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Phosphopantetheine adenylyltransferase (EC 2.7.7.3) (Dephospho-CoA pyrophosphorylase) (Pantetheine-phosphate adenylyltransferase) (PPAT)

 COAD_MYCTU              Reviewed;         161 AA.
P9WPA5; L0TCR8; O08023; P0A530; Q50452;
16-APR-2014, integrated into UniProtKB/Swiss-Prot.
16-APR-2014, sequence version 1.
25-OCT-2017, entry version 25.
RecName: Full=Phosphopantetheine adenylyltransferase {ECO:0000255|HAMAP-Rule:MF_00151, ECO:0000303|PubMed:15322293, ECO:0000303|Ref.5};
EC=2.7.7.3 {ECO:0000255|HAMAP-Rule:MF_00151, ECO:0000269|PubMed:20851704, ECO:0000269|Ref.5};
AltName: Full=Dephospho-CoA pyrophosphorylase {ECO:0000255|HAMAP-Rule:MF_00151};
AltName: Full=Pantetheine-phosphate adenylyltransferase {ECO:0000255|HAMAP-Rule:MF_00151};
Short=PPAT {ECO:0000255|HAMAP-Rule:MF_00151, ECO:0000303|PubMed:15322293, ECO:0000303|Ref.5};
Name=coaD {ECO:0000255|HAMAP-Rule:MF_00151};
Synonyms=kdtB {ECO:0000303|Ref.5}; OrderedLocusNames=Rv2965c;
ORFNames=MTCY349.22, u0002e;
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv).
Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
Mycobacterium; Mycobacterium tuberculosis complex.
NCBI_TaxID=83332;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Smith D.R., Robison K.;
Submitted (SEP-1994) to the EMBL/GenBank/DDBJ databases.
[2]
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).
[3]
ACETYLATION [LARGE SCALE ANALYSIS] AT THR-2, CLEAVAGE OF INITIATOR
METHIONINE [LARGE SCALE ANALYSIS], AND 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 (1.99 ANGSTROMS) OF 1-157, AND SUBUNIT.
PubMed=15322293; DOI=10.1110/ps.04816904;
Morris V.K., Izard T.;
"Substrate-induced asymmetry and channel closure revealed by the
apoenzyme structure of Mycobacterium tuberculosis phosphopantetheine
adenylyltransferase.";
Protein Sci. 13:2547-2552(2004).
[5]
X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) IN COMPLEX WITH THE NATURAL
INHIBITOR COENZYME A, FUNCTION, CATALYTIC ACTIVITY, ENZYME REGULATION,
AND SUBUNIT.
STRAIN=H37Rv;
DOI=10.1134/S1063774510060234;
Timofeev V.I., Smirnova E.A., Chupova L.A., Esipov R.S.,
Kuranova I.P.;
"Preparation of the crystal complex of phosphopantetheine
adenylyltransferase from Mycobacterium tuberculosis with Coenzyme A
and investigation of its three-dimensional structure at 2.1-A frame
resolution.";
Crystallogr. Rep. 55:1050-1059(2010).
[6]
X-RAY CRYSTALLOGRAPHY (1.58 ANGSTROMS) OF 1-157 IN COMPLEXES WITH
PHOSPHOPANTETHEINE AND A NON-HYDROLYZABLE ATP ANALOG, FUNCTION,
CATALYTIC ACTIVITY, AND BIOPHYSICOCHEMICAL PROPERTIES.
PubMed=20851704; DOI=10.1016/j.jmb.2010.09.002;
Wubben T.J., Mesecar A.D.;
"Kinetic, thermodynamic, and structural insight into the mechanism of
phosphopantetheine adenylyltransferase from Mycobacterium
tuberculosis.";
J. Mol. Biol. 404:202-219(2010).
[7]
X-RAY CRYSTALLOGRAPHY (2.11 ANGSTROMS) OF 1-157 IN COMPLEX WITH THE
NATURAL INHIBITOR COENZYME A, AND ENZYME REGULATION.
