MCAL_CERS4
ID MCAL_CERS4 Reviewed; 318 AA.
AC Q3J5L6; B8XVS9;
DT 08-FEB-2011, integrated into UniProtKB/Swiss-Prot.
DT 08-NOV-2005, sequence version 1.
DT 03-AUG-2022, entry version 98.
DE RecName: Full=L-malyl-CoA/beta-methylmalyl-CoA lyase {ECO:0000312|EMBL:ACJ71673.1};
DE EC=4.1.3.24 {ECO:0000269|PubMed:20047909};
DE AltName: Full=(3S)-malyl-CoA/beta-methylmalyl-CoA lyase {ECO:0000312|EMBL:ADC44453.1};
DE AltName: Full=(S)-citramalyl-CoA lyase;
DE EC=4.1.3.25 {ECO:0000269|PubMed:24206647};
GN Name=mcl1 {ECO:0000312|EMBL:ACJ71673.1}; OrderedLocusNames=RHOS4_03500;
GN ORFNames=RSP_1771;
OS Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG
OS 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.) (Rhodobacter
OS sphaeroides).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Rhodobacterales;
OC Rhodobacteraceae; Cereibacter.
OX NCBI_TaxID=272943;
RN [1] {ECO:0000312|EMBL:ACJ71673.1}
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RA Zarzycki J., Fuchs G., Alber B.E.;
RT "L-malyl-CoA/beta-methylmalyl-CoA lyase from Rhodobacter sphaeroides.";
RL Submitted (NOV-2008) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000305, ECO:0000312|EMBL:ADC44453.1}
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, CATALYTIC ACTIVITY, COFACTOR,
RP ACTIVITY REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, AND INDUCTION.
RC STRAIN=ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203
RC / NCIMB 8253 / ATH 2.4.1.;
RX PubMed=20047909; DOI=10.1128/jb.01267-09;
RA Erb T.J., Frerichs-Revermann L., Fuchs G., Alber B.E.;
RT "The apparent malate synthase activity of Rhodobacter sphaeroides is due to
RT two paralogous enzymes, (3S)-Malyl-coenzyme A (CoA)/{beta}-methylmalyl-CoA
RT lyase and (3S)- Malyl-CoA thioesterase.";
RL J. Bacteriol. 192:1249-1258(2010).
RN [3] {ECO:0000312|EMBL:ACJ71673.1}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203
RC / NCIMB 8253 / ATH 2.4.1.;
RA Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina T.,
RA Hammon N., Israni S., Pitluck S., Richardson P., Mackenzie C.,
RA Choudhary M., Larimer F., Hauser L.J., Land M., Donohue T.J., Kaplan S.;
RT "Complete sequence of chromosome 1 of Rhodobacter sphaeroides 2.4.1.";
RL Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS AND
RP MAGNESIUM ION, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, AND SUBUNIT.
RX PubMed=24206647; DOI=10.1186/1472-6807-13-28;
RA Zarzycki J., Kerfeld C.A.;
RT "The crystal structures of the tri-functional Chloroflexus aurantiacus and
RT bi-functional Rhodobacter sphaeroides malyl-CoA lyases and comparison with
RT CitE-like superfamily enzymes and malate synthases.";
RL BMC Struct. Biol. 13:28-28(2013).
CC -!- FUNCTION: Involved in the ethylmalonyl-CoA pathway for acetate
CC assimilation. Catalyzes the reversible condensation of glyoxylate and
CC acetyl-CoA to L-malyl-CoA and the reversible condensation of glyoxylate
CC and propionyl-CoA to yield beta-methylmalyl-CoA. It is also able to
CC catalyze the cleavage of (S)-citramalyl-CoA to yield acetyl-CoA and
CC pyruvate, although this reaction is not involved in the ethylmalonyl-
CC CoA pathway. {ECO:0000269|PubMed:20047909,
CC ECO:0000269|PubMed:24206647}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(S)-malyl-CoA = acetyl-CoA + glyoxylate; Xref=Rhea:RHEA:16629,
CC ChEBI:CHEBI:36655, ChEBI:CHEBI:57288, ChEBI:CHEBI:57317; EC=4.1.3.24;
CC Evidence={ECO:0000269|PubMed:20047909};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(2R,3S)-beta-methylmalyl-CoA = glyoxylate + propanoyl-CoA;
CC Xref=Rhea:RHEA:38259, ChEBI:CHEBI:36655, ChEBI:CHEBI:57392,
CC ChEBI:CHEBI:75634; EC=4.1.3.24;
CC Evidence={ECO:0000269|PubMed:20047909};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(3S)-citramalyl-CoA = acetyl-CoA + pyruvate;
CC Xref=Rhea:RHEA:22612, ChEBI:CHEBI:15361, ChEBI:CHEBI:57288,
CC ChEBI:CHEBI:58668; EC=4.1.3.25;
CC Evidence={ECO:0000269|PubMed:24206647};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:20047909, ECO:0000269|PubMed:24206647};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:20047909, ECO:0000269|PubMed:24206647};
CC Note=Divalent cations such as magnesium or manganese.
