AMACR_MYCTU
ID AMACR_MYCTU Reviewed; 360 AA.
AC O06543; I6XAR5;
DT 17-JUN-2020, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 3.
DT 03-AUG-2022, entry version 136.
DE RecName: Full=Alpha-methylacyl-CoA racemase {ECO:0000303|PubMed:12554951};
DE Short=AMACR {ECO:0000303|PubMed:12554951};
DE EC=5.1.99.4 {ECO:0000269|PubMed:15632186, ECO:0000269|PubMed:19854148, ECO:0000269|PubMed:26348625};
DE AltName: Full=MtMCR {ECO:0000303|PubMed:29502025};
GN Name=mcr {ECO:0000303|PubMed:12554951};
GN OrderedLocusNames=Rv1143 {ECO:0000312|EMBL:CCP43898.1};
OS Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv).
OC Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
OC Mycobacterium; Mycobacterium tuberculosis complex.
OX NCBI_TaxID=83332;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=9634230; DOI=10.1038/31159;
RA Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M., Harris D.E.,
RA Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III, Tekaia F., Badcock K.,
RA Basham D., Brown D., Chillingworth T., Connor R., Davies R.M., Devlin K.,
RA Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K.,
RA Krogh A., McLean J., Moule S., Murphy L.D., Oliver S., Osborne J.,
RA Quail M.A., Rajandream M.A., Rogers J., Rutter S., Seeger K., Skelton S.,
RA Squares S., Squares R., Sulston J.E., Taylor K., Whitehead S.,
RA Barrell B.G.;
RT "Deciphering the biology of Mycobacterium tuberculosis from the complete
RT genome sequence.";
RL Nature 393:537-544(1998).
RN [2]
RP SUBUNIT, AND CRYSTALLIZATION.
RX PubMed=12554951; DOI=10.1107/s0907444902020735;
RA Bhaumik P., Kursula P., Ratas V., Conzelmann E., Hiltunen J.K., Schmitz W.,
RA Wierenga R.K.;
RT "Crystallization and preliminary X-ray diffraction studies of an alpha-
RT methylacyl-CoA racemase from Mycobacterium tuberculosis.";
RL Acta Crystallogr. D 59:353-355(2003).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=19854148; DOI=10.1016/j.ab.2009.10.039;
RA Ouazia D., Bearne S.L.;
RT "A continuous assay for alpha-methylacyl-coenzyme A racemase using circular
RT dichroism.";
RL Anal. Biochem. 398:45-51(2010).
RN [4] {ECO:0007744|PubMed:21969609}
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=21969609; DOI=10.1074/mcp.m111.011627;
RA Kelkar D.S., Kumar D., Kumar P., Balakrishnan L., Muthusamy B., Yadav A.K.,
RA Shrivastava P., Marimuthu A., Anand S., Sundaram H., Kingsbury R.,
RA Harsha H.C., Nair B., Prasad T.S., Chauhan D.S., Katoch K., Katoch V.M.,
RA Kumar P., Chaerkady R., Ramachandran S., Dash D., Pandey A.;
RT "Proteogenomic analysis of Mycobacterium tuberculosis by high resolution
RT mass spectrometry.";
RL Mol. Cell. Proteomics 10:M111.011627-M111.011627(2011).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=26348625; DOI=10.1021/acs.biochem.5b00911;
RA Lu R., Schmitz W., Sampson N.S.;
RT "Alpha-methyl acyl CoA racemase provides Mycobacterium tuberculosis
RT catabolic access to cholesterol esters.";
RL Biochemistry 54:5669-5672(2015).
RN [6]
RP ACTIVITY REGULATION, AND BIOTECHNOLOGY.
RX PubMed=29502025; DOI=10.1016/j.bioorg.2018.01.041;
RA Pal M., Easton N.M., Yaphe H., Bearne S.L.;
RT "Potent dialkyl substrate-product analogue inhibitors and inactivators of
RT alpha-methylacyl-coenzyme A racemase from Mycobacterium tuberculosis by
RT rational design.";
RL Bioorg. Chem. 77:640-650(2018).
