ID C6PTP2_9CLOT Unreviewed; 641 AA.
AC C6PTP2;
DT 22-SEP-2009, integrated into UniProtKB/TrEMBL.
DT 22-SEP-2009, sequence version 1.
DT 24-JAN-2024, entry version 88.
DE RecName: Full=4-hydroxy-3-methylbut-2-enyl diphosphate reductase {ECO:0000256|HAMAP-Rule:MF_00191};
DE Short=HMBPP reductase {ECO:0000256|HAMAP-Rule:MF_00191};
DE EC=1.17.7.4 {ECO:0000256|HAMAP-Rule:MF_00191};
GN Name=ispH {ECO:0000256|HAMAP-Rule:MF_00191};
GN ORFNames=CcarbDRAFT_2159 {ECO:0000313|EMBL:EET87378.1};
OS Clostridium carboxidivorans P7.
OC Bacteria; Bacillota; Clostridia; Eubacteriales; Clostridiaceae;
OC Clostridium.
OX NCBI_TaxID=536227 {ECO:0000313|EMBL:EET87378.1, ECO:0000313|Proteomes:UP000004198};
RN [1] {ECO:0000313|EMBL:EET87378.1, ECO:0000313|Proteomes:UP000004198}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=P7 {ECO:0000313|EMBL:EET87378.1,
RC ECO:0000313|Proteomes:UP000004198};
RG US DOE Joint Genome Institute (JGI-PGF);
RA Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Tice H., Bruce D.,
RA Goodwin L., Pitluck S., Larimer F., Land M.L., Hauser L., Hemme C.L.;
RT "The draft genome of Clostridium carboxidivorans P7.";
RL Submitted (JUN-2009) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Catalyzes the conversion of 1-hydroxy-2-methyl-2-(E)-butenyl
CC 4-diphosphate (HMBPP) into a mixture of isopentenyl diphosphate (IPP)
CC and dimethylallyl diphosphate (DMAPP). Acts in the terminal step of the
CC DOXP/MEP pathway for isoprenoid precursor biosynthesis.
CC {ECO:0000256|HAMAP-Rule:MF_00191}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + isopentenyl diphosphate + 2 oxidized [2Fe-2S]-
CC [ferredoxin] = (2E)-4-hydroxy-3-methylbut-2-enyl diphosphate + 2 H(+)
CC + 2 reduced [2Fe-2S]-[ferredoxin]; Xref=Rhea:RHEA:24488, Rhea:RHEA-
CC COMP:10000, Rhea:RHEA-COMP:10001, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:33737, ChEBI:CHEBI:33738,
CC ChEBI:CHEBI:128753, ChEBI:CHEBI:128769; EC=1.17.7.4;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_00191};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=dimethylallyl diphosphate + H2O + 2 oxidized [2Fe-2S]-
CC [ferredoxin] = (2E)-4-hydroxy-3-methylbut-2-enyl diphosphate + 2 H(+)
CC + 2 reduced [2Fe-2S]-[ferredoxin]; Xref=Rhea:RHEA:24825, Rhea:RHEA-
CC COMP:10000, Rhea:RHEA-COMP:10001, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:33737, ChEBI:CHEBI:33738,
CC ChEBI:CHEBI:57623, ChEBI:CHEBI:128753; EC=1.17.7.4;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_00191};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_00191};
CC Note=Binds 1 [4Fe-4S] cluster per subunit. {ECO:0000256|HAMAP-
CC Rule:MF_00191};
CC -!- PATHWAY: Isoprenoid biosynthesis; dimethylallyl diphosphate
CC biosynthesis; dimethylallyl diphosphate from (2E)-4-hydroxy-3-
CC methylbutenyl diphosphate: step 1/1. {ECO:0000256|HAMAP-Rule:MF_00191}.
CC -!- PATHWAY: Isoprenoid biosynthesis; isopentenyl diphosphate biosynthesis
CC via DXP pathway; isopentenyl diphosphate from 1-deoxy-D-xylulose 5-
CC phosphate: step 6/6. {ECO:0000256|HAMAP-Rule:MF_00191}.
CC -!- SIMILARITY: Belongs to the IspH family. {ECO:0000256|HAMAP-
CC Rule:MF_00191}.
CC -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:EET87378.1}.
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DR EMBL; ACVI01000031; EET87378.1; -; Genomic_DNA.
DR RefSeq; WP_007061044.1; NZ_GG770701.1.
DR AlphaFoldDB; C6PTP2; -.
DR STRING; 536227.Ccar_07490; -.
DR KEGG; cck:Ccar_07490; -.
DR PATRIC; fig|536227.13.peg.1575; -.
DR eggNOG; COG0539; Bacteria.
DR eggNOG; COG0761; Bacteria.
DR OrthoDB; 9804077at2; -.
DR UniPathway; UPA00056; UER00097.
DR UniPathway; UPA00059; UER00105.
DR Proteomes; UP000004198; Unassembled WGS sequence.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-UniRule.
DR GO; GO:0051745; F:4-hydroxy-3-methylbut-2-en-1-yl diphosphate reductase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0003676; F:nucleic acid binding; IEA:InterPro.
DR GO; GO:0050992; P:dimethylallyl diphosphate biosynthetic process; IEA:UniProtKB-UniRule.
