ICMF_GEOKA
ID ICMF_GEOKA Reviewed; 1086 AA.
AC Q5KUG0;
DT 14-OCT-2015, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-2005, sequence version 1.
DT 03-AUG-2022, entry version 89.
DE RecName: Full=Fused isobutyryl-CoA mutase {ECO:0000255|HAMAP-Rule:MF_02050, ECO:0000303|PubMed:19864421};
DE Includes:
DE RecName: Full=Isobutyryl-CoA mutase {ECO:0000255|HAMAP-Rule:MF_02050, ECO:0000303|PubMed:19864421};
DE Short=ICM {ECO:0000255|HAMAP-Rule:MF_02050, ECO:0000303|PubMed:19864421};
DE EC=5.4.99.13 {ECO:0000255|HAMAP-Rule:MF_02050, ECO:0000269|PubMed:19864421, ECO:0000269|PubMed:22167181};
DE Includes:
DE RecName: Full=P-loop GTPase {ECO:0000255|HAMAP-Rule:MF_02050, ECO:0000303|PubMed:19864421};
DE EC=3.6.5.- {ECO:0000255|HAMAP-Rule:MF_02050, ECO:0000269|PubMed:19864421, ECO:0000269|PubMed:22167181};
DE AltName: Full=G-protein chaperone {ECO:0000255|HAMAP-Rule:MF_02050, ECO:0000303|PubMed:19864421};
GN Name=icmF {ECO:0000255|HAMAP-Rule:MF_02050, ECO:0000303|PubMed:19864421};
GN OrderedLocusNames=GK3391 {ECO:0000312|EMBL:BAD77676.1};
OS Geobacillus kaustophilus (strain HTA426).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Geobacillus;
OC Geobacillus thermoleovorans group.
OX NCBI_TaxID=235909;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=HTA426;
RX PubMed=15576355; DOI=10.1093/nar/gkh970;
RA Takami H., Takaki Y., Chee G.-J., Nishi S., Shimamura S., Suzuki H.,
RA Matsui S., Uchiyama I.;
RT "Thermoadaptation trait revealed by the genome sequence of thermophilic
RT Geobacillus kaustophilus.";
RL Nucleic Acids Res. 32:6292-6303(2004).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR,
RP SUBUNIT, AND DOMAIN.
RX PubMed=19864421; DOI=10.1074/jbc.m109.062182;
RA Cracan V., Padovani D., Banerjee R.;
RT "IcmF is a fusion between the radical B12 enzyme isobutyryl-CoA mutase and
RT its G-protein chaperone.";
RL J. Biol. Chem. 285:655-666(2010).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE
RP SPECIFICITY, COFACTOR, AND MUTAGENESIS OF LYS-213.
RX PubMed=22167181; DOI=10.1074/jbc.m111.320051;
RA Cracan V., Banerjee R.;
RT "Novel coenzyme B12-dependent interconversion of isovaleryl-CoA and
RT pivalyl-CoA.";
RL J. Biol. Chem. 287:3723-3732(2012).
CC -!- FUNCTION: Catalyzes the reversible interconversion of isobutyryl-CoA
CC and n-butyryl-CoA, and to a lesser extent, of pivalyl-CoA and
CC isovaleryl-CoA, using radical chemistry. Also exhibits GTPase activity,
CC associated with its G-protein domain (MeaI) that functions as a
CC chaperone that assists cofactor delivery and proper holo-enzyme
CC assembly. Also displays ATPase activity. Is not able to convert 3-
CC hydroxybutyryl-CoA to 2-hydroxyisobutyryl-CoA. Does not exhibit
CC methylmalonyl-CoA mutase (MCM) activity. {ECO:0000269|PubMed:19864421,
CC ECO:0000269|PubMed:22167181}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2-methylpropanoyl-CoA = butanoyl-CoA; Xref=Rhea:RHEA:13141,
CC ChEBI:CHEBI:57338, ChEBI:CHEBI:57371; EC=5.4.99.13;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_02050,
CC ECO:0000269|PubMed:19864421, ECO:0000269|PubMed:22167181};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=3-methylbutanoyl-CoA = 2,2-dimethylpropanoyl-CoA;
CC Xref=Rhea:RHEA:52620, ChEBI:CHEBI:57345, ChEBI:CHEBI:136712;
CC Evidence={ECO:0000269|PubMed:22167181};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=GTP + H2O = GDP + H(+) + phosphate; Xref=Rhea:RHEA:19669,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:37565,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:58189; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_02050, ECO:0000269|PubMed:19864421,
CC ECO:0000269|PubMed:22167181};
CC -!- COFACTOR:
CC Name=adenosylcob(III)alamin; Xref=ChEBI:CHEBI:18408;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_02050,