RN [7] {ECO:0007744|PDB:1X74}
RP X-RAY CRYSTALLOGRAPHY (1.79 ANGSTROMS), FUNCTION, CATALYTIC ACTIVITY,
RP BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, AND MUTAGENESIS OF ARG-52; ILE-56;
RP GLU-82; ARG-91; MET-111; HIS-126; ASP-156; ASP-190; GLU-241; CYS-297 AND
RP HIS-312.
RX PubMed=15632186; DOI=10.1074/jbc.m409704200;
RA Savolainen K., Bhaumik P., Schmitz W., Kotti T.J., Conzelmann E.,
RA Wierenga R.K., Hiltunen J.K.;
RT "Alpha-methylacyl-CoA racemase from Mycobacterium tuberculosis. Mutational
RT and structural characterization of the active site and the fold.";
RL J. Biol. Chem. 280:12611-12620(2005).
RN [8] {ECO:0000312|PDB:2GD2, ECO:0000312|PDB:2GD6, ECO:0007744|PDB:2GCE, ECO:0007744|PDB:2GCI, ECO:0007744|PDB:2GD0}
RP X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) IN COMPLEXES WITH SUBSTRATES AND
RP INHIBITORS, REACTION MECHANISM, AND ACTIVE SITE.
RX PubMed=17320106; DOI=10.1016/j.jmb.2007.01.062;
RA Bhaumik P., Schmitz W., Hassinen A., Hiltunen J.K., Conzelmann E.,
RA Wierenga R.K.;
RT "The catalysis of the 1,1-proton transfer by alpha-methyl-acyl-CoA racemase
RT is coupled to a movement of the fatty acyl moiety over a hydrophobic,
RT methionine-rich surface.";
RL J. Mol. Biol. 367:1145-1161(2007).
RN [9] {ECO:0007744|PDB:2YIM}
RP X-RAY CRYSTALLOGRAPHY (1.41 ANGSTROMS) IN COMPLEX WITH REACTION
RP INTERMEDIATE ANALOG, REACTION MECHANISM, AND ACTIVE SITE.
RX PubMed=22360758; DOI=10.1021/jp210185m;
RA Sharma S., Bhaumik P., Schmitz W., Venkatesan R., Hiltunen J.K.,
RA Conzelmann E., Juffer A.H., Wierenga R.K.;
RT "The enolization chemistry of a thioester-dependent racemase: the 1.4 A
RT crystal structure of a reaction intermediate complex characterized by
RT detailed QM/MM calculations.";
RL J. Phys. Chem. B 116:3619-3629(2012).
CC -!- FUNCTION: Catalyzes the epimerization of (2R)- and (2S)-methylacyl-
CC coenzyme A (CoA) thioesters (PubMed:15632186, PubMed:19854148,
CC PubMed:26348625). Accepts as substrates a wide range of alpha-
CC methylacyl-CoAs, including (2R)-2-methylmyristoyl-CoA and (2S)-2-
CC methylmyristoyl-CoA, (2R)-pristanoyl-CoA and (2S)-pristanoyl-CoA, and
CC the cholesterol esters (25R)-3-oxo-cholest-4-en-26-oyl-CoA and (25S)-3-
CC oxo-cholest-4-en-26-oyl-CoA (PubMed:15632186, PubMed:26348625). Can
CC also catalyze the interconversion of the non-physiologic substrates
CC (2R)-ibuprofenoyl-CoA and (2S)-ibuprofenoyl-CoA, which are potential
CC competitive inhibitors of the enzyme (PubMed:19854148).
