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Long-chain-fatty-acid--CoA ligase FadD13 (EC 6.2.1.3) (Fatty acyl-CoA ligase) (FACL) (FACL13) (Fatty acyl-CoA synthetase) (ACS) (FACS) (Very-long-chain fatty-acyl-CoA synthetase) (ACSVL)

 FAC13_MYCTU             Reviewed;         503 AA.
P9WQ37; F2GNX9; L0TEI7; O53306; Q7D654;
16-APR-2014, integrated into UniProtKB/Swiss-Prot.
16-APR-2014, sequence version 1.
23-MAY-2018, entry version 29.
RecName: Full=Long-chain-fatty-acid--CoA ligase FadD13;
EC=6.2.1.3;
AltName: Full=Fatty acyl-CoA ligase;
Short=FACL;
Short=FACL13;
AltName: Full=Fatty acyl-CoA synthetase;
Short=ACS;
Short=FACS;
AltName: Full=Very-long-chain fatty-acyl-CoA synthetase;
Short=ACSVL;
Name=fadD13; OrderedLocusNames=Rv3089;
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]
INDUCTION.
PubMed=14568148; DOI=10.1016/S0378-1097(03)00648-7;
Singh A., Jain S., Gupta S., Das T., Tyagi A.K.;
"mymA operon of Mycobacterium tuberculosis: its regulation and
importance in the cell envelope.";
FEMS Microbiol. Lett. 227:53-63(2003).
[3]
FUNCTION, AND DISRUPTION PHENOTYPE.
STRAIN=Erdman;
PubMed=15937179; DOI=10.1128/JB.187.12.4173-4186.2005;
Singh A., Gupta R., Vishwakarma R.A., Narayanan P.R.,
Paramasivan C.N., Ramanathan V.D., Tyagi A.K.;
"Requirement of the mymA operon for appropriate cell wall
ultrastructure and persistence of Mycobacterium tuberculosis in the
spleens of guinea pigs.";
J. Bacteriol. 187:4173-4186(2005).
[4]
DISRUPTION PHENOTYPE.
STRAIN=ATCC 25618 / H37Rv;
PubMed=16893682; DOI=10.1016/j.tube.2006.01.021;
Cheruvu M., Plikaytis B.B., Shinnick T.M.;
"The acid-induced operon Rv3083-Rv3089 is required for growth of
Mycobacterium tuberculosis in macrophages.";
Tuberculosis 87:12-20(2007).
[5]
FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF LYS-172; VAL-209;
ALA-211; ALA-302; TRP-377; ASP-382; SER-404 AND LYS-487,
BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE SPECIFICITY, AND SUBUNIT.
PubMed=20027301; DOI=10.1371/journal.pone.0008387;
Khare G., Gupta V., Gupta R.K., Gupta R., Bhat R., Tyagi A.K.;
"Dissecting the role of critical residues and substrate preference of
a fatty acyl-CoA synthetase (FadD13) of Mycobacterium tuberculosis.";
PLoS ONE 4:E8387-E8387(2009).
[6]
MUTAGENESIS OF ARG-397 AND LYS-487.
PubMed=20454815; DOI=10.1007/s00894-010-0727-3;
Jatana N., Jangid S., Khare G., Tyagi A.K., Latha N.;
"Molecular modeling studies of Fatty acyl-CoA synthetase (FadD13) from
Mycobacterium tuberculosis--a potential target for the development of
antitubercular drugs.";
J. Mol. Model. 17:301-313(2011).
[7]
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).
[8]
X-RAY CRYSTALLOGRAPHY (2.09 ANGSTROMS) OF 1-396, MUTAGENESIS OF
THR-214; ALA-302; GLY-406 AND LYS-487, BIOPHYSICOCHEMICAL PROPERTIES,
AND SUBSTRATE SELECTIVITY.