PubMed=21543857; DOI=10.1107/S1744309111010761;
Wubben T., Mesecar A.D.;
"Structure of Mycobacterium tuberculosis phosphopantetheine
adenylyltransferase in complex with the feedback inhibitor CoA reveals
only one active-site conformation.";
Acta Crystallogr. F 67:541-545(2011).
[8]
X-RAY CRYSTALLOGRAPHY (1.62 ANGSTROMS) IN THE APO FORM AND IN COMPLEX
WITH ATP.
STRAIN=H37Rv;
PubMed=23151631; DOI=10.1107/S0907444912040206;
Timofeev V., Smirnova E., Chupova L., Esipov R., Kuranova I.;
"X-ray study of the conformational changes in the molecule of
phosphopantetheine adenylyltransferase from Mycobacterium tuberculosis
during the catalyzed reaction.";
Acta Crystallogr. D 68:1660-1670(2012).
[9]
X-RAY CRYSTALLOGRAPHY (1.76 ANGSTROMS) OF 1-157 IN THE APO FORM AND IN
COMPLEXES WITH COA AND 3'-DEPHOSPHO-COA.
DOI=10.1134/S1063774512010142;
Timofeev V.I., Smirnova E.A., Chupova L.A., Esipov R.S.,
Kuranova I.P.;
"Three-dimensional structure of phosphopantetheine adenylyltransferase
from Mycobacterium Tuberculosis in the apo form and in complexes with
coenzyme A and dephosphocoenzyme A.";
Crystallogr. Rep. 57:96-104(2012).
-!- FUNCTION: Reversibly transfers an adenylyl group from ATP to 4'-
phosphopantetheine, yielding dephospho-CoA (dPCoA) and
pyrophosphate. {ECO:0000255|HAMAP-Rule:MF_00151,
ECO:0000269|PubMed:20851704, ECO:0000269|Ref.5}.
-!- CATALYTIC ACTIVITY: ATP + pantetheine 4'-phosphate = diphosphate +
3'-dephospho-CoA. {ECO:0000255|HAMAP-Rule:MF_00151,
ECO:0000269|PubMed:20851704, ECO:0000269|Ref.5}.
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
Evidence={ECO:0000255|HAMAP-Rule:MF_00151};
-!- ENZYME REGULATION: Regulated by Coenzyme A (CoA) through feedback
inhibition. {ECO:0000305|PubMed:21543857, ECO:0000305|Ref.5}.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=6.7 uM for 3'-dephospho-CoA {ECO:0000269|PubMed:20851704};
Note=kcat is 288.5 min(-1) for the reverse reaction, with
diphosphate and 3'-dephospho-CoA as substrates, which is nearly
identical to that of the forward reaction fitted to the Hill
equation. The enzyme seems to utilize a nonrapid-equilibrium
random bi-bi mechanism with a preferred pathway to the ternary
complex. A sigmoidal response is observed when ATP was varied at
different fixed concentrations of pantetheine 4'-phosphate. Also
exhibits nonhyperbolic kinetics when pantetheine 4'-phosphate
was varied at a fixed saturating concentration of ATP.
{ECO:0000269|PubMed:20851704};
-!- PATHWAY: Cofactor biosynthesis; coenzyme A biosynthesis; CoA from
(R)-pantothenate: step 4/5. {ECO:0000255|HAMAP-Rule:MF_00151}.
-!- SUBUNIT: Homohexamer; dimer of trimers. {ECO:0000255|HAMAP-
Rule:MF_00151, ECO:0000269|Ref.5, ECO:0000305|PubMed:15322293}.
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00151}.
-!- SIMILARITY: Belongs to the bacterial CoaD family.
{ECO:0000255|HAMAP-Rule:MF_00151}.
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EMBL; U00024; AAA50946.1; -; Genomic_DNA.
