidative mechanism
CC (PubMed:22564006, PubMed:24198335, PubMed:24706911). It reacts
CC stereospecifically with the R-enantiomer of (2-amino-1-
CC hydroxyethyl)phosphonic acid and is also able to use (R,R)-2-amino-1-
CC hydroxypropylphosphonate as substrate (PubMed:24706911).
CC {ECO:0000269|PubMed:22564006, ECO:0000269|PubMed:24198335,
CC ECO:0000269|PubMed:24706911, ECO:0000305|PubMed:19788654}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(1R)-(2-amino-1-hydroxyethyl)phosphonate + O2 = glycine + 2
CC H(+) + phosphate; Xref=Rhea:RHEA:41444, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:15379, ChEBI:CHEBI:43474, ChEBI:CHEBI:57305,
CC ChEBI:CHEBI:141612; EC=1.13.11.78;
CC Evidence={ECO:0000269|PubMed:22564006, ECO:0000269|PubMed:24198335,
CC ECO:0000269|PubMed:24706911};
CC -!- COFACTOR:
CC Name=Fe cation; Xref=ChEBI:CHEBI:24875;
CC Evidence={ECO:0000269|PubMed:22564006, ECO:0000269|PubMed:24198335,
CC ECO:0000269|PubMed:24706911};
CC Note=Binds 2 iron ions per subunit. During catalysis, PhnZ uses a
CC mixed-valent Fe(2+)/Fe(3+) cofactor. {ECO:0000269|PubMed:24198335,
CC ECO:0000269|PubMed:24706911};
CC -!- ACTIVITY REGULATION: Inhibited by EDTA. {ECO:0000269|PubMed:22564006}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.16 mM for (R,R)-2-amino-1-hydroxypropylphosphonic acid
CC {ECO:0000269|PubMed:24706911};
CC KM=0.17 mM for (R)-2-amino-1-hydroxyethylphosphonic acid
CC {ECO:0000269|PubMed:24706911};
CC Note=kcat is 11 min(-1) for (R)-2-amino-1-hydroxyethylphosphonic acid
CC as substrate. kcat is 7 min(-1) for (R,R)-2-amino-1-
CC hydroxypropylphosphonic acid as substrate.
CC {ECO:0000269|PubMed:24706911};
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:24198335,
CC ECO:0000269|PubMed:24706911}.
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DR EMBL; GQ422594; ACU83550.1; -; Genomic_DNA.
DR PDB; 4MLM; X-ray; 1.70 A; A/B=1-190.
DR PDB; 4MLN; X-ray; 2.10 A; A/B=1-190.
DR PDB; 4N6W; X-ray; 1.85 A; A=1-190.
DR PDB; 4N71; X-ray; 2.98 A; A/B/D/E=1-190.
DR PDBsum; 4MLM; -.
DR PDBsum; 4MLN; -.
DR PDBsum; 4N6W; -.
DR PDBsum; 4N71; -.
DR AlphaFoldDB; D0E8I5; -.
DR SMR; D0E8I5; -.
DR KEGG; ag:ACU83550; -.
DR BioCyc; MetaCyc:MON-18485; -.
DR BRENDA; 1.13.11.78; 744.
DR GO; GO:0016787; F:hydrolase activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0016491; F:oxidoreductase activity; IEA:UniProtKB-KW.
DR CDD; cd00077; HDc; 1.
DR InterPro; IPR003607; HD/PDEase_dom.
DR InterPro; IPR006674; HD_domain.
DR InterPro; IPR006675; HDIG_dom.
DR Pfam; PF01966; HD; 1.
DR TIGRFAMs; TIGR00277; HDIG; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Hydrolase; Iron; Metal-binding; Oxidoreductase.