PubMed=22206988; DOI=10.1016/j.jmb.2011.12.031;
Goyal A., Verma P., Anandhakrishnan M., Gokhale R.S.,
Sankaranarayanan R.;
"Molecular basis of the functional divergence of fatty acyl-AMP ligase
biosynthetic enzymes of Mycobacterium tuberculosis.";
J. Mol. Biol. 416:221-238(2012).
[9]
X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS), FUNCTION, SUBCELLULAR
LOCATION, MUTAGENESIS OF ARG-9; ARG-17; ARG-195; ARG-197 AND ARG-244,
AND LIPID ACCOMMODATION.
PubMed=22560731; DOI=10.1016/j.str.2012.03.012;
Andersson C.S., Lundgren C.A., Magnusdottir A., Ge C., Wieslander A.,
Martinez Molina D., Hogbom M.;
"The Mycobacterium tuberculosis very-long-chain fatty acyl-CoA
synthetase: structural basis for housing lipid substrates longer than
the enzyme.";
Structure 20:1062-1070(2012).
-!- FUNCTION: Required for maintaining the appropriate mycolic acid
composition and permeability of the envelope on its exposure to
acidic pH. Catalyzes the activation of long-chain fatty acids as
acyl-coenzyme A (acyl-CoA), which are then transferred to the
multifunctional polyketide synthase (PKS) type III for further
chain extension. It has preference for the fatty acid with long
chain length in the following order: hexacosanoic acid (C26),
tetracosanoic acid (C24) and palmitic acid (C16).
{ECO:0000269|PubMed:15937179, ECO:0000269|PubMed:20027301,
ECO:0000269|PubMed:22560731}.
-!- CATALYTIC ACTIVITY: ATP + a long-chain fatty acid + CoA = AMP +
diphosphate + an acyl-CoA. {ECO:0000269|PubMed:20027301}.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=0.13 mM for CoA (at pH 8 and at 37 degrees Celsius)
{ECO:0000269|PubMed:20027301, ECO:0000269|PubMed:22206988};
KM=0.11 mM for CoASH (at pH 8 and at 30 degrees Celsius)
{ECO:0000269|PubMed:20027301, ECO:0000269|PubMed:22206988};
KM=19.79 uM for palmitic acid (at pH 8 and at 37 degrees
Celsius) {ECO:0000269|PubMed:20027301,
ECO:0000269|PubMed:22206988};
KM=0.23 mM for ATP (at pH 8 and at 37 degrees Celsius)
{ECO:0000269|PubMed:20027301, ECO:0000269|PubMed:22206988};
KM=0.25 mM for ATP (at pH 8 and at 30 degrees Celsius)
{ECO:0000269|PubMed:20027301, ECO:0000269|PubMed:22206988};
Vmax=14.62 pmol/min/ug enzyme (at pH 8 and at 37 degrees
Celsius) {ECO:0000269|PubMed:20027301,
ECO:0000269|PubMed:22206988};
Note=Kcat is 0.03 sec(-1) for palmitic acid (at pH 8 and at 37
degrees Celsius).;
-!- PATHWAY: Lipid metabolism; fatty acid biosynthesis.
-!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:20027301}.
-!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000269|PubMed:22560731};
Peripheral membrane protein {ECO:0000269|PubMed:22560731}.
Note=Membrane-associated through distinctive regions rich in
arginine and aromatic residues.
-!- INDUCTION: Expression is controlled by VirS. Induced at acidic pH
and in macrophages. {ECO:0000269|PubMed:14568148}.
-!- DISRUPTION PHENOTYPE: Inactivation of the mymA operon causes
altered cell wall structure, reduced contents and altered
composition of mycolic acids along with the accumulation of
saturated C24 and C26 fatty acids, and enhanced susceptibility to
antibiotics, detergents and acidic pH. Also impairs ability to
survive in macrophages. {ECO:0000269|PubMed:15937179,
ECO:0000269|PubMed:16893682}.
-!- SIMILARITY: Belongs to the ATP-dependent AMP-binding enzyme
family. {ECO:0000305}.