EMBL; AL123456; CCP45769.1; -; Genomic_DNA.
PIR; B70671; B70671.
RefSeq; NP_217481.1; NC_000962.3.
RefSeq; WP_003414998.1; NZ_KK339370.1.
PDB; 1TFU; X-ray; 1.99 A; A=1-157.
PDB; 3LCJ; X-ray; 2.10 A; A=1-161.
PDB; 3NBA; X-ray; 2.68 A; A/B/C/D=1-157.
PDB; 3NBK; X-ray; 1.58 A; A/B/C/D=1-157.
PDB; 3PNB; X-ray; 2.11 A; A/B/C/D=1-157.
PDB; 3RBA; X-ray; 1.59 A; A=1-157.
PDB; 3RFF; X-ray; 1.76 A; A=1-157.
PDB; 3RHS; X-ray; 1.59 A; A=1-157.
PDB; 3UC5; X-ray; 1.70 A; A=1-157.
PDB; 4E1A; X-ray; 1.62 A; A=1-161.
PDB; 4R0N; X-ray; 2.00 A; A/C/E/G/I/K=2-157.
PDBsum; 1TFU; -.
PDBsum; 3LCJ; -.
PDBsum; 3NBA; -.
PDBsum; 3NBK; -.
PDBsum; 3PNB; -.
PDBsum; 3RBA; -.
PDBsum; 3RFF; -.
PDBsum; 3RHS; -.
PDBsum; 3UC5; -.
PDBsum; 4E1A; -.
PDBsum; 4R0N; -.
ProteinModelPortal; P9WPA5; -.
SMR; P9WPA5; -.
STRING; 83332.Rv2965c; -.
iPTMnet; P9WPA5; -.
PaxDb; P9WPA5; -.
EnsemblBacteria; CCP45769; CCP45769; Rv2965c.
GeneID; 888423; -.
KEGG; mtu:Rv2965c; -.
TubercuList; Rv2965c; -.
eggNOG; ENOG4108ZEF; Bacteria.
eggNOG; COG0669; LUCA.
KO; K00954; -.
OMA; EFQMALM; -.
PhylomeDB; P9WPA5; -.
UniPathway; UPA00241; UER00355.
Proteomes; UP000001584; Chromosome.
GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
GO; GO:0004595; F:pantetheine-phosphate adenylyltransferase activity; IDA:MTBBASE.
GO; GO:0015937; P:coenzyme A biosynthetic process; IDA:MTBBASE.
GO; GO:0034214; P:protein hexamerization; IDA:MTBBASE.
CDD; cd02163; PPAT; 1.
Gene3D; 3.40.50.620; -; 1.
HAMAP; MF_00151; PPAT_bact; 1.
InterPro; IPR004821; Cyt_trans-like.
InterPro; IPR001980; PPAT.
InterPro; IPR014729; Rossmann-like_a/b/a_fold.
PANTHER; PTHR21342:SF1; PTHR21342:SF1; 1.
Pfam; PF01467; CTP_transf_like; 1.
PRINTS; PR01020; LPSBIOSNTHSS.
TIGRFAMs; TIGR01510; coaD_prev_kdtB; 1.
TIGRFAMs; TIGR00125; cyt_tran_rel; 1.
1: Evidence at protein level;
3D-structure; Acetylation; ATP-binding; Coenzyme A biosynthesis;
Complete proteome; Cytoplasm; Magnesium; Nucleotide-binding;
Nucleotidyltransferase; Reference proteome; Transferase.
INIT_MET 1 1 Removed. {ECO:0000244|PubMed:21969609}.
CHAIN 2 161 Phosphopantetheine adenylyltransferase.
/FTId=PRO_0000156242.
NP_BIND 9 10 ATP. {ECO:0000244|PDB:3NBA,
ECO:0000244|PDB:3UC5, ECO:0000255|HAMAP-
Rule:MF_00151,
ECO:0000269|PubMed:23151631,
ECO:0000305|PubMed:20851704}.
