35NBP_CHRVO
ID 35NBP_CHRVO Reviewed; 285 AA.
AC Q7NXD4;
DT 16-SEP-2015, integrated into UniProtKB/Swiss-Prot.
DT 15-DEC-2003, sequence version 1.
DT 03-AUG-2022, entry version 108.
DE RecName: Full=3',5'-nucleoside bisphosphate phosphatase {ECO:0000303|PubMed:24401123};
DE EC=3.1.3.97 {ECO:0000269|PubMed:24401123};
GN OrderedLocusNames=CV_1693 {ECO:0000312|EMBL:AAQ59368.1};
OS Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / NBRC
OS 12614 / NCIMB 9131 / NCTC 9757).
OC Bacteria; Proteobacteria; Betaproteobacteria; Neisseriales;
OC Chromobacteriaceae; Chromobacterium.
OX NCBI_TaxID=243365;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC
RC 9757 {ECO:0000312|Proteomes:UP000001424};
RX PubMed=14500782; DOI=10.1073/pnas.1832124100;
RA Vasconcelos A.T.R., de Almeida D.F., Hungria M., Guimaraes C.T.,
RA Antonio R.V., Almeida F.C., de Almeida L.G.P., de Almeida R.,
RA Alves-Gomes J.A., Andrade E.M., Araripe J., de Araujo M.F.F.,
RA Astolfi-Filho S., Azevedo V., Baptista A.J., Bataus L.A.M., Batista J.S.,
RA Belo A., van den Berg C., Bogo M., Bonatto S., Bordignon J., Brigido M.M.,
RA Brito C.A., Brocchi M., Burity H.A., Camargo A.A., Cardoso D.D.P.,
RA Carneiro N.P., Carraro D.M., Carvalho C.M.B., Cascardo J.C.M., Cavada B.S.,
RA Chueire L.M.O., Creczynski-Pasa T.B., Cunha-Junior N.C., Fagundes N.,
RA Falcao C.L., Fantinatti F., Farias I.P., Felipe M.S.S., Ferrari L.P.,
RA Ferro J.A., Ferro M.I.T., Franco G.R., Freitas N.S.A., Furlan L.R.,
RA Gazzinelli R.T., Gomes E.A., Goncalves P.R., Grangeiro T.B.,
RA Grattapaglia D., Grisard E.C., Hanna E.S., Jardim S.N., Laurino J.,
RA Leoi L.C.T., Lima L.F.A., Loureiro M.F., Lyra M.C.C.P., Madeira H.M.F.,
RA Manfio G.P., Maranhao A.Q., Martins W.S., di Mauro S.M.Z.,
RA de Medeiros S.R.B., Meissner R.V., Moreira M.A.M., Nascimento F.F.,
RA Nicolas M.F., Oliveira J.G., Oliveira S.C., Paixao R.F.C., Parente J.A.,
RA Pedrosa F.O., Pena S.D.J., Pereira J.O., Pereira M., Pinto L.S.R.C.,
RA Pinto L.S., Porto J.I.R., Potrich D.P., Ramalho-Neto C.E., Reis A.M.M.,
RA Rigo L.U., Rondinelli E., Santos E.B.P., Santos F.R., Schneider M.P.C.,
RA Seuanez H.N., Silva A.M.R., da Silva A.L.C., Silva D.W., Silva R.,
RA Simoes I.C., Simon D., Soares C.M.A., Soares R.B.A., Souza E.M.,
RA Souza K.R.L., Souza R.C., Steffens M.B.R., Steindel M., Teixeira S.R.,
RA Urmenyi T., Vettore A., Wassem R., Zaha A., Simpson A.J.G.;
RT "The complete genome sequence of Chromobacterium violaceum reveals
RT remarkable and exploitable bacterial adaptability.";
RL Proc. Natl. Acad. Sci. U.S.A. 100:11660-11665(2003).
RN [2] {ECO:0007744|PDB:2YB1, ECO:0007744|PDB:2YB4}
RP X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) IN COMPLEX WITH AMP AND MANGANESE,
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, AND
RP SUBUNIT.
RX PubMed=24401123; DOI=10.1021/bi401640r;
RA Cummings J.A., Vetting M., Ghodge S.V., Xu C., Hillerich B., Seidel R.D.,
RA Almo S.C., Raushel F.M.;
RT "Prospecting for unannotated enzymes: discovery of a 3',5'-nucleotide
RT bisphosphate phosphatase within the amidohydrolase superfamily.";
RL Biochemistry 53:591-600(2014).