CC {ECO:0000269|PubMed:20047909, ECO:0000269|PubMed:24206647};
CC -!- ACTIVITY REGULATION: Inhibited by EDTA. {ECO:0000269|PubMed:20047909}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=3.1 mM for glyoxylate (for L-malyl-CoA formation)
CC {ECO:0000269|PubMed:20047909};
CC KM=0.07 mM for acetyl-CoA (for L-malyl-CoA formation)
CC {ECO:0000269|PubMed:20047909};
CC KM=4.1 mM for glyoxylate (for beta-methylmalyl-CoA formation)
CC {ECO:0000269|PubMed:20047909};
CC KM=0.2 mM for propionyl-CoA (for beta-methylmalyl-CoA formation)
CC {ECO:0000269|PubMed:20047909};
CC KM=0.02 mM for (3S)-malyl-CoA {ECO:0000269|PubMed:20047909};
CC KM=0.01 mM for beta-methylmalyl-CoA {ECO:0000269|PubMed:20047909};
CC -!- SUBUNIT: Homohexamer. Dimer of trimers. {ECO:0000269|PubMed:20047909,
CC ECO:0000269|PubMed:24206647}.
CC -!- INDUCTION: By growth on acetate. {ECO:0000269|PubMed:20047909}.
CC -!- SIMILARITY: Belongs to the HpcH/HpaI aldolase family. {ECO:0000305}.
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DR EMBL; GU320612; ADC44453.1; -; Genomic_DNA.
DR EMBL; FJ445415; ACJ71673.1; -; Genomic_DNA.
DR EMBL; CP000143; ABA77918.1; -; Genomic_DNA.
DR RefSeq; WP_011336971.1; NZ_CP030271.1.
DR RefSeq; YP_351819.1; NC_007493.2.
DR PDB; 4L9Y; X-ray; 2.10 A; A/B/C/D/E/F=1-318.
DR PDB; 4L9Z; X-ray; 2.01 A; A/B/C/D/E/F=1-318.
DR PDBsum; 4L9Y; -.
DR PDBsum; 4L9Z; -.
DR AlphaFoldDB; Q3J5L6; -.
DR SMR; Q3J5L6; -.
DR STRING; 272943.RSP_1771; -.
DR EnsemblBacteria; ABA77918; ABA77918; RSP_1771.
DR GeneID; 57469111; -.
DR GeneID; 67445557; -.
DR KEGG; rsp:RSP_1771; -.
DR PATRIC; fig|272943.9.peg.650; -.
DR eggNOG; COG2301; Bacteria.
DR OMA; WDIHYLD; -.
DR PhylomeDB; Q3J5L6; -.
DR BRENDA; 4.1.3.24; 5383.
DR SABIO-RK; Q3J5L6; -.
DR Proteomes; UP000002703; Chromosome 1.
DR GO; GO:0047777; F:(S)-citramalyl-CoA lyase activity; IDA:UniProtKB.
DR GO; GO:0043959; F:L-erythro-3-methylmalyl-CoA lyase activity; IEA:UniProtKB-EC.
DR GO; GO:0050083; F:malyl-CoA lyase activity; IDA:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IDA:UniProtKB.
DR Gene3D; 3.20.20.60; -; 1.
DR InterPro; IPR005000; Aldolase/citrate-lyase_domain.
DR InterPro; IPR011206; Citrate_lyase_beta/mcl1/mcl2.
DR InterPro; IPR015813; Pyrv/PenolPyrv_Kinase-like_dom.
DR InterPro; IPR040442; Pyrv_Kinase-like_dom_sf.
DR Pfam; PF03328; HpcH_HpaI; 1.
DR PIRSF; PIRSF015582; Cit_lyase_B; 1.
