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3',5'-cyclic adenosine monophosphate phosphodiesterase CpdA (3',5'-cyclic AMP phosphodiesterase) (cAMP phosphodiesterase) (EC 3.1.4.53)

 CPDA_MYCTU              Reviewed;         318 AA.
P9WP65; L0T7J7; O06629; Q7D993;
16-APR-2014, integrated into UniProtKB/Swiss-Prot.
16-APR-2014, sequence version 1.
28-MAR-2018, entry version 26.
RecName: Full=3',5'-cyclic adenosine monophosphate phosphodiesterase CpdA {ECO:0000255|HAMAP-Rule:MF_00905};
Short=3',5'-cyclic AMP phosphodiesterase {ECO:0000255|HAMAP-Rule:MF_00905};
Short=cAMP phosphodiesterase {ECO:0000255|HAMAP-Rule:MF_00905};
EC=3.1.4.53 {ECO:0000255|HAMAP-Rule:MF_00905};
Name=cpdA {ECO:0000255|HAMAP-Rule:MF_00905}; Synonyms=icc;
OrderedLocusNames=Rv0805;
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv).
Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
Mycobacterium; Mycobacterium tuberculosis complex.
NCBI_TaxID=83332;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 25618 / H37Rv;
PubMed=9634230; DOI=10.1038/31159;
Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M.,
Harris D.E., Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III,
Tekaia F., Badcock K., Basham D., Brown D., Chillingworth T.,
Connor R., Davies R.M., Devlin K., Feltwell T., Gentles S., Hamlin N.,
Holroyd S., Hornsby T., Jagels K., Krogh A., McLean J., Moule S.,
Murphy L.D., Oliver S., Osborne J., Quail M.A., Rajandream M.A.,
Rogers J., Rutter S., Seeger K., Skelton S., Squares S., Squares R.,
Sulston J.E., Taylor K., Whitehead S., Barrell B.G.;
"Deciphering the biology of Mycobacterium tuberculosis from the
complete genome sequence.";
Nature 393:537-544(1998).
[2]
FUNCTION, CATALYTIC ACTIVITY, COFACTOR, ENZYME REGULATION,
BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, MUTAGENESIS OF ASP-21; HIS-23;
ASP-66; ASN-97; HIS-169 AND HIS-207, AND HOMOLOGY MODELING.
PubMed=16313172; DOI=10.1021/bi0512391;
Shenoy A.R., Sreenath N., Podobnik M., Kovacevic M.,
Visweswariah S.S.;
"The Rv0805 gene from Mycobacterium tuberculosis encodes a 3',5'-
cyclic nucleotide phosphodiesterase: biochemical and mutational
analysis.";
Biochemistry 44:15695-15704(2005).
[3]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
STRAIN=ATCC 25618 / H37Rv;
PubMed=21969609; DOI=10.1074/mcp.M111.011627;
Kelkar D.S., Kumar D., Kumar P., Balakrishnan L., Muthusamy B.,
Yadav A.K., Shrivastava P., Marimuthu A., Anand S., Sundaram H.,
Kingsbury R., Harsha H.C., Nair B., Prasad T.S., Chauhan D.S.,
Katoch K., Katoch V.M., Kumar P., Chaerkady R., Ramachandran S.,
Dash D., Pandey A.;
"Proteogenomic analysis of Mycobacterium tuberculosis by high
resolution mass spectrometry.";
Mol. Cell. Proteomics 10:M111.011627-M111.011627(2011).
[4]
X-RAY CRYSTALLOGRAPHY (1.93 ANGSTROMS) OF 3-278 OF WILD-TYPE; MUTANT
ALA-66 AND MUTANT ALA-97 IN COMPLEXES WITH IRON AND MANGANESE,
COFACTOR, SUBUNIT, AND MUTAGENESIS OF HIS-140.
PubMed=17059828; DOI=10.1016/j.jmb.2006.10.005;
Shenoy A.R., Capuder M., Draskovic P., Lamba D., Visweswariah S.S.,
Podobnik M.;
"Structural and biochemical analysis of the Rv0805 cyclic nucleotide
phosphodiesterase from Mycobacterium tuberculosis.";
J. Mol. Biol. 365:211-225(2007).
[5]
X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) OF 2-318 IN COMPLEX WITH IRON;
MANGANESE AND AMP, FUNCTION, CATALYTIC ACTIVITY, COFACTOR,
BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, SUBCELLULAR LOCATION, DOMAIN,
AND MUTAGENESIS OF ASN-97; HIS-98; HIS-140; HIS-209 AND TYR-229.