CC {ECO:0000269|PubMed:15632186, ECO:0000269|PubMed:19854148,
CC ECO:0000269|PubMed:26348625}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a (2S)-2-methylacyl-CoA = a (2R)-2-methylacyl-CoA;
CC Xref=Rhea:RHEA:12657, ChEBI:CHEBI:57313, ChEBI:CHEBI:57314;
CC EC=5.1.99.4; Evidence={ECO:0000269|PubMed:15632186};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(2S)-2-methyltetradecanoyl-CoA = (2R)-2-methyltetradecanoyl-
CC CoA; Xref=Rhea:RHEA:46724, ChEBI:CHEBI:86520, ChEBI:CHEBI:86521;
CC Evidence={ECO:0000269|PubMed:15632186};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(2R)-pristanoyl-CoA = (2S)-pristanoyl-CoA;
CC Xref=Rhea:RHEA:40447, ChEBI:CHEBI:77099, ChEBI:CHEBI:77275;
CC Evidence={ECO:0000269|PubMed:15632186};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(25S)-3-oxocholest-4-en-26-oyl-CoA = (25R)-3-oxocholest-4-en-
CC 26-oyl-CoA; Xref=Rhea:RHEA:63172, ChEBI:CHEBI:83819,
CC ChEBI:CHEBI:146202; Evidence={ECO:0000269|PubMed:26348625};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(2S)-ibuprofenoyl-CoA = (2R)-ibuprofenoyl-CoA;
CC Xref=Rhea:RHEA:63176, ChEBI:CHEBI:146203, ChEBI:CHEBI:146204;
CC Evidence={ECO:0000269|PubMed:19854148};
CC -!- ACTIVITY REGULATION: Inactivated by N,N-dialkylcarbamoyl-CoA substrate-
CC product analogs. {ECO:0000269|PubMed:29502025}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=41 uM for (R)-pristanoyl-CoA {ECO:0000269|PubMed:15632186};
CC KM=6.5 uM for (25R)-3-oxo-cholest-4-en-26-oyl-CoA
CC {ECO:0000269|PubMed:26348625};
CC KM=86 uM for (2S)-ibuprofenoyl-CoA {ECO:0000269|PubMed:19854148};
CC KM=48 uM for (2R)-ibuprofenoyl-CoA {ECO:0000269|PubMed:19854148};
CC Vmax=214 umol/min/mg enzyme with (R)-pristanoyl-CoA as substrate
CC {ECO:0000269|PubMed:15632186};
CC Note=kcat is 3.7 sec(-1) with (25R)-3-oxo-cholest-4-en-26-oyl-CoA as
CC substrate (PubMed:26348625). kcat is 450 sec(-1) with (2S)-
CC ibuprofenoyl-CoA as substrate (PubMed:19854148). kcat is 291 sec(-1)
CC with (2R)-ibuprofenoyl-CoA as substrate (PubMed:19854148).
CC {ECO:0000269|PubMed:19854148, ECO:0000269|PubMed:26348625};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:12554951,
CC ECO:0000269|PubMed:15632186}.
CC -!- BIOTECHNOLOGY: Development of gem-disubstituted substrate-product
CC analogs as inhibitors of racemases and epimerases is elaborated using
CC alpha-methylacyl-CoA racemase from Mycobacterium tuberculosis as a
CC model enzyme. These non-physiologic substrates could be used as a
CC therapeutic agent to inhibit human AMACR, which is overexpressed in
CC prostate cancer. {ECO:0000269|PubMed:29502025}.
CC -!- MISCELLANEOUS: Interconversion is achieved via a planar enolate
CC intermediate. {ECO:0000269|PubMed:22360758}.
CC -!- SIMILARITY: Belongs to the CoA-transferase III family. {ECO:0000305}.
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DR EMBL; AL123456; CCP43898.1; -; Genomic_DNA.
DR RefSeq; NP_215659.1; NC_000962.3.
DR RefSeq; WP_003898740.1; NZ_NVQJ01000021.1.
DR PDB; 1X74; X-ray; 1.79 A; A/B/C/D=1-360.
DR PDB; 2GCE; X-ray; 1.85 A; A/B/C/D=1-360.
DR PDB; 2GCI; X-ray; 1.60 A; A/B/C/D=1-360.
DR PDB; 2GD0; X-ray; 1.70 A; A/B/C/D=1-360.
DR PDB; 2GD2; X-ray; 1.70 A; A/B/C/D=1-360.
DR PDB; 2GD6; X-ray; 2.30 A; A/B/C/D=1-360.
DR PDB; 2YIM; X-ray; 1.41 A; A/B/C/D=1-360.
DR PDBsum; 1X74; -.
DR PDBsum; 2GCE; -.
DR PDBsum; 2GCI; -.
DR PDBsum; 2GD0; -.
DR PDBsum; 2GD2; -.
DR PDBsum; 2GD6; -.
DR PDBsum; 2YIM; -.
DR AlphaFoldDB; O06543; -.
DR SMR; O06543; -.
DR STRING; 83332.Rv1143; -.
DR SwissLipids; SLP:000001290; -.
DR PaxDb; O06543; -.