DR SUPFAM; SSF51621; SSF51621; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Lyase; Magnesium; Manganese; Metal-binding;
KW Reference proteome.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000250|UniProtKB:B6E2X2"
FT CHAIN 2..318
FT /note="L-malyl-CoA/beta-methylmalyl-CoA lyase"
FT /id="PRO_0000404701"
FT BINDING 19
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:24206647,
FT ECO:0007744|PDB:4L9Y"
FT BINDING 24
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:24206647,
FT ECO:0007744|PDB:4L9Y"
FT BINDING 30
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:24206647,
FT ECO:0007744|PDB:4L9Z"
FT BINDING 76
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:24206647,
FT ECO:0007744|PDB:4L9Y, ECO:0007744|PDB:4L9Z"
FT BINDING 141
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:24206647,
FT ECO:0007744|PDB:4L9Y, ECO:0007744|PDB:4L9Z"
FT BINDING 167..168
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:24206647,
FT ECO:0007744|PDB:4L9Z"
FT BINDING 168
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:24206647,
FT ECO:0007744|PDB:4L9Y, ECO:0007744|PDB:4L9Z"
FT BINDING 251..252
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:24206647,
FT ECO:0007744|PDB:4L9Z"
FT STRAND 15..21
FT /evidence="ECO:0007829|PDB:4L9Z"
FT HELIX 25..27
FT /evidence="ECO:0007829|PDB:4L9Z"
FT HELIX 28..32
FT /evidence="ECO:0007829|PDB:4L9Z"
FT STRAND 37..44
FT /evidence="ECO:0007829|PDB:4L9Z"
FT HELIX 49..51
FT /evidence="ECO:0007829|PDB:4L9Z"
FT HELIX 52..65
FT /evidence="ECO:0007829|PDB:4L9Z"
FT STRAND 72..76
FT /evidence="ECO:0007829|PDB:4L9Z"
FT STRAND 82..84
FT /evidence="ECO:0007829|PDB:4L9Z"
FT HELIX 85..95
FT /evidence="ECO:0007829|PDB:4L9Z"
FT STRAND 102..105
FT /evidence="ECO:0007829|PDB:4L9Z"
FT HELIX 111..128
FT /evidence="ECO:0007829|PDB:4L9Z"
FT STRAND 135..140
FT /evidence="ECO:0007829|PDB:4L9Z"
FT HELIX 143..147
FT /evidence="ECO:0007829|PDB:4L9Z"
FT HELIX 149..153
FT /evidence="ECO:0007829|PDB:4L9Z"
FT STRAND 159..164
FT /evidence="ECO:0007829|PDB:4L9Z"
FT HELIX 166..173
FT /evidence="ECO:0007829|PDB:4L9Z"
FT STRAND 179..182
FT /evidence="ECO:0007829|PDB:4L9Y"
FT STRAND 188..191
FT /evidence="ECO:0007829|PDB:4L9Z"
FT STRAND 194..197
FT /evidence="ECO:0007829|PDB:4L9Z"
FT HELIX 202..215
FT /evidence="ECO:0007829|PDB:4L9Z"
FT STRAND 218..221
FT /evidence="ECO:0007829|PDB:4L9Z"
FT HELIX 230..243
FT /evidence="ECO:0007829|PDB:4L9Z"
FT STRAND 248..252
FT /evidence="ECO:0007829|PDB:4L9Z"
FT HELIX 255..262
FT /evidence="ECO:0007829|PDB:4L9Z"
FT HELIX 267..285
FT /evidence="ECO:0007829|PDB:4L9Z"
FT STRAND 289..293
FT /evidence="ECO:0007829|PDB:4L9Z"
FT STRAND 296..299
FT /evidence="ECO:0007829|PDB:4L9Z"
FT HELIX 300..314
FT /evidence="ECO:0007829|PDB:4L9Z"
SQ SEQUENCE 318 AA; 34288 MW; E366B25B7A193AC1 CRC64;
MSFRLQPAPP ARPNRCQLFG PGSRPALFEK MAASAADVIN LDLEDSVAPD DKAQARANII
EAINGLDWGR KYLSVRINGL DTPFWYRDVV DLLEQAGDRL DQIMIPKVGC AADVYAVDAL
VTAIERAKGR TKPLSFEVII ESAAGIAHVE EIAASSPRLQ AMSLGAADFA ASMGMQTTGI
GGTQENYYML HDGQKHWSDP WHWAQAAIVA ACRTHGILPV DGPFGDFSDD EGFRAQARRS
ATLGMVGKWA IHPKQVALAN EVFTPSETAV TEAREILAAM DAAKARGEGA TVYKGRLVDI
ASIKQAEVIV RQAEMISA
