CUPIN_RHORT
ID CUPIN_RHORT Reviewed; 156 AA.
AC Q2RSU5;
DT 10-OCT-2018, integrated into UniProtKB/Swiss-Prot.
DT 24-JAN-2006, sequence version 1.
DT 03-AUG-2022, entry version 88.
DE RecName: Full=1-methylthio-D-xylulose 5-phosphate methylsulfurylase {ECO:0000303|PubMed:23035785};
DE Short=MTXu 5-P methylsulfurylase {ECO:0000303|PubMed:23035785};
DE EC=4.4.1.- {ECO:0000269|PubMed:23035785, ECO:0000269|PubMed:23042035};
DE AltName: Full=1-methylthio-xylulose 5-phosphate sulfo-lyase {ECO:0000305};
GN Name=cupin {ECO:0000303|PubMed:23042035};
GN OrderedLocusNames=Rru_A2000 {ECO:0000312|EMBL:ABC22800.1};
OS Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 /
OS NCIMB 8255 / S1).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Rhodospirillales;
OC Rhodospirillaceae; Rhodospirillum.
OX NCBI_TaxID=269796;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1;
RX PubMed=21886856; DOI=10.4056/sigs.1804360;
RA Munk A.C., Copeland A., Lucas S., Lapidus A., Del Rio T.G., Barry K.,
RA Detter J.C., Hammon N., Israni S., Pitluck S., Brettin T., Bruce D.,
RA Han C., Tapia R., Gilna P., Schmutz J., Larimer F., Land M., Kyrpides N.C.,
RA Mavromatis K., Richardson P., Rohde M., Goeker M., Klenk H.P., Zhang Y.,
RA Roberts G.P., Reslewic S., Schwartz D.C.;
RT "Complete genome sequence of Rhodospirillum rubrum type strain (S1).";
RL Stand. Genomic Sci. 4:293-302(2011).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, PATHWAY, MUTAGENESIS OF CYS-121, AND ACTIVE
RP SITE.
RX PubMed=23035785; DOI=10.1021/bi301215g;
RA Warlick B.P., Evans B.S., Erb T.J., Ramagopal U.A., Sriram J., Imker H.J.,
RA Sauder J.M., Bonanno J.B., Burley S.K., Tabita F.R., Almo S.C.,
RA Sweedler J.S., Gerlt J.A.;
RT "1-methylthio-D-xylulose 5-phosphate methylsulfurylase: a novel route to 1-
RT deoxy-D-xylulose 5-phosphate in Rhodospirillum rubrum.";
RL Biochemistry 51:8324-8326(2012).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, PATHWAY, AND DISRUPTION PHENOTYPE.
RC STRAIN=ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1;
RX PubMed=23042035; DOI=10.1038/nchembio.1087;
RA Erb T.J., Evans B.S., Cho K., Warlick B.P., Sriram J., Wood B.M.,
RA Imker H.J., Sweedler J.V., Tabita F.R., Gerlt J.A.;
RT "A RubisCO-like protein links SAM metabolism with isoprenoid
RT biosynthesis.";
RL Nat. Chem. Biol. 8:926-932(2012).
RN [4]
RP PATHWAY, AND DISRUPTION PHENOTYPE.
RX PubMed=29133429; DOI=10.1073/pnas.1711625114;
RA North J.A., Miller A.R., Wildenthal J.A., Young S.J., Tabita F.R.;
RT "Microbial pathway for anaerobic 5'-methylthioadenosine metabolism coupled
RT to ethylene formation.";
RL Proc. Natl. Acad. Sci. U.S.A. 114:E10455-E10464(2017).
RN [5] {ECO:0007744|PDB:3JZV}
RP X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) OF 2-156 IN COMPLEX WITH MANGANESE.
RA Ramagopal U.A., Toro R., Burley S.K., Almo S.C.;
RT "Crystal structure of Rru_A2000 from Rhodospirillum rubrum: A cupin-2
RT domain.";
RL Submitted (SEP-2009) to the PDB data bank.
CC -!- FUNCTION: Catalyzes the formation of methanethiol and 1-deoxy-D-
CC xylulose 5-phosphate (DXP) from 1-methylthioxylulose 5-phosphate (MTXu-
CC 5P) (PubMed:23042035, PubMed:23035785). Involved in the MTA-isoprenoid
CC shunt of the methionine salvage pathway (PubMed:23042035).
CC {ECO:0000269|PubMed:23035785, ECO:0000269|PubMed:23042035}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=AH2 + S-methyl-1-thio-D-xylulose 5-phosphate = 1-deoxy-D-
CC xylulose 5-phosphate + A + methanethiol; Xref=Rhea:RHEA:57096,
CC ChEBI:CHEBI:13193, ChEBI:CHEBI:16007, ChEBI:CHEBI:17499,
CC ChEBI:CHEBI:57792, ChEBI:CHEBI:141466;
CC Evidence={ECO:0000269|PubMed:23035785, ECO:0000269|PubMed:23042035};
CC -!- PATHWAY: Amino-acid biosynthesis; L-methionine biosynthesis via salvage
CC pathway. {ECO:0000305|PubMed:29133429}.
