RLPMH_RHIL3
ID RLPMH_RHIL3 Reviewed; 514 AA.
AC Q1M964;
DT 20-DEC-2017, integrated into UniProtKB/Swiss-Prot.
DT 30-MAY-2006, sequence version 1.
DT 03-AUG-2022, entry version 97.
DE RecName: Full=Multifunctional alkaline phosphatase superfamily protein pRL90232 {ECO:0000305};
DE AltName: Full=Phosphodiesterase {ECO:0000303|PubMed:18793651};
DE EC=3.1.4.- {ECO:0000269|PubMed:18793651};
DE AltName: Full=Phosphonate monoester hydrolase {ECO:0000303|PubMed:18793651};
DE Short=RlPMH {ECO:0000303|PubMed:18793651};
DE EC=3.1.3.- {ECO:0000269|PubMed:18793651};
GN OrderedLocusNames=pRL90232 {ECO:0000312|EMBL:CAK03956.1};
OS Rhizobium leguminosarum bv. viciae (strain 3841).
OG Plasmid pRL9 {ECO:0000312|EMBL:CAK03956.1,
OG ECO:0000312|Proteomes:UP000006575}.
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Rhizobiaceae; Rhizobium/Agrobacterium group; Rhizobium.
OX NCBI_TaxID=216596 {ECO:0000312|EMBL:CAK03956.1};
RN [1] {ECO:0000312|EMBL:CAK03956.1, ECO:0000312|Proteomes:UP000006575}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=3841 {ECO:0000312|EMBL:CAK03956.1,
RC ECO:0000312|Proteomes:UP000006575};
RX PubMed=16640791; DOI=10.1186/gb-2006-7-4-r34;
RA Young J.P.W., Crossman L.C., Johnston A.W.B., Thomson N.R., Ghazoui Z.F.,
RA Hull K.H., Wexler M., Curson A.R.J., Todd J.D., Poole P.S., Mauchline T.H.,
RA East A.K., Quail M.A., Churcher C., Arrowsmith C., Cherevach I.,
RA Chillingworth T., Clarke K., Cronin A., Davis P., Fraser A., Hance Z.,
RA Hauser H., Jagels K., Moule S., Mungall K., Norbertczak H.,
RA Rabbinowitsch E., Sanders M., Simmonds M., Whitehead S., Parkhill J.;
RT "The genome of Rhizobium leguminosarum has recognizable core and accessory
RT components.";
RL Genome Biol. 7:R34.1-R34.20(2006).
RN [2] {ECO:0007744|PDB:2VQR}
RP X-RAY CRYSTALLOGRAPHY (1.42 ANGSTROMS) IN COMPLEX WITH CALCIUM OR
RP MANGANESE, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL
RP PROPERTIES, SUBSTRATE SPECIFICITY, REACTION MECHANISM, SUBUNIT, OXOALANINE
RP AT CYS-57, ACTIVE SITE, AND MUTAGENESIS OF GLN-13; CYS-57; ASN-78; TYR-105;
RP THR-107; HIS-218 AND LYS-337.
RC STRAIN=3841 {ECO:0000303|PubMed:18793651};
RX PubMed=18793651; DOI=10.1016/j.jmb.2008.08.072;
RA Jonas S., van Loo B., Hyvonen M., Hollfelder F.;
RT "A new member of the alkaline phosphatase superfamily with a formylglycine
RT nucleophile: structural and kinetic characterisation of a phosphonate
RT monoester hydrolase/phosphodiesterase from Rhizobium leguminosarum.";
RL J. Mol. Biol. 384:120-136(2008).
CC -!- FUNCTION: Hydrolytic enzyme with a broad substrate specificity acting
CC on phosphate diesters and phosphonate monoesters.
CC {ECO:0000269|PubMed:18793651}.
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:18793651};
CC Note=Mn(2+) is probably the active metal ion. Other metals such as Zn,
CC Ca and Fe can also act as cofactors. {ECO:0000303|PubMed:18793651};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=3.0 mM for phosphonate monoester p-nitrophenyl phenyl phosphonate
CC (at 30 degrees Celsius and pH 7.5) {ECO:0000269|PubMed:18793651};
CC KM=2.3 mM for phosphate diester p-nitrophenyl ethyl phosphate (at 30
CC degrees Celsius and pH 7.5) {ECO:0000269|PubMed:18793651};
CC Note=kcat is 16 sec(-1) with p-nitrophenyl phenyl phosphonate as
CC substrate. kcat is 9.5 sec(-1) with p-nitrophenyl ethyl phosphate as
CC substrate. {ECO:0000269|PubMed:18793651};
CC pH dependence:
CC Optimum pH is 7.5. {ECO:0000269|PubMed:18793651};
CC -!- SUBUNIT: Homotetramer. {ECO:0000269|PubMed:18793651}.
CC -!- PTM: The conversion to 3-oxoalanine (also known as C-formylglycine,
CC FGly), of a serine or cysteine residue in prokaryotes and of a cysteine
CC residue in eukaryotes, is critical for catalytic activity.
CC {ECO:0000255|PIRSR:PIRSR600917-51, ECO:0000269|PubMed:18793651}.
CC -!- SIMILARITY: Belongs to the alkaline phosphatase superfamily.
CC {ECO:0000303|PubMed:18793651}.
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DR EMBL; AM236083; CAK03956.1; -; Genomic_DNA.
DR RefSeq; WP_011649751.1; NC_008379.1.
DR PDB; 2VQR; X-ray; 1.42 A; A=1-514.
DR PDBsum; 2VQR; -.