CC ECO:0000269|PubMed:19864421, ECO:0000269|PubMed:22167181};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_02050};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=20.1 uM for isobutyryl-CoA (in the absence of nucleotides, at pH
CC 7.5 and 37 degrees Celsius) {ECO:0000269|PubMed:19864421};
CC KM=45.3 uM for isobutyryl-CoA (in the presence of GDP, at pH 7.5 and
CC 37 degrees Celsius) {ECO:0000269|PubMed:19864421};
CC KM=50.8 uM for isobutyryl-CoA (in the presence of GTP, at pH 7.5 and
CC 37 degrees Celsius) {ECO:0000269|PubMed:19864421};
CC KM=51 uM for GTP (at 37 degrees Celsius)
CC {ECO:0000269|PubMed:19864421, ECO:0000269|PubMed:22167181};
CC KM=62 uM for isovaleryl-CoA (at 37 degrees Celsius)
CC {ECO:0000269|PubMed:22167181};
CC KM=1290 uM for ATP (at 37 degrees Celsius)
CC {ECO:0000269|PubMed:22167181};
CC Vmax=0.021 umol/min/mg enzyme for isovaleryl-CoA isomerization (at 37
CC degrees Celsius) {ECO:0000269|PubMed:22167181};
CC Vmax=1.2 umol/min/mg enzyme for isobutyryl-CoA isomerization (at 37
CC degrees Celsius) {ECO:0000269|PubMed:22167181};
CC Vmax=3.3 umol/min/mg enzyme for n-butyryl-CoA isomerization (at 37
CC degrees Celsius) {ECO:0000269|PubMed:22167181};
CC Note=kcat is 3.1 sec(-1) for ICM activity in the absence of
CC nucleotides, at pH 7.5 and 37 degrees Celsius. Activity might be 4-
CC fold higher at 60 degrees Celsius, the optimal growth temperature for
CC this organism. kcat is 1.96 sec(-1) for ICM activity in the presence
CC of GDP, at pH 7.5 and 37 degrees Celsius. kcat is 1.88 sec(-1) for
CC ICM activity in the presence of GTP, at pH 7.5 and 37 degrees Celsius
CC (PubMed:19864421). kcat is 10 min(-1) for GTPase activity and 19
CC min(-1) for ATPase activity (at 37 degrees Celsius)
CC (PubMed:22167181). {ECO:0000269|PubMed:19864421,
CC ECO:0000269|PubMed:22167181};
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_02050,
CC ECO:0000269|PubMed:19864421}.
CC -!- DOMAIN: Is composed of four functional domains: the N-terminal 5'-
CC deoxyadenosylcobalamin binding region that is homologous to the small
CC subunit of ICM (IcmB), a middle P-loop GTPase domain (MeaI) that likely
CC acts as a chaperone for ICM, a structured linker region involved in
CC dimer formation, and a C-terminal part that is homologous to the large
CC substrate-binding subunit of ICM (IcmA). {ECO:0000255|HAMAP-
CC Rule:MF_02050, ECO:0000269|PubMed:19864421}.
CC -!- SIMILARITY: Belongs to the IcmF family. {ECO:0000255|HAMAP-
CC Rule:MF_02050, ECO:0000305}.
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DR EMBL; BA000043; BAD77676.1; -; Genomic_DNA.
DR RefSeq; WP_011232858.1; NC_006510.1.
DR AlphaFoldDB; Q5KUG0; -.
DR SMR; Q5KUG0; -.
DR STRING; 235909.GK3391; -.
DR EnsemblBacteria; BAD77676; BAD77676; GK3391.
DR KEGG; gka:GK3391; -.
DR eggNOG; COG1703; Bacteria.
DR eggNOG; COG1884; Bacteria.
DR eggNOG; COG2185; Bacteria.
DR HOGENOM; CLU_009523_2_0_9; -.
DR OMA; LAMFMNT; -.
DR Proteomes; UP000001172; Chromosome.
DR GO; GO:0031419; F:cobalamin binding; IDA:UniProtKB.
DR GO; GO:0005525; F:GTP binding; IDA:UniProtKB.
DR GO; GO:0003924; F:GTPase activity; IDA:UniProtKB.
DR GO; GO:0047727; F:isobutyryl-CoA mutase activity; IDA:UniProtKB.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0034784; F:pivalyl-CoA mutase activity; IDA:UniProtKB.
DR GO; GO:0042803; F:protein homodimerization activity; IDA:UniProtKB.
DR GO; GO:0006637; P:acyl-CoA metabolic process; IDA:UniProtKB.
DR Gene3D; 3.40.50.300; -; 1.
DR HAMAP; MF_02050; IcmF; 1.
DR InterPro; IPR006159; Acid_CoA_mut_C.
DR InterPro; IPR016176; Cbl-dep_enz_cat.
DR InterPro; IPR006158; Cobalamin-bd.
DR InterPro; IPR036724; Cobalamin-bd_sf.
DR InterPro; IPR033669; IcmF.
DR InterPro; IPR006099; MeMalonylCoA_mutase_a/b_cat.
DR InterPro; IPR027417; P-loop_NTPase.