CC -!- PATHWAY: Metabolic intermediate biosynthesis; 1-deoxy-D-xylulose 5-
CC phosphate biosynthesis. {ECO:0000305|PubMed:23035785,
CC ECO:0000305|PubMed:23042035}.
CC -!- DISRUPTION PHENOTYPE: Mutant does not release methanethiol and does not
CC show an increase in 1-deoxy-D-xylulose 5-phosphate formation after 5'-
CC methylthioadenosine (MTA) feeding. Mutant accumulates a mixture of 1-
CC methylthioxylulose 5-phosphate (MTXu-5P) and 1-methylthioribulose 5-
CC phosphate (MTRu-5P) (PubMed:23042035). Inactivation of the gene
CC increases ethylene production from MTA-grown cells (PubMed:29133429).
CC {ECO:0000269|PubMed:23042035, ECO:0000269|PubMed:29133429}.
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DR EMBL; CP000230; ABC22800.1; -; Genomic_DNA.
DR RefSeq; WP_011389753.1; NC_007643.1.
DR RefSeq; YP_427087.1; NC_007643.1.
DR PDB; 3JZV; X-ray; 2.30 A; A=2-156.
DR PDBsum; 3JZV; -.
DR AlphaFoldDB; Q2RSU5; -.
DR SMR; Q2RSU5; -.
DR STRING; 269796.Rru_A2000; -.
DR DNASU; 3835425; -.
DR EnsemblBacteria; ABC22800; ABC22800; Rru_A2000.
DR KEGG; rru:Rru_A2000; -.
DR PATRIC; fig|269796.9.peg.2084; -.
DR eggNOG; COG0662; Bacteria.
DR HOGENOM; CLU_116722_1_0_5; -.
DR OMA; WHQFRAN; -.
DR OrthoDB; 1928636at2; -.
DR PhylomeDB; Q2RSU5; -.
DR BioCyc; MetaCyc:MON-17872; -.
DR UniPathway; UPA00064; -.
DR UniPathway; UPA00904; -.
DR EvolutionaryTrace; Q2RSU5; -.
DR Proteomes; UP000001929; Chromosome.
DR GO; GO:0016829; F:lyase activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0052865; P:1-deoxy-D-xylulose 5-phosphate biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0019509; P:L-methionine salvage from methylthioadenosine; IEA:UniProtKB-UniPathway.
DR Gene3D; 2.60.120.10; -; 1.
DR InterPro; IPR013096; Cupin_2.
DR InterPro; IPR014710; RmlC-like_jellyroll.
DR InterPro; IPR011051; RmlC_Cupin_sf.
DR Pfam; PF07883; Cupin_2; 1.
DR SUPFAM; SSF51182; SSF51182; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Amino-acid biosynthesis; Lyase; Manganese; Metal-binding;
KW Methionine biosynthesis; Reference proteome.
FT CHAIN 1..156
FT /note="1-methylthio-D-xylulose 5-phosphate
FT methylsulfurylase"
FT /id="PRO_0000445436"
FT ACT_SITE 121
FT /evidence="ECO:0000305|PubMed:23035785"
FT BINDING 67
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000269|Ref.5, ECO:0007744|PDB:3JZV"
FT BINDING 69
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000269|Ref.5, ECO:0007744|PDB:3JZV"
FT BINDING 73
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000269|Ref.5, ECO:0007744|PDB:3JZV"
FT BINDING 107
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000269|Ref.5, ECO:0007744|PDB:3JZV"
FT MUTAGEN 121
FT /note="C->A: Loss of activity."
FT /evidence="ECO:0000269|PubMed:23035785"
FT STRAND 24..26
FT /evidence="ECO:0007829|PDB:3JZV"
FT STRAND 36..44
FT /evidence="ECO:0007829|PDB:3JZV"
FT STRAND 50..63
FT /evidence="ECO:0007829|PDB:3JZV"
FT STRAND 73..80
FT /evidence="ECO:0007829|PDB:3JZV"
FT STRAND 82..86
FT /evidence="ECO:0007829|PDB:3JZV"
FT STRAND 89..93
FT /evidence="ECO:0007829|PDB:3JZV"
FT STRAND 98..101
FT /evidence="ECO:0007829|PDB:3JZV"
FT STRAND 107..110
FT /evidence="ECO:0007829|PDB:3JZV"
FT STRAND 117..126
FT /evidence="ECO:0007829|PDB:3JZV"
FT HELIX 135..142
FT /evidence="ECO:0007829|PDB:3JZV"
FT HELIX 145..151
FT /evidence="ECO:0007829|PDB:3JZV"
SQ SEQUENCE 156 AA; 17124 MW; 2685A30A37280CEE CRC64;
MSDSNDDRPF RPFQSQYRWP GVDLLAYKEE GSAPFRSVTR QVLFSGNGLT GELRYFEVGP
GGHSTLERHQ HAHGVMILKG RGHAMVGRAV SAVAPYDLVT IPGWSWHQFR APADEALGFL
CMVNAERDKP QLPTEADLAM LRADDAVAAF LDGLAG