PubMed=19801656; DOI=10.1074/jbc.M109.049635;
Podobnik M., Tyagi R., Matange N., Dermol U., Gupta A.K., Mattoo R.,
Seshadri K., Visweswariah S.S.;
"A mycobacterial cyclic AMP phosphodiesterase that moonlights as a
modifier of cell wall permeability.";
J. Biol. Chem. 284:32846-32857(2009).
-!- FUNCTION: Hydrolyzes cAMP to 5'-AMP. Plays an important regulatory
role in modulating the intracellular concentration of cAMP,
thereby influencing cAMP-dependent processes. Can also hydrolyze
cGMP, p-nitrophenyl phosphate (pNPP), bis-(p-nitrophenyl
phosphate) (bis(pNPP)), p-nitrophenyl phenylphosphonate (pNPPP)
and 2',3'-cAMP. May play a role in pathogenicity, not only by
hydrolyzing cAMP, but also by altering properties of the cell
wall. {ECO:0000255|HAMAP-Rule:MF_00905,
ECO:0000269|PubMed:16313172, ECO:0000269|PubMed:19801656}.
-!- CATALYTIC ACTIVITY: Adenosine 3',5'-cyclic phosphate + H(2)O =
adenosine 5'-phosphate. {ECO:0000255|HAMAP-Rule:MF_00905,
ECO:0000269|PubMed:16313172, ECO:0000269|PubMed:19801656}.
-!- COFACTOR:
Name=Fe(3+); Xref=ChEBI:CHEBI:29034;
Evidence={ECO:0000269|PubMed:16313172,
ECO:0000269|PubMed:17059828, ECO:0000269|PubMed:19801656};
Note=Binds 1 Fe(3+) ion per subunit. {ECO:0000269|PubMed:17059828,
ECO:0000269|PubMed:19801656};
-!- COFACTOR:
Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
Evidence={ECO:0000269|PubMed:16313172,
ECO:0000269|PubMed:17059828, ECO:0000269|PubMed:19801656};
Note=Binds 1 Mn(2+) ion per subunit. {ECO:0000269|PubMed:17059828,
ECO:0000269|PubMed:19801656};
-!- ENZYME REGULATION: Enhanced by magnesium or manganese. Activity
decreases in the presence of orthovanadate and phosphotyrosine.
{ECO:0000269|PubMed:16313172}.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=5.5 mM for 3',5'-cAMP {ECO:0000269|PubMed:19801656};
KM=0.9 mM for bis(pNPP) {ECO:0000269|PubMed:19801656};
KM=0.9 mM for pNPPP {ECO:0000269|PubMed:19801656};
KM=1 mM for 2',3'-cAMP {ECO:0000269|PubMed:19801656};
Vmax=1.1 umol/min/mg enzyme with 3',5'-cAMP as substrate
{ECO:0000269|PubMed:19801656};
Vmax=74 umol/min/mg enzyme with bis(pNPP) as substrate
{ECO:0000269|PubMed:19801656};
Vmax=112.7 umol/min/mg enzyme with pNPPP as substrate
{ECO:0000269|PubMed:19801656};
Vmax=14.7 umol/min/mg enzyme with 2',3'-cAMP as substrate
{ECO:0000269|PubMed:19801656};
Vmax=0.017 umol/min/mg enzyme with pNPP as substrate
{ECO:0000269|PubMed:19801656};
pH dependence:
Optimum pH is 8.5-9.5. {ECO:0000269|PubMed:16313172};
-!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:16313172,
ECO:0000269|PubMed:17059828, ECO:0000269|PubMed:19801656}.
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:19801656}.
Cell membrane {ECO:0000269|PubMed:19801656}. Secreted, cell wall
{ECO:0000269|PubMed:19801656}. Note=Localization to the cell
membrane and cell wall could be due to a specialized secretion
system operative in mycobacteria. {ECO:0000305|PubMed:19801656}.
-!- DOMAIN: The C-terminal domain is used to better adjust the
substrates into the active sites and to facilitate subcellular
localization of the protein. {ECO:0000269|PubMed:19801656}.
-!- SIMILARITY: Belongs to the cAMP phosphodiesterase class-III
family. {ECO:0000255|HAMAP-Rule:MF_00905}.
-----------------------------------------------------------------------
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EMBL; AL123456; CCP43553.1; -; Genomic_DNA.
PIR; F70536; F70536.
RefSeq; NP_215320.1; NC_000962.3.
RefSeq; WP_003404120.1; NZ_KK339370.1.
PDB; 2HY1; X-ray; 1.93 A; A=3-278.
PDB; 2HYO; X-ray; 2.25 A; A=3-278.
PDB; 2HYP; X-ray; 2.05 A; A=3-278.
PDB; 3IB7; X-ray; 1.60 A; A=2-318.