DR GO; GO:0019288; P:isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway; IEA:UniProtKB-UniRule.
DR GO; GO:0016114; P:terpenoid biosynthetic process; IEA:UniProtKB-UniRule.
DR CDD; cd13944; lytB_ispH; 1.
DR CDD; cd05687; S1_RPS1_repeat_ec1_hs1; 1.
DR CDD; cd04465; S1_RPS1_repeat_ec2_hs2; 1.
DR CDD; cd05688; S1_RPS1_repeat_ec3; 1.
DR Gene3D; 3.40.50.11270; -; 1.
DR Gene3D; 3.40.1010.20; 4-hydroxy-3-methylbut-2-enyl diphosphate reductase, catalytic domain; 2.
DR Gene3D; 2.40.50.140; Nucleic acid-binding proteins; 3.
DR HAMAP; MF_00191; IspH; 1.
DR InterPro; IPR003451; LytB/IspH.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR InterPro; IPR035104; Ribosomal_protein_S1-like.
DR InterPro; IPR003029; S1_domain.
DR NCBIfam; TIGR00216; ispH_lytB; 1.
DR PANTHER; PTHR30426; 4-HYDROXY-3-METHYLBUT-2-ENYL DIPHOSPHATE REDUCTASE; 1.
DR PANTHER; PTHR30426:SF0; 4-HYDROXY-3-METHYLBUT-2-ENYL DIPHOSPHATE REDUCTASE; 1.
DR Pfam; PF02401; LYTB; 1.
DR Pfam; PF00575; S1; 3.
DR PRINTS; PR00681; RIBOSOMALS1.
DR SMART; SM00316; S1; 4.
DR SUPFAM; SSF50249; Nucleic acid-binding proteins; 4.
DR PROSITE; PS50126; S1; 4.
PE 3: Inferred from homology;
KW 4Fe-4S {ECO:0000256|ARBA:ARBA00022485, ECO:0000256|HAMAP-Rule:MF_00191};
KW Iron {ECO:0000256|ARBA:ARBA00023004, ECO:0000256|HAMAP-Rule:MF_00191};
KW Iron-sulfur {ECO:0000256|ARBA:ARBA00023014, ECO:0000256|HAMAP-
KW Rule:MF_00191}; Isoprene biosynthesis {ECO:0000256|HAMAP-Rule:MF_00191};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723, ECO:0000256|HAMAP-
KW Rule:MF_00191}; Oxidoreductase {ECO:0000256|HAMAP-Rule:MF_00191};
KW Reference proteome {ECO:0000313|Proteomes:UP000004198}.
FT DOMAIN 301..370
FT /note="S1 motif"
FT /evidence="ECO:0000259|PROSITE:PS50126"
FT DOMAIN 387..456
FT /note="S1 motif"
FT /evidence="ECO:0000259|PROSITE:PS50126"
FT DOMAIN 477..545
FT /note="S1 motif"
FT /evidence="ECO:0000259|PROSITE:PS50126"
FT DOMAIN 567..636
FT /note="S1 motif"
FT /evidence="ECO:0000259|PROSITE:PS50126"
FT ACT_SITE 128
FT /note="Proton donor"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00191"
FT BINDING 12
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00191"
FT BINDING 41
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00191"
FT BINDING 76
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00191"
FT BINDING 98
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00191"
FT BINDING 126
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00191"
FT BINDING 162
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00191"
FT BINDING 190
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00191"
FT BINDING 218..220
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00191"
FT BINDING 263
FT /ligand="substrate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00191"
SQ SEQUENCE 641 AA; 71858 MW; CFD431A33183A323 CRC64;
MKIVLADEAG FCFGVKRAVE EAENVQKKYN KKVFTLGPLI HNSDVVNYLK EKNIYPIELD
TINDLNKDDI VIIRSHGVPR KTIELLQSKS LNIVDATCPY VANIHKKVDE YYKLGYSILI
VGDKNHPEVV GINGWCENKA IISKDGSDLK NLPSKICVVS QTTEKQENWK RVLSIIVKNC
KEIVAFNTIC SATELRQNSA EKLSKKVDFM VVLGGRNSSN TTKLYEICKN NCSNTIHVEN
SGEIPDDIIN SKINTIGVTA GASTPHWIIK EAISKMCEGK NLEMSEQLAY MEQNDRQIIV
GQVITGTVIT VNEKEAFLNI GYKSDGLLPK SEVTKDVNLN LADLIQVGNE LEVKVIRRKN
EDGYVVLSKI ELQRESAFKE IKEASENKIS LKVLVKDAVK GGLVATYKGI RIFIPASHVE
LFHVNDLSSY IGKELEVNII EFKEDRKGRR IVASRRELLK SEKEVKEEGT WNSLEKDTVV
EGEVKRLTNF GAFVDVQGVD GLLHVSEISW GRVEKPEDSL KIGKKVKVYI LDIDKEKKKL
SLSIKKTIED PWTNVEIKYP VGNIVLGNIV LGKVVRFANF GAFVELEPGV DALVHISQIS
HKRINKPEDA LKIGEEIKAK ILEVNKENKK IGLSIKEVDE I
//