NP_BIND 88 90 ATP. {ECO:0000244|PDB:3NBA,
ECO:0000244|PDB:3UC5, ECO:0000255|HAMAP-
Rule:MF_00151,
ECO:0000269|PubMed:23151631,
ECO:0000305|PubMed:20851704}.
NP_BIND 122 128 ATP. {ECO:0000244|PDB:3NBA,
ECO:0000244|PDB:3UC5, ECO:0000255|HAMAP-
Rule:MF_00151,
ECO:0000269|PubMed:23151631,
ECO:0000305|PubMed:20851704}.
BINDING 9 9 Substrate. {ECO:0000244|PDB:3NBK,
ECO:0000255|HAMAP-Rule:MF_00151,
ECO:0000269|PubMed:20851704}.
BINDING 17 17 ATP. {ECO:0000244|PDB:3NBA,
ECO:0000244|PDB:3UC5, ECO:0000255|HAMAP-
Rule:MF_00151,
ECO:0000269|PubMed:23151631,
ECO:0000305|PubMed:20851704}.
BINDING 41 41 Substrate. {ECO:0000255|HAMAP-
Rule:MF_00151}.
BINDING 73 73 Substrate; via amide nitrogen.
{ECO:0000244|PDB:3NBK, ECO:0000255|HAMAP-
Rule:MF_00151,
ECO:0000269|PubMed:20851704}.
BINDING 87 87 Substrate. {ECO:0000255|HAMAP-
Rule:MF_00151}.
BINDING 98 98 ATP. {ECO:0000244|PDB:3UC5,
ECO:0000255|HAMAP-Rule:MF_00151,
ECO:0000269|PubMed:23151631}.
BINDING 105 105 Substrate. {ECO:0000244|PDB:3NBK,
ECO:0000269|PubMed:20851704}.
BINDING 118 118 ATP. {ECO:0000244|PDB:3NBA,
ECO:0000244|PDB:3UC5,
ECO:0000269|PubMed:23151631,
ECO:0000305|PubMed:20851704}.
SITE 17 17 Transition state stabilizer.
{ECO:0000255|HAMAP-Rule:MF_00151}.
MOD_RES 2 2 N-acetylthreonine.
{ECO:0000244|PubMed:21969609}.
STRAND 3 8 {ECO:0000244|PDB:3NBK}.
HELIX 15 27 {ECO:0000244|PDB:3NBK}.
STRAND 28 35 {ECO:0000244|PDB:3NBK}.
STRAND 39 41 {ECO:0000244|PDB:3RHS}.
HELIX 47 57 {ECO:0000244|PDB:3NBK}.
STRAND 64 68 {ECO:0000244|PDB:3NBK}.
HELIX 73 79 {ECO:0000244|PDB:3NBK}.
STRAND 84 89 {ECO:0000244|PDB:3NBK}.
HELIX 95 109 {ECO:0000244|PDB:3NBK}.
STRAND 112 117 {ECO:0000244|PDB:3NBK}.
HELIX 120 122 {ECO:0000244|PDB:3NBK}.
HELIX 127 135 {ECO:0000244|PDB:3NBK}.
HELIX 141 143 {ECO:0000244|PDB:3NBK}.
HELIX 146 156 {ECO:0000244|PDB:3NBK}.
SEQUENCE 161 AA; 17628 MW; DE9F12E18D0C1721 CRC64;
MTGAVCPGSF DPVTLGHVDI FERAAAQFDE VVVAILVNPA KTGMFDLDER IAMVKESTTH
LPNLRVQVGH GLVVDFVRSC GMTAIVKGLR TGTDFEYELQ MAQMNKHIAG VDTFFVATAP
RYSFVSSSLA KEVAMLGGDV SELLPEPVNR RLRDRLNTER T


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