NIRJ_PARPN
ID NIRJ_PARPN Reviewed; 407 AA.
AC A0A1I5E523;
DT 02-JUN-2021, integrated into UniProtKB/Swiss-Prot.
DT 12-APR-2017, sequence version 1.
DT 03-AUG-2022, entry version 24.
DE RecName: Full=Pre-heme d1 synthase {ECO:0000305};
GN Name=nirJ {ECO:0000303|PubMed:20420837};
GN ORFNames=BDE18_2053 {ECO:0000312|EMBL:RKS52721.1},
GN HYQ43_08945 {ECO:0000312|EMBL:QLH14439.1};
OS Paracoccus pantotrophus (Thiosphaera pantotropha).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Rhodobacterales;
OC Rhodobacteraceae; Paracoccus.
OX NCBI_TaxID=82367;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 35512 / DSM 2944 / CIP 106514 / LMD 82.5 / NBRC 102493 / NCCB
RC 82005 / GB17;
RA Goeker M.;
RT "Genomic Encyclopedia of Archaeal and Bacterial Type Strains, Phase II
RT (KMG-II): from individual species to whole genera.";
RL Submitted (OCT-2018) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ACCC 10489;
RA Si Y.;
RT "The complete genome of Paracoccus pantotrophus ACCC 10489.";
RL Submitted (JUL-2020) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP COFACTOR, AND SUBUNIT.
RX PubMed=20420837; DOI=10.1016/j.febslet.2010.04.053;
RA Brindley A.A., Zajicek R., Warren M.J., Ferguson S.J., Rigby S.E.;
RT "NirJ, a radical SAM family member of the d1 heme biogenesis cluster.";
RL FEBS Lett. 584:2461-2466(2010).
RN [4]
RP FUNCTION, AND PATHWAY.
RC STRAIN=ATCC 35512 / DSM 2944 / CIP 106514 / LMD 82.5 / NBRC 102493 / NCCB
RC 82005 / GB17;
RX PubMed=21969545; DOI=10.1073/pnas.1108228108;
RA Bali S., Lawrence A.D., Lobo S.A., Saraiva L.M., Golding B.T., Palmer D.J.,
RA Howard M.J., Ferguson S.J., Warren M.J.;
RT "Molecular hijacking of siroheme for the synthesis of heme and d1 heme.";
RL Proc. Natl. Acad. Sci. U.S.A. 108:18260-18265(2011).
CC -!- FUNCTION: Involved in heme d1 biosynthesis (Probable). Radical SAM
CC enzyme that catalyzes the removal of two propionate side chains from
CC the intermediate 12,18-didecarboxysiroheme (DDSH) and may introduce the
CC keto functions on rings A and B, yielding the heme d1 precursor
CC dihydro-heme d1 (By similarity). {ECO:0000250|UniProtKB:A8LLZ7,
CC ECO:0000305|PubMed:21969545}.
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000255|PROSITE-ProRule:PRU01266,
CC ECO:0000269|PubMed:20420837};
CC Note=Binds 2 [4Fe-4S] clusters per subunit.
CC {ECO:0000250|UniProtKB:A8LLZ7};
CC -!- PATHWAY: Porphyrin-containing compound metabolism.
CC {ECO:0000305|PubMed:21969545}.
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:20420837}.
CC -!- SIMILARITY: Belongs to the radical SAM superfamily. {ECO:0000305}.
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DR EMBL; CP058690; QLH14439.1; -; Genomic_DNA.
DR EMBL; RBLI01000001; RKS52721.1; -; Genomic_DNA.
DR RefSeq; WP_024843016.1; NZ_RIAQ01000012.1.
DR AlphaFoldDB; A0A1I5E523; -.
DR SMR; A0A1I5E523; -.
DR Proteomes; UP000273626; Unassembled WGS sequence.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0003824; F:catalytic activity; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR Gene3D; 3.20.20.70; -; 1.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR006638; Elp3/MiaB/NifB.
DR InterPro; IPR023992; HemeD1_Synth_NirJ.
DR InterPro; IPR017200; PqqE-like.
DR InterPro; IPR007197; rSAM.
DR Pfam; PF04055; Radical_SAM; 1.
DR PIRSF; PIRSF037420; PQQ_syn_pqqE; 1.
DR SFLD; SFLDF00393; heme_D1_biosynthesis_(NirJ-lik; 1.
DR SMART; SM00729; Elp3; 1.
DR TIGRFAMs; TIGR04051; rSAM_NirJ; 1.
DR PROSITE; PS51918; RADICAL_SAM; 1.
PE 1: Evidence at protein level;
KW 4Fe-4S; Iron; Iron-sulfur; Metal-binding; S-adenosyl-L-methionine.
FT CHAIN 1..407
FT /note="Pre-heme d1 synthase"
FT /id="PRO_0000452838"
FT DOMAIN 24..236
FT /note="Radical SAM core"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT BINDING 38
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT BINDING 42
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT BINDING 45
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="1"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT BINDING 342
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:A8LLZ7"
FT BINDING 345
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:A8LLZ7"
FT BINDING 351
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:A8LLZ7"
FT BINDING 373
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:A8LLZ7"
SQ SEQUENCE 407 AA; 45072 MW; AE701AB6B01D72FB CRC64;
MFRLTQYMHQ LLDPSPPRRR SRPDAVRPVV IWNLTRSCNL KCRHCYTVSA DRPFPGELSH
DQAMAVLRDL SDFRIPALIL SGGEPMSRFD FWELAEEARR LDFRHLSLST NGTKIDAGNV
ERLAGLGFDY VGISLDGIGA VNDWFRGVEG AFDQALAGVR ACKAQGVKVG LRFTITEGNA
HHLPAMLDLC RDEGVDKFYL SHLVYAGRGD KHRGEDTEHA RTRRAMDLLI ARAWQAVERG
EPLEVVTGNN DADAVYFLRW AETRFAPAAV AHLRAHLQAW GGNSSGLGVG NIDPQGRVHP
DTYWSDYTLG SVKERPFSAI WTGDDPILAT LRTRPRPLKG RCGACAYQAV CGGNTRIRAL
QLTGDPWAED PACYLSGSEI GAEGADLDRL AVTPFRGKSH DPAHRFL