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EMBL; AL123456; CCP45898.1; -; Genomic_DNA.
PIR; E70853; E70853.
RefSeq; NP_217605.1; NC_000962.3.
RefSeq; WP_003416081.1; NZ_KK339370.1.
PDB; 3R44; X-ray; 1.80 A; A=1-503.
PDB; 3T5B; X-ray; 2.35 A; A=1-396.
PDB; 3T5C; X-ray; 2.09 A; A/B=1-396.
PDBsum; 3R44; -.
PDBsum; 3T5B; -.
PDBsum; 3T5C; -.
ProteinModelPortal; P9WQ37; -.
SMR; P9WQ37; -.
STRING; 83332.Rv3089; -.
SwissLipids; SLP:000000980; -.
PaxDb; P9WQ37; -.
PRIDE; P9WQ37; -.
EnsemblBacteria; CCP45898; CCP45898; Rv3089.
GeneID; 888666; -.
KEGG; mtu:Rv3089; -.
TubercuList; Rv3089; -.
eggNOG; ENOG4105CEY; Bacteria.
eggNOG; COG0318; LUCA.
OMA; FYYTANG; -.
PhylomeDB; P9WQ37; -.
UniPathway; UPA00094; -.
Proteomes; UP000001584; Chromosome.
GO; GO:0005618; C:cell wall; IDA:MTBBASE.
GO; GO:0005829; C:cytosol; IDA:MTBBASE.
GO; GO:0005886; C:plasma membrane; IEA:UniProtKB-SubCell.
GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
GO; GO:0102391; F:decanoate-CoA ligase activity; IEA:UniProtKB-EC.
GO; GO:0004321; F:fatty-acyl-CoA synthase activity; IDA:MTBBASE.
GO; GO:0004467; F:long-chain fatty acid-CoA ligase activity; IEA:UniProtKB-EC.
GO; GO:0006633; P:fatty acid biosynthetic process; IEA:UniProtKB-UniPathway.
GO; GO:0044119; P:growth of symbiont in host cell; IMP:MTBBASE.
GO; GO:0010447; P:response to acidic pH; IEP:MTBBASE.
InterPro; IPR025110; AMP-bd_C.
InterPro; IPR020845; AMP-binding_CS.
InterPro; IPR000873; AMP-dep_Synth/Lig.
Pfam; PF00501; AMP-binding; 1.
Pfam; PF13193; AMP-binding_C; 1.
PROSITE; PS00455; AMP_BINDING; 1.
1: Evidence at protein level;
3D-structure; ATP-binding; Cell membrane; Complete proteome;
Fatty acid metabolism; Ligase; Lipid metabolism; Membrane;
Nucleotide-binding; Reference proteome.
CHAIN 1 503 Long-chain-fatty-acid--CoA ligase FadD13.
/FTId=PRO_0000420960.
SITE 9 9 Membrane interaction.
SITE 17 17 Membrane interaction.
SITE 195 195 Membrane interaction.
SITE 197 197 Membrane interaction.
SITE 214 214 Important for substrate selectivity.
SITE 244 244 Membrane interaction.
SITE 302 302 Important for substrate selectivity.
MUTAGEN 9 9 R->A: Alteration of the strength of the
membrane binding; when associated with A-
9; A-195; A-197 and A-244.
{ECO:0000269|PubMed:22560731}.
MUTAGEN 17 17 R->A: Alteration of the strength of the
membrane binding; when associated with A-
9; A-17; A-197 and A-244.
{ECO:0000269|PubMed:22560731}.
MUTAGEN 172 172 K->A: Slight reduction of the fatty acyl-
CoA ligase activity. Slight increase of
susceptibility to proteolysis.
{ECO:0000269|PubMed:20027301}.
MUTAGEN 195 195 R->A: Alteration of the strength of the
membrane binding; when associated with A-
9; A-17; A-197 and A-244.
{ECO:0000269|PubMed:22560731}.