FT CHAIN 1..190
FT /note="2-amino-1-hydroxyethylphosphonate dioxygenase
FT (glycine-forming)"
FT /id="PRO_0000445271"
FT BINDING 24
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:24706911,
FT ECO:0007744|PDB:4MLM, ECO:0007744|PDB:4MLN"
FT BINDING 27
FT /ligand="(1R)-(2-amino-1-hydroxyethyl)phosphonate"
FT /ligand_id="ChEBI:CHEBI:141612"
FT /evidence="ECO:0000269|PubMed:24198335,
FT ECO:0007744|PDB:4N71"
FT BINDING 34
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:24198335,
FT ECO:0000269|PubMed:24706911, ECO:0007744|PDB:4MLM,
FT ECO:0007744|PDB:4MLN, ECO:0007744|PDB:4N6W,
FT ECO:0007744|PDB:4N71"
FT BINDING 58
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:24198335,
FT ECO:0000269|PubMed:24706911, ECO:0007744|PDB:4MLM,
FT ECO:0007744|PDB:4MLN, ECO:0007744|PDB:4N6W,
FT ECO:0007744|PDB:4N71"
FT BINDING 59
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:24198335,
FT ECO:0000269|PubMed:24706911, ECO:0007744|PDB:4MLM,
FT ECO:0007744|PDB:4MLN, ECO:0007744|PDB:4N6W,
FT ECO:0007744|PDB:4N71"
FT BINDING 59
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:24198335,
FT ECO:0000269|PubMed:24706911, ECO:0007744|PDB:4MLM,
FT ECO:0007744|PDB:4MLN, ECO:0007744|PDB:4N6W,
FT ECO:0007744|PDB:4N71"
FT BINDING 62
FT /ligand="(1R)-(2-amino-1-hydroxyethyl)phosphonate"
FT /ligand_id="ChEBI:CHEBI:141612"
FT /evidence="ECO:0000269|PubMed:24198335,
FT ECO:0000269|PubMed:24706911, ECO:0007744|PDB:4MLM,
FT ECO:0007744|PDB:4MLN, ECO:0007744|PDB:4N6W,
FT ECO:0007744|PDB:4N71"
FT BINDING 80
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:24198335,
FT ECO:0000269|PubMed:24706911, ECO:0007744|PDB:4MLM,
FT ECO:0007744|PDB:4MLN, ECO:0007744|PDB:4N6W,
FT ECO:0007744|PDB:4N71"
FT BINDING 104
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:24198335,
FT ECO:0000269|PubMed:24706911, ECO:0007744|PDB:4MLM,
FT ECO:0007744|PDB:4MLN, ECO:0007744|PDB:4N6W,
FT ECO:0007744|PDB:4N71"
FT BINDING 108
FT /ligand="(1R)-(2-amino-1-hydroxyethyl)phosphonate"
FT /ligand_id="ChEBI:CHEBI:141612"
FT /evidence="ECO:0000269|PubMed:24198335,
FT ECO:0000269|PubMed:24706911, ECO:0007744|PDB:4MLM,
FT ECO:0007744|PDB:4MLN, ECO:0007744|PDB:4N6W,
FT ECO:0007744|PDB:4N71"
FT BINDING 126..133
FT /ligand="(1R)-(2-amino-1-hydroxyethyl)phosphonate"
FT /ligand_id="ChEBI:CHEBI:141612"
FT /evidence="ECO:0000269|PubMed:24198335,
FT ECO:0000269|PubMed:24706911, ECO:0007744|PDB:4MLM,
FT ECO:0007744|PDB:4MLN, ECO:0007744|PDB:4N6W,
FT ECO:0007744|PDB:4N71"
FT BINDING 158
FT /ligand="(1R)-(2-amino-1-hydroxyethyl)phosphonate"
FT /ligand_id="ChEBI:CHEBI:141612"
FT /evidence="ECO:0000269|PubMed:24198335,
FT ECO:0000269|PubMed:24706911, ECO:0007744|PDB:4MLM,
FT ECO:0007744|PDB:4MLN, ECO:0007744|PDB:4N6W,
FT ECO:0007744|PDB:4N71"
FT BINDING 161
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:24198335,
FT ECO:0000269|PubMed:24706911, ECO:0007744|PDB:4MLM,
FT ECO:0007744|PDB:4MLN, ECO:0007744|PDB:4N6W,
FT ECO:0007744|PDB:4N71"
FT SITE 27
FT /note="Important for stereospecificity with the R-
FT enantiomer"
FT /evidence="ECO:0000269|PubMed:24706911"
FT MUTAGEN 24
FT /note="Y->E: Slight decrease of the catalytic efficiency
FT and of the affinity for (R)-2-amino-1-
FT hydroxyethylphosphonic acid."
