P936_METJA
ID P936_METJA Reviewed; 166 AA.
AC Q58346;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 126.
DE RecName: Full=Phosphodiesterase MJ0936;
DE EC=3.1.4.-;
GN OrderedLocusNames=MJ0936;
OS Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM
OS 10045 / NBRC 100440) (Methanococcus jannaschii).
OC Archaea; Euryarchaeota; Methanomada group; Methanococci; Methanococcales;
OC Methanocaldococcaceae; Methanocaldococcus.
OX NCBI_TaxID=243232;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440;
RX PubMed=8688087; DOI=10.1126/science.273.5278.1058;
RA Bult C.J., White O., Olsen G.J., Zhou L., Fleischmann R.D., Sutton G.G.,
RA Blake J.A., FitzGerald L.M., Clayton R.A., Gocayne J.D., Kerlavage A.R.,
RA Dougherty B.A., Tomb J.-F., Adams M.D., Reich C.I., Overbeek R.,
RA Kirkness E.F., Weinstock K.G., Merrick J.M., Glodek A., Scott J.L.,
RA Geoghagen N.S.M., Weidman J.F., Fuhrmann J.L., Nguyen D., Utterback T.R.,
RA Kelley J.M., Peterson J.D., Sadow P.W., Hanna M.C., Cotton M.D.,
RA Roberts K.M., Hurst M.A., Kaine B.P., Borodovsky M., Klenk H.-P.,
RA Fraser C.M., Smith H.O., Woese C.R., Venter J.C.;
RT "Complete genome sequence of the methanogenic archaeon, Methanococcus
RT jannaschii.";
RL Science 273:1058-1073(1996).
RN [2] {ECO:0007744|PDB:1S3L, ECO:0007744|PDB:1S3M, ECO:0007744|PDB:1S3N}
RP X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF 1-165 OF NATIVE PROTEIN AND IN
RP COMPLEXES WITH NICKEL AND MANGANESE, FUNCTION, COFACTOR, AND
RP BIOPHYSICOCHEMICAL PROPERTIES.
RC STRAIN=ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440;
RX PubMed=15128743; DOI=10.1074/jbc.m401059200;
RA Chen S., Yakunin A.F., Kuznetsova E., Busso D., Pufan R., Proudfoot M.,
RA Kim R., Kim S.-H.;
RT "Structural and functional characterization of a novel phosphodiesterase
RT from Methanococcus jannaschii.";
RL J. Biol. Chem. 279:31854-31862(2004).
CC -!- FUNCTION: Shows phosphodiesterase activity, hydrolyzing phosphodiesters
CC bonds in the artificial chromogenic substrates bis-p-nitrophenyl
CC phosphate (bis-pNPP), and less efficiently thymidine 5'-monophosphate
CC p-nitrophenyl ester (pNP-TMP) and p-nitrophenylphosphorylcholine
CC (pNPPC). No catalytic activity was found toward cAMP or cGMP,
CC nucleotides or phospholipase substrates such as phosphatidylcholine.
CC The physiological substrate is unknown. {ECO:0000269|PubMed:15128743}.
CC -!- COFACTOR:
CC Name=Ni(2+); Xref=ChEBI:CHEBI:49786;
CC Evidence={ECO:0000269|PubMed:15128743};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:15128743};
CC Note=Binds 2 divalent metal ions per subunit. Most effective are nickel
CC and manganese. {ECO:0000269|PubMed:15128743};
CC -!- ACTIVITY REGULATION: Competitively inhibited by phosphate.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.15 mM for bis-pNPP (in the presence of Ni(2+))
CC {ECO:0000269|PubMed:15128743};
CC KM=0.035 mM for pNP-TMP (in the presence of Ni(2+))
CC {ECO:0000269|PubMed:15128743};
CC KM=3.33 mM for pNPPC (in the presence of Ni(2+))
CC {ECO:0000269|PubMed:15128743};
CC KM=1.53 mM for pNPPC (in the presence of Mn(2+))
CC {ECO:0000269|PubMed:15128743};
CC pH dependence:
CC Optimum pH is 9.4-9.8. {ECO:0000269|PubMed:15128743};
CC -!- SUBUNIT: Monomer. {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the metallophosphoesterase superfamily. YfcE
CC family. {ECO:0000305}.
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DR EMBL; L77117; AAB98941.1; -; Genomic_DNA.
DR PIR; H64416; H64416.
DR RefSeq; WP_010870450.1; NC_000909.1.
DR PDB; 1S3L; X-ray; 2.40 A; A/B=1-165.
DR PDB; 1S3M; X-ray; 2.50 A; A/B=1-165.
DR PDB; 1S3N; X-ray; 2.50 A; A/B=1-165.
DR PDB; 2AHD; X-ray; 3.00 A; A/B/C/D=1-165.
DR PDBsum; 1S3L; -.
DR PDBsum; 1S3M; -.
DR PDBsum; 1S3N; -.
DR PDBsum; 2AHD; -.
DR AlphaFoldDB; Q58346; -.
DR SMR; Q58346; -.
DR STRING; 243232.MJ_0936; -.
DR EnsemblBacteria; AAB98941; AAB98941; MJ_0936.
DR GeneID; 1451832; -.
DR KEGG; mja:MJ_0936; -.
DR eggNOG; arCOG01141; Archaea.
DR HOGENOM; CLU_063749_4_0_2; -.
DR InParanoid; Q58346; -.
DR OMA; IHCGDFV; -.
DR OrthoDB; 78782at2157; -.
DR PhylomeDB; Q58346; -.