MUTAGEN 197 197 R->A: Alteration of the strength of the
membrane binding; when associated with A-
9; A-17; A-195 and A-244.
{ECO:0000269|PubMed:22560731}.
MUTAGEN 209 209 V->D: Strong reduction of the fatty acyl-
CoA ligase activity. No significant
change in the total expression level,
however the cytoplasmic expression is
reduced. Slight increase of
susceptibility to proteolysis.
{ECO:0000269|PubMed:20027301}.
MUTAGEN 211 211 A->G: Slight increase of the fatty acyl-
CoA ligase activity. Reduced rate of
proteolytic degradation.
{ECO:0000269|PubMed:20027301}.
MUTAGEN 214 214 T->W: Shows a marked decrease in the
activity with lauric and palmitic acid
(C12 and C16 fatty acid) with a
simultaneous increase in the activity
with caprylic acid (C8 fatty acid).
{ECO:0000269|PubMed:22206988}.
MUTAGEN 244 244 R->A: Alteration of the strength of the
membrane binding; when associated with A-
17; A-195; A-195 and A-197.
{ECO:0000269|PubMed:22560731}.
MUTAGEN 302 302 A->G: Slight increase of the fatty acyl-
CoA ligase activity. Reduced rate of
proteolytic degradation.
{ECO:0000269|PubMed:20027301,
ECO:0000269|PubMed:22206988}.
MUTAGEN 302 302 A->W: Does not show activity with small,
medium or long acyl chains.
{ECO:0000269|PubMed:20027301,
ECO:0000269|PubMed:22206988}.
MUTAGEN 377 377 W->A: Strong reduction of the fatty acyl-
CoA ligase activity. Enhanced affinity
towards palmitic acid binding. No
significant change in the total
expression level, however the cytoplasmic
expression is low. Slight increase of
susceptibility to proteolysis.
{ECO:0000269|PubMed:20027301}.
MUTAGEN 382 382 D->A: Strong reduction of the fatty acyl-
CoA ligase activity. No significant
change in the total expression level,
however the cytoplasmic expression is
reduced. {ECO:0000269|PubMed:20027301}.
MUTAGEN 397 397 R->A: Reduction of binding affinity for
fatty acids.
{ECO:0000269|PubMed:20454815}.
MUTAGEN 404 404 S->A: Slight reduction of the fatty acyl-
CoA ligase activity. Enhanced affinity
towards palmitic acid binding.
{ECO:0000269|PubMed:20027301}.
MUTAGEN 406 406 G->L: No effect on the formation of acyl-
adenylate intermediate. However, it shows
very poor catalytic efficiency to form
acyl-CoA. {ECO:0000269|PubMed:22206988}.
MUTAGEN 487 487 K->A: Strong reduction of the fatty acyl-
CoA ligase activity. Reduction of binding
affinity for ATP.
{ECO:0000269|PubMed:20027301,
ECO:0000269|PubMed:20454815,
ECO:0000269|PubMed:22206988}.
HELIX 4 14 {ECO:0000244|PDB:3R44}.
STRAND 18 23 {ECO:0000244|PDB:3R44}.
HELIX 24 26 {ECO:0000244|PDB:3R44}.
STRAND 28 31 {ECO:0000244|PDB:3R44}.
HELIX 32 48 {ECO:0000244|PDB:3R44}.
STRAND 56 60 {ECO:0000244|PDB:3R44}.
HELIX 65 77 {ECO:0000244|PDB:3R44}.
STRAND 80 83 {ECO:0000244|PDB:3R44}.
HELIX 90 100 {ECO:0000244|PDB:3R44}.
STRAND 103 107 {ECO:0000244|PDB:3R44}.
HELIX 109 111 {ECO:0000244|PDB:3R44}.
HELIX 112 120 {ECO:0000244|PDB:3R44}.
STRAND 121 123 {ECO:0000244|PDB:3R44}.
STRAND 130 133 {ECO:0000244|PDB:3R44}.
HELIX 134 143 {ECO:0000244|PDB:3R44}.