DR Pfam; PF02310; B12-binding; 1.
DR Pfam; PF01642; MM_CoA_mutase; 1.
DR SUPFAM; SSF51703; SSF51703; 1.
DR SUPFAM; SSF52242; SSF52242; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR TIGRFAMs; TIGR00640; acid_CoA_mut_C; 1.
DR PROSITE; PS51332; B12_BINDING; 1.
PE 1: Evidence at protein level;
KW Chaperone; Cobalamin; Cobalt; GTP-binding; Hydrolase; Isomerase; Magnesium;
KW Metal-binding; Multifunctional enzyme; Nucleotide-binding;
KW Reference proteome.
FT CHAIN 1..1086
FT /note="Fused isobutyryl-CoA mutase"
FT /id="PRO_0000434127"
FT DOMAIN 10..140
FT /note="B12-binding"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02050"
FT REGION 153..407
FT /note="GTPase chaperone MeaI"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02050"
FT REGION 408..570
FT /note="Linker"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02050"
FT BINDING 23
FT /ligand="adenosylcob(III)alamin"
FT /ligand_id="ChEBI:CHEBI:18408"
FT /ligand_part="Co"
FT /ligand_part_id="ChEBI:CHEBI:27638"
FT /note="axial binding residue"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02050"
FT BINDING 210..215
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02050"
FT BINDING 214
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02050"
FT BINDING 238
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02050"
FT BINDING 239
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02050"
FT BINDING 252
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02050"
FT BINDING 252
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02050"
FT BINDING 255
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02050"
FT BINDING 300
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02050"
FT BINDING 300
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02050"
FT BINDING 301
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02050"
FT BINDING 347..350
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02050"
FT BINDING 578
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02050"
FT BINDING 613
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02050"
FT BINDING 719
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02050"
FT BINDING 763
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02050"
FT BINDING 812
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02050"
FT BINDING 847
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02050"
FT BINDING 852
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02050"
FT BINDING 964
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02050"
FT BINDING 1085
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02050"
FT MUTAGEN 213
FT /note="K->A: Loss of GTPase and ATPase activities. No
FT effect on the mutase activity."
FT /evidence="ECO:0000269|PubMed:22167181"
SQ SEQUENCE 1086 AA; 122429 MW; 073D27235443416F CRC64;
MAHIYRPKHH VRFVTASSLF DGHDASINIM RRILQASGAE VIHLGHNRSV EEIVNAAIQE
DVQGIAVSSY QGGHMEFFKY MYDLLQERGA SHIRIYGGGG GVIIPREIKE LHEYGIARIF
SPEDGRRLGL QGMINVMLEE CDFPTVTVVT DELERLPSGD VQAIARLITL CEYRAEGENK
EAAAAAEAAI EQVKALEKRV PVLGITGTGG AGKSSLTDEL VRRFLNEIPD IKIAILSVDP
TKQKTGGALL GDRIRMNSIN SPRVYMRSLA TRHSRTELSP AIRDAISVVK AAGFDLVIIE
TSGIGQGDAA ITEVCDVSMY VMTSEFGAPT QLEKIDMIDY ADLIVINKFE RKGSEDAKRQ
VQKQYQRSHQ LFDRDVSEMP VYGTIASQFN DPGTNTLFVA LVDTINKKAG TNWKTSLKTV
ANVEKHNVII PNERRYYLRE IAETVRSYHR RAEQQVEVAR RLFQIEGAIE AAKERGEAED
VIRALETLKA DYEAKLTPES KRILATWEET KAKYAAKQFV TKVRDKEIVT ELTTKTLSGL
DIPKVVLPKF KDYGEILRWV YKENVPGSFP YTAGVFPFKR QGEDPKRQFA GEGTPERTNR
RFHYLCKEDK AKRLSTAFDS VTLYGEDPDY RPDIFGKVGE SGVSVCTLDD MKKLYKGFDL
CDPLTSVSMT INGPAPILLA MFMNTAIDQQ VEKKEAELGR PLTPEEYEQV KEWTLQTVRG
TVQADILKED QGQNTCIFST DFALKMMGDI QEYFIKHRVR NYYSVSISGY HIAEAGANPI
TQLAFTLANG FTYVEYYLSR GMHIDDFAPN LSFFFSNGLD PEYSVIGRVA RRIWAIVMRE
KYGANERSQK LKYHIQTSGR SLHAQEIDFN DIRTTLQALL AIYDNCNSLH TNAYDEAITT
PTEESVRRAM AIQLIITKEF GLTKNENPLQ GSFIIEELTD LVEEAVLQEF ERLNDRGGVL
GAMEMQYQRG KIQDESLYYE TKKHTGELPI IGVNTFLNPN PPSEDELNNI QLARATYEEK
ETQIRNLREF QERNKDKAGP ALERLKQVAT SGGNIFEELM ETVKVASLGQ ITRALYEVGG
QYRRNM