DR BRENDA; 3.1.4.1; 3260.
DR SABIO-RK; Q58346; -.
DR EvolutionaryTrace; Q58346; -.
DR Proteomes; UP000000805; Chromosome.
DR GO; GO:0110165; C:cellular anatomical entity; IEA:UniProt.
DR GO; GO:0016787; F:hydrolase activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR CDD; cd00841; MPP_YfcE; 1.
DR Gene3D; 3.60.21.10; -; 1.
DR InterPro; IPR024654; Calcineurin-like_PHP_lpxH.
DR InterPro; IPR029052; Metallo-depent_PP-like.
DR InterPro; IPR041802; MPP_YfcE.
DR InterPro; IPR020935; PdiEstase_YfcE_CS.
DR InterPro; IPR000979; Phosphodiesterase_MJ0936/Vps29.
DR Pfam; PF12850; Metallophos_2; 1.
DR SUPFAM; SSF56300; SSF56300; 1.
DR TIGRFAMs; TIGR00040; yfcE; 1.
DR PROSITE; PS01269; UPF0025; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Hydrolase; Manganese; Metal-binding; Nickel;
KW Reference proteome.
FT CHAIN 1..166
FT /note="Phosphodiesterase MJ0936"
FT /id="PRO_0000155612"
FT BINDING 8
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:15128743,
FT ECO:0007744|PDB:1S3N"
FT BINDING 8
FT /ligand="Ni(2+)"
FT /ligand_id="ChEBI:CHEBI:49786"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:15128743,
FT ECO:0007744|PDB:1S3M"
FT BINDING 10
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:15128743,
FT ECO:0007744|PDB:1S3N"
FT BINDING 10
FT /ligand="Ni(2+)"
FT /ligand_id="ChEBI:CHEBI:49786"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:15128743,
FT ECO:0007744|PDB:1S3M"
FT BINDING 36
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:15128743,
FT ECO:0007744|PDB:1S3N"
FT BINDING 36
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:15128743,
FT ECO:0007744|PDB:1S3N"
FT BINDING 36
FT /ligand="Ni(2+)"
FT /ligand_id="ChEBI:CHEBI:49786"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:15128743,
FT ECO:0007744|PDB:1S3M"
FT BINDING 36
FT /ligand="Ni(2+)"
FT /ligand_id="ChEBI:CHEBI:49786"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:15128743,
FT ECO:0007744|PDB:1S3M"
FT BINDING 59
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:15128743,
FT ECO:0007744|PDB:1S3N"
FT BINDING 59
FT /ligand="Ni(2+)"
FT /ligand_id="ChEBI:CHEBI:49786"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:15128743,
FT ECO:0007744|PDB:1S3M"
FT BINDING 97
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:15128743,
FT ECO:0007744|PDB:1S3N"
FT BINDING 97
FT /ligand="Ni(2+)"
FT /ligand_id="ChEBI:CHEBI:49786"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:15128743,
FT ECO:0007744|PDB:1S3M"
FT BINDING 120
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:15128743,
FT ECO:0007744|PDB:1S3N"
FT BINDING 120
FT /ligand="Ni(2+)"
FT /ligand_id="ChEBI:CHEBI:49786"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:15128743,
FT ECO:0007744|PDB:1S3M"
FT BINDING 122
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:15128743,
FT ECO:0007744|PDB:1S3N"
FT BINDING 122
FT /ligand="Ni(2+)"
FT /ligand_id="ChEBI:CHEBI:49786"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:15128743,
FT ECO:0007744|PDB:1S3M"
FT STRAND 2..6
FT /evidence="ECO:0007829|PDB:1S3L"
FT HELIX 13..25
FT /evidence="ECO:0007829|PDB:1S3L"
FT STRAND 29..33
FT /evidence="ECO:0007829|PDB:1S3L"
FT HELIX 41..45
FT /evidence="ECO:0007829|PDB:1S3L"
FT HELIX 46..48
FT /evidence="ECO:0007829|PDB:1S3L"
FT STRAND 50..56
FT /evidence="ECO:0007829|PDB:1S3L"
FT HELIX 64..74
FT /evidence="ECO:0007829|PDB:1S3L"
FT STRAND 79..88
FT /evidence="ECO:0007829|PDB:1S3L"
FT STRAND 91..98
FT /evidence="ECO:0007829|PDB:1S3L"
FT HELIX 101..110
FT /evidence="ECO:0007829|PDB:1S3L"
FT STRAND 114..119
FT /evidence="ECO:0007829|PDB:1S3L"
FT STRAND 125..129
FT /evidence="ECO:0007829|PDB:1S3L"
FT STRAND 132..136
FT /evidence="ECO:0007829|PDB:1S3L"
FT TURN 143..145
FT /evidence="ECO:0007829|PDB:1S3L"
FT STRAND 149..154
FT /evidence="ECO:0007829|PDB:1S3L"
FT TURN 155..158
FT /evidence="ECO:0007829|PDB:1S3L"
FT STRAND 159..164
FT /evidence="ECO:0007829|PDB:1S3L"
SQ SEQUENCE 166 AA; 19039 MW; 1F92D7A501EEA315 CRC64;
MKIGIMSDTH DHLPNIRKAI EIFNDENVET VIHCGDFVSL FVIKEFENLN ANIIATYGNN
DGERCKLKEW LKDINEENII DDFISVEIDD LKFFITHGHH QSVLEMAIKS GLYDVVIYGH
THERVFEEVD DVLVINPGEC CGYLTGIPTI GILDTEKKEY REIVLE