FT /evidence="ECO:0000269|PubMed:24706911"
FT MUTAGEN 24
FT /note="Y->F: Slight decrease of the catalytic efficiency
FT and of the affinity for (R)-2-amino-1-
FT hydroxyethylphosphonic acid. 3-fold decrease of the Fe-
FT enzyme molar ratios."
FT /evidence="ECO:0000269|PubMed:24706911"
FT MUTAGEN 27
FT /note="E->A: 4-fold decrease of the catalytic efficiency
FT and 3-fold decrease of the affinity for (R)-2-amino-1-
FT hydroxyethylphosphonic acid. 6-fold decrease of the Fe-
FT enzyme molar ratios."
FT /evidence="ECO:0000269|PubMed:24706911"
FT MUTAGEN 34
FT /note="H->A: Loss of dioxygenase activity."
FT /evidence="ECO:0000269|PubMed:24706911"
FT MUTAGEN 58
FT /note="H->A: Loss of dioxygenase activity."
FT /evidence="ECO:0000269|PubMed:24706911"
FT MUTAGEN 59
FT /note="D->A: Loss of dioxygenase activity."
FT /evidence="ECO:0000269|PubMed:24706911"
FT MUTAGEN 62
FT /note="H->A: 6-fold decrease of the catalytic efficiency
FT and 2.5-fold decrease of the affinity for (R)-2-amino-1-
FT hydroxyethylphosphonic acid."
FT /evidence="ECO:0000269|PubMed:24706911"
FT MUTAGEN 80
FT /note="H->A: 3-fold decrease of the catalytic efficiency
FT and 3.5-fold decrease of the affinity for (R)-2-amino-1-
FT hydroxyethylphosphonic acid. 2.5-fold decrease of the Fe-
FT enzyme molar ratios."
FT /evidence="ECO:0000269|PubMed:24706911"
FT MUTAGEN 104
FT /note="H->A: Loss of dioxygenase activity."
FT /evidence="ECO:0000269|PubMed:24706911"
FT MUTAGEN 161
FT /note="D->A: Loss of dioxygenase activity."
FT /evidence="ECO:0000269|PubMed:24706911"
FT HELIX 5..18
FT /evidence="ECO:0007829|PDB:4MLM"
FT HELIX 19..21
FT /evidence="ECO:0007829|PDB:4MLM"
FT STRAND 22..25
FT /evidence="ECO:0007829|PDB:4MLM"
FT TURN 26..28
FT /evidence="ECO:0007829|PDB:4MLM"
FT HELIX 31..44
FT /evidence="ECO:0007829|PDB:4MLM"
FT HELIX 49..57
FT /evidence="ECO:0007829|PDB:4MLM"
FT TURN 58..61
FT /evidence="ECO:0007829|PDB:4MLM"
FT HELIX 66..72
FT /evidence="ECO:0007829|PDB:4MLM"
FT TURN 75..77
FT /evidence="ECO:0007829|PDB:4MLM"
FT HELIX 80..91
FT /evidence="ECO:0007829|PDB:4MLM"
FT HELIX 95..102
FT /evidence="ECO:0007829|PDB:4MLM"
FT HELIX 104..114
FT /evidence="ECO:0007829|PDB:4MLM"
FT HELIX 116..121
FT /evidence="ECO:0007829|PDB:4MLM"
FT HELIX 124..129
FT /evidence="ECO:0007829|PDB:4MLM"
FT HELIX 130..132
FT /evidence="ECO:0007829|PDB:4MLM"
FT HELIX 139..147
FT /evidence="ECO:0007829|PDB:4MLM"
FT HELIX 151..163
FT /evidence="ECO:0007829|PDB:4MLM"
FT HELIX 174..177
FT /evidence="ECO:0007829|PDB:4MLM"
FT HELIX 178..187
FT /evidence="ECO:0007829|PDB:4MLM"
SQ SEQUENCE 190 AA; 21586 MW; 34F63C582F08EBB5 CRC64;
MSLSNSSKVS VLISLLEKSR DLDYIGEAIN QLEHSLQCAY FAQRSGADNE MVLAALLHDL
GHYCNDTSFE DMGGYGVWQH EKVGADYLRG LGFSERVACL IEGHVAAKRY LVSSKASYLK
NLSDASRKTL EYQGGPMDEG ERRLFEERED FKDCLKIRAW DEKGKQTDLK VPGPEHYRKM
MEEHLSENQN