PDB; 3IB8; X-ray; 1.80 A; A=2-318.
PDBsum; 2HY1; -.
PDBsum; 2HYO; -.
PDBsum; 2HYP; -.
PDBsum; 3IB7; -.
PDBsum; 3IB8; -.
ProteinModelPortal; P9WP65; -.
SMR; P9WP65; -.
STRING; 83332.Rv0805; -.
PaxDb; P9WP65; -.
EnsemblBacteria; CCP43553; CCP43553; Rv0805.
GeneID; 885326; -.
KEGG; mtu:Rv0805; -.
TubercuList; Rv0805; -.
eggNOG; ENOG41070EG; Bacteria.
eggNOG; COG1409; LUCA.
KO; K03651; -.
OMA; CAWLDQH; -.
PhylomeDB; P9WP65; -.
Proteomes; UP000001584; Chromosome.
GO; GO:0005618; C:cell wall; IDA:MTBBASE.
GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
GO; GO:0005576; C:extracellular region; IEA:UniProtKB-KW.
GO; GO:0005886; C:plasma membrane; IEA:UniProtKB-SubCell.
GO; GO:0008663; F:2',3'-cyclic-nucleotide 2'-phosphodiesterase activity; IDA:MTBBASE.
GO; GO:0004115; F:3',5'-cyclic-AMP phosphodiesterase activity; IDA:MTBBASE.
GO; GO:0008199; F:ferric iron binding; IDA:MTBBASE.
GO; GO:0005506; F:iron ion binding; IDA:MTBBASE.
GO; GO:0030145; F:manganese ion binding; IDA:MTBBASE.
GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
GO; GO:0016791; F:phosphatase activity; IDA:MTBBASE.
GO; GO:0042301; F:phosphate ion binding; IDA:MTBBASE.
GO; GO:0006198; P:cAMP catabolic process; IDA:MTBBASE.
GO; GO:0042545; P:cell wall modification; IDA:MTBBASE.
GO; GO:0009405; P:pathogenesis; IMP:MTBBASE.
CDD; cd07402; MPP_GpdQ; 1.
Gene3D; 3.60.21.10; -; 1.
HAMAP; MF_00905; cAMP_phophodiest_CpdA; 1.
InterPro; IPR004843; Calcineurin-like_PHP_ApaH.
InterPro; IPR026575; cAMP_Pdiest_CpdA.
InterPro; IPR029052; Metallo-depent_PP-like.
Pfam; PF00149; Metallophos; 1.
1: Evidence at protein level;
3D-structure; cAMP; Cell membrane; Cell wall; Complete proteome;
Cytoplasm; Hydrolase; Iron; Manganese; Membrane; Metal-binding;
Nucleotide-binding; Reference proteome; Secreted.
CHAIN 1 318 3',5'-cyclic adenosine monophosphate
phosphodiesterase CpdA.
/FTId=PRO_0000413370.
NP_BIND 97 98 cAMP. {ECO:0000255|HAMAP-Rule:MF_00905,
ECO:0000305|PubMed:19801656}.
METAL 21 21 Iron. {ECO:0000269|PubMed:17059828,
ECO:0000269|PubMed:19801656}.
METAL 23 23 Iron. {ECO:0000269|PubMed:17059828,
ECO:0000269|PubMed:19801656}.
METAL 63 63 Iron. {ECO:0000269|PubMed:17059828,
ECO:0000269|PubMed:19801656}.
METAL 63 63 Manganese. {ECO:0000269|PubMed:17059828,
ECO:0000269|PubMed:19801656}.
METAL 97 97 Manganese. {ECO:0000269|PubMed:17059828,
ECO:0000269|PubMed:19801656}.
METAL 169 169 Manganese. {ECO:0000269|PubMed:17059828,
ECO:0000269|PubMed:19801656}.
METAL 207 207 Manganese. {ECO:0000269|PubMed:17059828,
ECO:0000269|PubMed:19801656}.
METAL 209 209 Iron. {ECO:0000269|PubMed:17059828,
ECO:0000269|PubMed:19801656}.
BINDING 23 23 cAMP. {ECO:0000255|HAMAP-Rule:MF_00905,
ECO:0000305|PubMed:19801656}.
BINDING 63 63 cAMP. {ECO:0000255|HAMAP-Rule:MF_00905,
ECO:0000305|PubMed:19801656}.
BINDING 209 209 cAMP. {ECO:0000255|HAMAP-Rule:MF_00905,
ECO:0000305|PubMed:19801656}.
MUTAGEN 21 21 D->A: 90% decrease in bis(pNPP)
hydrolysis. Does not affect cAMP
hydrolysis.