CC -!- FUNCTION: Hydrolyzes 3',5'-bisphosphonucleosides (pGp, pCp, pUp, and
CC pIp) to nucleoside 5'-phosphate and orthophosphate. Has similar
CC catalytic efficiencies with all the bases. Also shows activity with
CC ribonucleoside 2'-deoxyribonucleoside 3',5'-bisphosphates. Does not
CC show activity with nucleoside 2',5'-bisphosphates.
CC {ECO:0000269|PubMed:24401123}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a ribonucleoside 3',5'-bisphosphate + H2O = a ribonucleoside
CC 5'-phosphate + phosphate; Xref=Rhea:RHEA:43532, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:58043, ChEBI:CHEBI:83402; EC=3.1.3.97;
CC Evidence={ECO:0000269|PubMed:24401123};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:24401123};
CC Note=Binds 3 Mn(2+) ions per subunit. {ECO:0000269|PubMed:24401123};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=15.5 uM for pAp {ECO:0000269|PubMed:24401123};
CC KM=10.2 uM for 2'-deoxy-pAp {ECO:0000269|PubMed:24401123};
CC KM=14 uM for pCp {ECO:0000269|PubMed:24401123};
CC KM=26 uM for 2'-deoxy-pCp {ECO:0000269|PubMed:24401123};
CC KM=17.3 uM for pGp {ECO:0000269|PubMed:24401123};
CC KM=5.2 uM for 2'-deoxy-pGp {ECO:0000269|PubMed:24401123};
CC KM=8.8 uM for pUp {ECO:0000269|PubMed:24401123};
CC KM=29 uM for 2'-deoxy-pUp {ECO:0000269|PubMed:24401123};
CC KM=9.3 uM for pTp {ECO:0000269|PubMed:24401123};
CC KM=22 uM for 2'-deoxy-pIp {ECO:0000269|PubMed:24401123};
CC KM=1.6 uM for pApA {ECO:0000269|PubMed:24401123};
CC KM=5.4 uM for N(6)-methyl-3',5'-pAp {ECO:0000269|PubMed:24401123};
CC Note=kcat is 22 sec(-1) for pAp. kcat is 7.1 sec(-1) for 2'-deoxy-
CC pAp. kcat is 8.6 sec(-1) for pCp. kcat is 9.4 sec(-1) for 2'-deoxy-
CC pCp. kcat is 12.3 sec(-1) for pGp. kcat is 4.2 sec(-1) for 2'-deoxy-
CC pGp. kcat is 5.4 sec(-1) for pUp. kcat is 5.2 sec(-1) for 2'-deoxy-
CC pUp. kcat is 3.3 sec(-1) for pTp. kcat is 4.3 sec(-1) for 2'-deoxy-
CC pIp. kcat is 0.05 sec(-1) for pApA. kcat is 11.6 sec(-1) for N(6)-
CC methyl-3',5'-pAp. {ECO:0000269|PubMed:24401123};
CC -!- SUBUNIT: Monomer. {ECO:0000305|PubMed:24401123}.
CC -!- SIMILARITY: Belongs to the PHP family. {ECO:0000305}.
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DR EMBL; AE016825; AAQ59368.1; -; Genomic_DNA.
DR RefSeq; WP_011135245.1; NC_005085.1.
DR PDB; 2YB1; X-ray; 1.90 A; A=1-285.
DR PDB; 2YB4; X-ray; 2.20 A; A=1-285.
DR PDBsum; 2YB1; -.
DR PDBsum; 2YB4; -.
DR AlphaFoldDB; Q7NXD4; -.
DR SMR; Q7NXD4; -.
DR STRING; 243365.CV_1693; -.
DR EnsemblBacteria; AAQ59368; AAQ59368; CV_1693.
DR KEGG; cvi:CV_1693; -.
DR eggNOG; COG0613; Bacteria.
DR HOGENOM; CLU_067347_0_0_4; -.
DR OMA; CTWGGAT; -.
DR OrthoDB; 1309717at2; -.
DR BRENDA; 3.1.3.7; 1370.
DR SABIO-RK; Q7NXD4; -.
DR Proteomes; UP000001424; Chromosome.
DR GO; GO:0097657; F:3',5'-nucleotide bisphosphate phosphatase activity; IDA:UniProtKB.
DR GO; GO:0030145; F:manganese ion binding; IDA:UniProtKB.
DR GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
DR GO; GO:0016311; P:dephosphorylation; IDA:UniProtKB.
DR InterPro; IPR004013; PHP_dom.
DR InterPro; IPR003141; Pol/His_phosphatase_N.
DR InterPro; IPR016195; Pol/histidinol_Pase-like.
DR Pfam; PF02811; PHP; 1.
DR SMART; SM00481; POLIIIAc; 1.
DR SUPFAM; SSF89550; SSF89550; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Hydrolase; Manganese; Metal-binding; Nucleotide-binding;
KW Reference proteome.