DR AlphaFoldDB; Q1M964; -.
DR SMR; Q1M964; -.
DR EnsemblBacteria; CAK03956; CAK03956; pRL90232.
DR KEGG; rle:pRL90232; -.
DR HOGENOM; CLU_006332_9_2_5; -.
DR OMA; VHYEEAM; -.
DR OrthoDB; 1067869at2; -.
DR EvolutionaryTrace; Q1M964; -.
DR Proteomes; UP000006575; Plasmid pRL9.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0008484; F:sulfuric ester hydrolase activity; IEA:InterPro.
DR Gene3D; 3.40.720.10; -; 1.
DR InterPro; IPR017850; Alkaline_phosphatase_core_sf.
DR InterPro; IPR032506; DUF4976.
DR InterPro; IPR000917; Sulfatase_N.
DR Pfam; PF16347; DUF4976; 1.
DR Pfam; PF00884; Sulfatase; 1.
DR SUPFAM; SSF53649; SSF53649; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Calcium; Hydrolase; Manganese; Metal-binding; Plasmid.
FT CHAIN 1..514
FT /note="Multifunctional alkaline phosphatase superfamily
FT protein pRL90232"
FT /id="PRO_0000442719"
FT ACT_SITE 57
FT /note="Nucleophile"
FT /evidence="ECO:0000269|PubMed:18793651"
FT BINDING 12
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000269|PubMed:18793651,
FT ECO:0007744|PDB:2VQR"
FT BINDING 57
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /note="via 3-oxoalanine"
FT /evidence="ECO:0000269|PubMed:18793651"
FT BINDING 324
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000269|PubMed:18793651,
FT ECO:0007744|PDB:2VQR"
FT BINDING 325
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000269|PubMed:18793651,
FT ECO:0007744|PDB:2VQR"
FT MOD_RES 57
FT /note="3-oxoalanine (Cys)"
FT /evidence="ECO:0000255|PIRSR:PIRSR600917-51,
FT ECO:0000269|PubMed:18793651"
FT MUTAGEN 13
FT /note="Q->A: Kcat increases 1.6-fold and affinity reduces
FT 14-fold with phosphonate monoester as substrate. kcat
FT increases 1.9-fold and affinity reduces 21.7-fold with
FT phosphate diester as substrate."
FT MUTAGEN 57
FT /note="C->A: Kcat reduces 1818-fold and affinity increases
FT 1.1-fold with phosphonate monoester as substrate. kcat
FT reduces 2021-fold and affinity reduces 1.3-fold with
FT phosphate diester as substrate."
FT MUTAGEN 57
FT /note="C->S: Kcat reduces 4.8-fold and affinity reduces
FT 1.3-fold with phosphonate monoester as substrate. kcat
FT reduces 5.9-fold and affinity increases 1.4-fold with
FT phosphate diester as substrate."
FT MUTAGEN 78
FT /note="N->A: Kcat reduces 10.7-fold and affinity reduces
FT 1.3-fold with phosphonate monoester as substrate. kcat
FT reduces 8.6-fold and affinity reduces 19.6-fold with
FT phosphate diester as substrate."
FT MUTAGEN 105
FT /note="Y->A: Kcat reduces 5.9-fold and affinity reduces
FT 9.3-fold with phosphonate monoester as substrate. kcat
FT reduces over 55.9-fold and affinity reduces over 30.4-fold
FT with phosphate diester as substrate."
FT MUTAGEN 107
FT /note="T->A: Kcat reduces 6.7-fold and affinity increases
FT 9.7-fold with phosphonate monoester as substrate. kcat
FT reduces 16.7-fold and affinity reduces 2.1-fold with
FT phosphate diester as substrate."
FT MUTAGEN 218
FT /note="H->A: Kcat reduces 16.0-fold and affinity reduces 5-
FT fold with phosphonate monoester as substrate. kcat reduces
FT 31.7-fold and affinity reduces 24.8-fold with phosphate
FT diester as substrate."
FT MUTAGEN 337
FT /note="K->A: Kcat reduces 1.3-fold and affinity reduces
FT 4.7-fold with phosphonate monoester as substrate. kcat
FT reduces 3.3-fold and affinity reduces 31.7-fold with
FT phosphate diester as substrate."
SQ SEQUENCE 514 AA; 58054 MW; 43F86726346FB4EB CRC64;
MRKKNVLLIV VDQWRADFVP HVLRADGKID FLKTPNLDRL CREGVTFRNH VTTCVPCGPA
RASLLTGLYL MNHRAVQNTV PLDQRHLNLG KALRGVGYDP ALIGYTTTVP DPRTTSPNDP
RFRVLGDLMD GFHPVGAFEP NMEGYFGWVA QNGFDLPEHR PDIWLPEGED AVAGATDRPS
RIPKEFSDST FFTERALTYL KGRDGKPFFL HLGYYRPHPP FVASAPYHAM YRPEDMPAPI
RAANPDIEAA QHPLMKFYVD SIRRGSFFQG AEGSGATLDE AELRQMRATY CGLITEVDDC
LGRVFSYLDE TGQWDDTLII FTSDHGEQLG DHHLLGKIGY NDPSFRIPLV IKDAGENARA
GAIESGFTES IDVMPTILDW LGGKIPHACD GLSLLPFLSE GRPQDWRTEL HYEYDFRDVY
YSEPQSFLGL GMNDCSLCVI QDERYKYVHF AALPPLFFDL RHDPNEFTNL ADDPAYAALV
RDYAQKALSW RLKHADRTLT HYRSGPEGLS ERSH