STRAND 157 164 {ECO:0000244|PDB:3R44}.
STRAND 172 177 {ECO:0000244|PDB:3R44}.
HELIX 178 191 {ECO:0000244|PDB:3R44}.
STRAND 199 202 {ECO:0000244|PDB:3R44}.
HELIX 209 221 {ECO:0000244|PDB:3R44}.
STRAND 224 227 {ECO:0000244|PDB:3R44}.
HELIX 233 242 {ECO:0000244|PDB:3R44}.
STRAND 247 250 {ECO:0000244|PDB:3R44}.
HELIX 252 260 {ECO:0000244|PDB:3R44}.
HELIX 262 266 {ECO:0000244|PDB:3R44}.
STRAND 274 277 {ECO:0000244|PDB:3R44}.
HELIX 284 292 {ECO:0000244|PDB:3R44}.
STRAND 296 302 {ECO:0000244|PDB:3R44}.
HELIX 304 306 {ECO:0000244|PDB:3R44}.
STRAND 310 313 {ECO:0000244|PDB:3R44}.
HELIX 315 317 {ECO:0000244|PDB:3R44}.
TURN 318 323 {ECO:0000244|PDB:3R44}.
STRAND 326 328 {ECO:0000244|PDB:3R44}.
STRAND 332 337 {ECO:0000244|PDB:3R44}.
STRAND 343 355 {ECO:0000244|PDB:3R44}.
STRAND 360 362 {ECO:0000244|PDB:3R44}.
HELIX 366 371 {ECO:0000244|PDB:3R44}.
STRAND 377 386 {ECO:0000244|PDB:3R44}.
STRAND 392 396 {ECO:0000244|PDB:3R44}.
HELIX 398 400 {ECO:0000244|PDB:3R44}.
STRAND 402 404 {ECO:0000244|PDB:3R44}.
STRAND 407 409 {ECO:0000244|PDB:3R44}.
HELIX 411 418 {ECO:0000244|PDB:3R44}.
STRAND 424 434 {ECO:0000244|PDB:3R44}.
TURN 435 437 {ECO:0000244|PDB:3R44}.
STRAND 438 447 {ECO:0000244|PDB:3R44}.
TURN 449 451 {ECO:0000244|PDB:3R44}.
HELIX 454 464 {ECO:0000244|PDB:3R44}.
HELIX 467 469 {ECO:0000244|PDB:3R44}.
STRAND 472 476 {ECO:0000244|PDB:3R44}.
HELIX 490 497 {ECO:0000244|PDB:3R44}.
HELIX 498 500 {ECO:0000244|PDB:3R44}.
SEQUENCE 503 AA; 54459 MW; B4CF011549E7B620 CRC64;
MKNIGWMLRQ RATVSPRLQA YVEPSTDVRM TYAQMNALAN RCADVLTALG IAKGDRVALL
MPNSVEFCCL FYGAAKLGAV AVPINTRLAA PEVSFILSDS GSKVVIYGAP SAPVIDAIRA
QADPPGTVTD WIGADSLAER LRSAAADEPA VECGGDDNLF IMYTSGTTGH PKGVVHTHES
VHSAASSWAS TIDVRYRDRL LLPLPMFHVA ALTTVIFSAM RGVTLISMPQ FDATKVWSLI
VEERVCIGGA VPAILNFMRQ VPEFAELDAP DFRYFITGGA PMPEALIKIY AAKNIEVVQG
YALTESCGGG TLLLSEDALR KAGSAGRATM FTDVAVRGDD GVIREHGEGE VVIKSDILLK
EYWNRPEATR DAFDNGWFRT GDIGEIDDEG YLYIKDRLKD MIISGGENVY PAEIESVIIG
VPGVSEVAVI GLPDEKWGEI AAAIVVADQN EVSEQQIVEY CGTRLARYKL PKKVIFAEAI
PRNPTGKILK TVLREQYSAT VPK


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