FT CHAIN 1..285
FT /note="3',5'-nucleoside bisphosphate phosphatase"
FT /id="PRO_0000433638"
FT BINDING 7
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:24401123,
FT ECO:0007744|PDB:2YB1"
FT BINDING 9
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:24401123,
FT ECO:0007744|PDB:2YB1"
FT BINDING 14
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:24401123,
FT ECO:0007744|PDB:2YB1"
FT BINDING 14
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:24401123,
FT ECO:0007744|PDB:2YB1"
FT BINDING 39
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:24401123,
FT ECO:0007744|PDB:2YB1"
FT BINDING 39
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:24401123,
FT ECO:0007744|PDB:2YB1"
FT BINDING 64
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:24401123,
FT ECO:0007744|PDB:2YB1"
FT BINDING 64
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="3"
FT /evidence="ECO:0000269|PubMed:24401123,
FT ECO:0007744|PDB:2YB1"
FT BINDING 75
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="3"
FT /evidence="ECO:0000269|PubMed:24401123,
FT ECO:0007744|PDB:2YB1"
FT BINDING 99..102
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:24401123,
FT ECO:0007744|PDB:2YB1"
FT BINDING 134..135
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:24401123,
FT ECO:0007744|PDB:2YB1"
FT BINDING 191
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="3"
FT /evidence="ECO:0000269|PubMed:24401123,
FT ECO:0007744|PDB:2YB1"
FT BINDING 248
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:24401123,
FT ECO:0007744|PDB:2YB1"
FT BINDING 250
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:24401123,
FT ECO:0007744|PDB:2YB1"
FT BINDING 250
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:24401123,
FT ECO:0007744|PDB:2YB1"
FT TURN 11..14
FT /evidence="ECO:0007829|PDB:2YB1"
FT HELIX 19..27
FT /evidence="ECO:0007829|PDB:2YB1"
FT STRAND 32..36
FT /evidence="ECO:0007829|PDB:2YB1"
FT HELIX 45..54
FT /evidence="ECO:0007829|PDB:2YB1"
FT STRAND 59..69
FT /evidence="ECO:0007829|PDB:2YB1"
FT STRAND 72..80
FT /evidence="ECO:0007829|PDB:2YB1"
FT HELIX 86..96
FT /evidence="ECO:0007829|PDB:2YB1"
FT HELIX 99..112
FT /evidence="ECO:0007829|PDB:2YB1"
FT HELIX 118..123
FT /evidence="ECO:0007829|PDB:2YB1"
FT HELIX 129..131
FT /evidence="ECO:0007829|PDB:2YB1"
FT HELIX 134..143
FT /evidence="ECO:0007829|PDB:2YB1"
FT STRAND 146..149
FT /evidence="ECO:0007829|PDB:2YB1"
FT HELIX 150..156
FT /evidence="ECO:0007829|PDB:2YB1"
FT STRAND 157..159
FT /evidence="ECO:0007829|PDB:2YB1"
FT HELIX 173..182
FT /evidence="ECO:0007829|PDB:2YB1"
FT STRAND 186..189
FT /evidence="ECO:0007829|PDB:2YB1"
FT HELIX 192..194
FT /evidence="ECO:0007829|PDB:2YB1"
FT HELIX 199..211
FT /evidence="ECO:0007829|PDB:2YB1"
FT STRAND 216..221
FT /evidence="ECO:0007829|PDB:2YB1"
FT HELIX 226..239
FT /evidence="ECO:0007829|PDB:2YB1"
FT STRAND 242..246
FT /evidence="ECO:0007829|PDB:2YB1"
FT HELIX 272..275
FT /evidence="ECO:0007829|PDB:2YB1"
FT HELIX 277..279
FT /evidence="ECO:0007829|PDB:2YB1"
FT STRAND 283..285
FT /evidence="ECO:0007829|PDB:2YB4"
SQ SEQUENCE 285 AA; 30456 MW; 5BA7E0385B6AD657 CRC64;
MANIDLHFHS RTSDGALTPT EVIDRAAARA PALLALTDHD CTGGLAEAAA AAARRGIPFL
NGVEVSVSWG RHTVHIVGLG IDPAEPALAA GLKSIREGRL ERARQMGASL EAAGIAGCFD
GAMRWCDNPE MISRTHFARH LVDSGAVKDM RTVFRKYLTP GKPGYVSHQW ASLEDAVGWI
VGAGGMAVIA HPGRYDMGRT LIERLILDFQ AAGGQGIEVA SGSHSLDDMH KFALHADRHG
LYASSGSDFH APGEGGRDVG HTEDLPPICR PIWRELEARI LRPAD