{ECO:0000269|PubMed:16313172}.
MUTAGEN 23 23 H->A: 50% decrease in bis(pNPP)
hydrolysis. Does not affect cAMP
hydrolysis.
{ECO:0000269|PubMed:16313172}.
MUTAGEN 66 66 D->A: 25% decrease in bis(pNPP)
hydrolysis. 70% decrease in cAMP
hydrolysis.
{ECO:0000269|PubMed:16313172}.
MUTAGEN 97 97 N->A: Loss of bis(pNPP) and 3',5'-cAMP
hydrolysis. Strong decrease in 2',3'-cAMP
hydrolysis. {ECO:0000269|PubMed:16313172,
ECO:0000269|PubMed:19801656}.
MUTAGEN 98 98 H->A: 40% decrease in bis(pNPP)
hydrolysis. Strong decrease in 3',5'-cAMP
and 2',3'-cAMP hydrolysis.
{ECO:0000269|PubMed:19801656}.
MUTAGEN 140 140 H->A: No change in activity.
{ECO:0000269|PubMed:17059828,
ECO:0000269|PubMed:19801656}.
MUTAGEN 169 169 H->A: 50% decrease in bis(pNPP)
hydrolysis. Does not affect cAMP
hydrolysis.
{ECO:0000269|PubMed:16313172}.
MUTAGEN 207 207 H->A: 75% decrease in bis(pNPP)
hydrolysis. Does not affect cAMP
hydrolysis.
{ECO:0000269|PubMed:16313172}.
MUTAGEN 209 209 H->A: 80% decrease in hydrolysis of
3',5'-cAMP and bis(pNPP). 40% decrease in
2',3'-cAMP hydrolysis.
{ECO:0000269|PubMed:19801656}.
MUTAGEN 229 229 Y->A: 40% decrease in bis(pNPP)
hydrolysis. 80% decrease in 3',5'-cAMP
and 2',3'-cAMP hydrolysis.
{ECO:0000269|PubMed:19801656}.
STRAND 13 19 {ECO:0000244|PDB:3IB7}.
STRAND 26 28 {ECO:0000244|PDB:3IB7}.
TURN 32 34 {ECO:0000244|PDB:3IB7}.
HELIX 37 51 {ECO:0000244|PDB:3IB7}.
STRAND 56 60 {ECO:0000244|PDB:3IB7}.
STRAND 65 67 {ECO:0000244|PDB:2HY1}.
HELIX 70 87 {ECO:0000244|PDB:3IB7}.
STRAND 90 93 {ECO:0000244|PDB:3IB7}.
HELIX 101 109 {ECO:0000244|PDB:3IB7}.
STRAND 120 124 {ECO:0000244|PDB:3IB7}.
STRAND 127 131 {ECO:0000244|PDB:3IB7}.
STRAND 140 142 {ECO:0000244|PDB:2HY1}.
HELIX 146 155 {ECO:0000244|PDB:3IB7}.
STRAND 164 167 {ECO:0000244|PDB:3IB7}.
HELIX 178 183 {ECO:0000244|PDB:3IB7}.
STRAND 184 186 {ECO:0000244|PDB:3IB7}.
HELIX 188 195 {ECO:0000244|PDB:3IB7}.
STRAND 198 205 {ECO:0000244|PDB:3IB7}.
STRAND 207 210 {ECO:0000244|PDB:3IB7}.
STRAND 212 216 {ECO:0000244|PDB:3IB7}.
STRAND 219 223 {ECO:0000244|PDB:3IB7}.
STRAND 242 244 {ECO:0000244|PDB:3IB7}.
STRAND 248 254 {ECO:0000244|PDB:3IB7}.
STRAND 259 265 {ECO:0000244|PDB:3IB7}.
HELIX 278 287 {ECO:0000244|PDB:3IB7}.
SEQUENCE 318 AA; 34233 MW; 7C1B683C5E375B3F CRC64;
MHRLRAAEHP RPDYVLLHIS DTHLIGGDRR LYGAVDADDR LGELLEQLNQ SGLRPDAIVF
TGDLADKGEP AAYRKLRGLV EPFAAQLGAE LVWVMGNHDD RAELRKFLLD EAPSMAPLDR
VCMIDGLRII VLDTSVPGHH HGEIRASQLG WLAEELATPA PDGTILALHH PPIPSVLDMA
VTVELRDQAA LGRVLRGTDV RAILAGHLHY STNATFVGIP VSVASATCYT QDLTVAAGGT
RGRDGAQGCN LVHVYPDTVV HSVIPLGGGE TVGTFVSPGQ ARRKIAESGI FIEPSRRDSL
FKHPPMVLTS SAPRSPVD


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