DR PRIDE; O06543; -.
DR DNASU; 885067; -.
DR GeneID; 885067; -.
DR KEGG; mtu:Rv1143; -.
DR PATRIC; fig|83332.111.peg.1277; -.
DR TubercuList; Rv1143; -.
DR eggNOG; COG1804; Bacteria.
DR InParanoid; O06543; -.
DR OMA; ASWLFMS; -.
DR PhylomeDB; O06543; -.
DR BioCyc; MetaCyc:G185E-5310-MON; -.
DR BRENDA; 5.1.99.4; 3445.
DR EvolutionaryTrace; O06543; -.
DR Proteomes; UP000001584; Chromosome.
DR GO; GO:0008111; F:alpha-methylacyl-CoA racemase activity; IDA:MTBBASE.
DR GO; GO:0042803; F:protein homodimerization activity; IPI:MTBBASE.
DR GO; GO:0006637; P:acyl-CoA metabolic process; IDA:MTBBASE.
DR GO; GO:0006629; P:lipid metabolic process; IEA:UniProtKB-KW.
DR Gene3D; 3.30.1540.10; -; 1.
DR Gene3D; 3.40.50.10540; -; 1.
DR InterPro; IPR003673; CoA-Trfase_fam_III.
DR InterPro; IPR044855; CoA-Trfase_III_dom3_sf.
DR InterPro; IPR023606; CoA-Trfase_III_dom_1_sf.
DR Pfam; PF02515; CoA_transf_3; 1.
DR SUPFAM; SSF89796; SSF89796; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Isomerase; Lipid metabolism; Reference proteome.
FT CHAIN 1..360
FT /note="Alpha-methylacyl-CoA racemase"
FT /id="PRO_0000449922"
FT ACT_SITE 126
FT /note="Proton acceptor"
FT /evidence="ECO:0000305|PubMed:17320106,
FT ECO:0000305|PubMed:22360758"
FT ACT_SITE 156
FT /note="Proton donor"
FT /evidence="ECO:0000305|PubMed:17320106,
FT ECO:0000305|PubMed:22360758"
FT BINDING 38
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:17320106,
FT ECO:0000269|PubMed:22360758"
FT BINDING 59..62
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:17320106,
FT ECO:0000269|PubMed:22360758"
FT BINDING 83..85
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:17320106,
FT ECO:0000269|PubMed:22360758"
FT BINDING 91
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:17320106,
FT ECO:0000269|PubMed:22360758"
FT BINDING 125..130
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:17320106,
FT ECO:0000269|PubMed:22360758"
FT MUTAGEN 52
FT /note="R->A: 15.7% of wild-type activity."
FT /evidence="ECO:0000269|PubMed:15632186"
FT MUTAGEN 56
FT /note="I->P: 28.8% of wild-type activity."
FT /evidence="ECO:0000269|PubMed:15632186"
FT MUTAGEN 82
FT /note="E->A: 12.5% of wild-type activity."
FT /evidence="ECO:0000269|PubMed:15632186"
FT MUTAGEN 91
FT /note="R->A: 19.9% of wild-type activity."
FT /evidence="ECO:0000269|PubMed:15632186"
FT MUTAGEN 111
FT /note="M->P: 5.2% of wild-type activity."
FT /evidence="ECO:0000269|PubMed:15632186"
FT MUTAGEN 126
FT /note="H->A: 4.5% of wild-type activity."
FT /evidence="ECO:0000269|PubMed:15632186"
FT MUTAGEN 156
FT /note="D->A: 17.6 of wild-type activity."
FT /evidence="ECO:0000269|PubMed:15632186"
FT MUTAGEN 190
FT /note="D->A: 3.3% of wild-type activity."
FT /evidence="ECO:0000269|PubMed:15632186"
FT MUTAGEN 241
FT /note="E->A: 2.1% of wild-type activity."
FT /evidence="ECO:0000269|PubMed:15632186"
FT MUTAGEN 297
FT /note="C->A: 6.2% of wild-type activity."
FT /evidence="ECO:0000269|PubMed:15632186"
FT MUTAGEN 312
FT /note="H->A: 10.1% of wild-type activity."
FT /evidence="ECO:0000269|PubMed:15632186"
FT TURN 4..7
FT /evidence="ECO:0007829|PDB:2YIM"
FT STRAND 9..13
FT /evidence="ECO:0007829|PDB:2YIM"
FT HELIX 18..28
FT /evidence="ECO:0007829|PDB:2YIM"
FT STRAND 32..37
FT /evidence="ECO:0007829|PDB:2YIM"
FT HELIX 49..51
FT /evidence="ECO:0007829|PDB:2YIM"
FT STRAND 55..58
FT /evidence="ECO:0007829|PDB:2YIM"
FT HELIX 64..74
FT /evidence="ECO:0007829|PDB:2YIM"
FT STRAND 78..82
FT /evidence="ECO:0007829|PDB:2YIM"
FT HELIX 88..92
FT /evidence="ECO:0007829|PDB:2YIM"
FT HELIX 96..102
FT /evidence="ECO:0007829|PDB:2YIM"
FT STRAND 107..114
FT /evidence="ECO:0007829|PDB:2YIM"
FT STRAND 116..118
FT /evidence="ECO:0007829|PDB:2YIM"
FT TURN 119..122
FT /evidence="ECO:0007829|PDB:2YIM"
FT HELIX 127..132
FT /evidence="ECO:0007829|PDB:2YIM"
FT TURN 133..136
FT /evidence="ECO:0007829|PDB:2GCE"
FT HELIX 137..139
FT /evidence="ECO:0007829|PDB:2YIM"
FT HELIX 153..160
FT /evidence="ECO:0007829|PDB:2YIM"
FT HELIX 161..178
FT /evidence="ECO:0007829|PDB:2YIM"
FT STRAND 182..187
FT /evidence="ECO:0007829|PDB:2YIM"
FT HELIX 188..195
FT /evidence="ECO:0007829|PDB:2YIM"
FT HELIX 197..204
FT /evidence="ECO:0007829|PDB:2YIM"
FT TURN 216..219
FT /evidence="ECO:0007829|PDB:2YIM"
FT STRAND 224..228
FT /evidence="ECO:0007829|PDB:2YIM"
FT STRAND 234..238
FT /evidence="ECO:0007829|PDB:2YIM"
FT HELIX 242..252
FT /evidence="ECO:0007829|PDB:2YIM"
FT HELIX 256..258
FT /evidence="ECO:0007829|PDB:2YIM"
FT HELIX 265..267
FT /evidence="ECO:0007829|PDB:2YIM"
FT HELIX 268..280
FT /evidence="ECO:0007829|PDB:2YIM"
FT HELIX 284..290
FT /evidence="ECO:0007829|PDB:2YIM"
FT STRAND 292..296
FT /evidence="ECO:0007829|PDB:2YIM"
FT STRAND 298..300
FT /evidence="ECO:0007829|PDB:2YIM"
FT HELIX 304..309
FT /evidence="ECO:0007829|PDB:2YIM"
FT HELIX 311..315
FT /evidence="ECO:0007829|PDB:2YIM"
FT STRAND 319..322
FT /evidence="ECO:0007829|PDB:2YIM"
FT STRAND 325..328
FT /evidence="ECO:0007829|PDB:2YIM"
FT STRAND 331..337
FT /evidence="ECO:0007829|PDB:2YIM"
FT HELIX 351..358
FT /evidence="ECO:0007829|PDB:2YIM"
SQ SEQUENCE 360 AA; 38685 MW; 52633107358AC843 CRC64;
MAGPLSGLRV VELAGIGPGP HAAMILGDLG ADVVRIDRPS SVDGISRDAM LRNRRIVTAD
LKSDQGLELA LKLIAKADVL IEGYRPGVTE RLGLGPEECA KVNDRLIYAR MTGWGQTGPR
SQQAGHDINY ISLNGILHAI GRGDERPVPP LNLVGDFGGG SMFLLVGILA ALWERQSSGK
GQVVDAAMVD GSSVLIQMMW AMRATGMWTD TRGANMLDGG APYYDTYECA DGRYVAVGAI
EPQFYAAMLA GLGLDAAELP PQNDRARWPE LRALLTEAFA SHDRDHWGAV FANSDACVTP
VLAFGEVHNE PHIIERNTFY EANGGWQPMP APRFSRTASS QPRPPAATID IEAVLTDWDG
