ID   NIRJ_DINSH              Reviewed;         404 AA.
AC   A8LLZ7;
DT   02-JUN-2021, integrated into UniProtKB/Swiss-Prot.
DT   04-DEC-2007, sequence version 1.
DT   03-AUG-2022, entry version 68.
DE   RecName: Full=Pre-heme d1 synthase {ECO:0000305};
GN   Name=nirJ {ECO:0000303|PubMed:29076625};
GN   OrderedLocusNames=Dshi_3173 {ECO:0000312|EMBL:ABV94906.1};
OS   Dinoroseobacter shibae (strain DSM 16493 / NCIMB 14021 / DFL 12).
OC   Bacteria; Proteobacteria; Alphaproteobacteria; Rhodobacterales;
OC   Roseobacteraceae; Dinoroseobacter.
OX   NCBI_TaxID=398580;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=DSM 16493 / NCIMB 14021 / DFL 12;
RX   PubMed=19741735; DOI=10.1038/ismej.2009.94;
RA   Wagner-Dobler I., Ballhausen B., Berger M., Brinkhoff T., Buchholz I.,
RA   Bunk B., Cypionka H., Daniel R., Drepper T., Gerdts G., Hahnke S., Han C.,
RA   Jahn D., Kalhoefer D., Kiss H., Klenk H.P., Kyrpides N., Liebl W.,
RA   Liesegang H., Meincke L., Pati A., Petersen J., Piekarski T.,
RA   Pommerenke C., Pradella S., Pukall R., Rabus R., Stackebrandt E., Thole S.,
RA   Thompson L., Tielen P., Tomasch J., von Jan M., Wanphrut N., Wichels A.,
RA   Zech H., Simon M.;
RT   "The complete genome sequence of the algal symbiont Dinoroseobacter shibae:
RT   a hitchhiker's guide to life in the sea.";
RL   ISME J. 4:61-77(2010).
RN   [2]
RP   FUNCTION, COFACTOR, PATHWAY, AND MUTAGENESIS OF CYS-36; CYS-40 AND CYS-43.
RC   STRAIN=DSM 16493 / NCIMB 14021 / DFL 12;
RX   PubMed=29076625; DOI=10.1111/febs.14307;
RA   Boss L., Oehme R., Billig S., Birkemeyer C., Layer G.;
RT   "The radical SAM enzyme NirJ catalyzes the removal of two propionate side
RT   chains during heme d1 biosynthesis.";
RL   FEBS J. 284:4314-4327(2017).
CC   -!- FUNCTION: Involved in heme d1 biosynthesis (PubMed:29076625). Radical
CC       SAM enzyme that catalyzes the removal of two propionate side chains
CC       from the intermediate 12,18-didecarboxysiroheme (DDSH) and may
CC       introduce the keto functions on rings A and B, yielding the heme d1
CC       precursor dihydro-heme d1 (PubMed:29076625).
CC       {ECO:0000269|PubMed:29076625}.
CC   -!- COFACTOR:
CC       Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC         Evidence={ECO:0000255|PROSITE-ProRule:PRU01266,
CC         ECO:0000269|PubMed:29076625};
CC       Note=Binds 2 [4Fe-4S] clusters per subunit.
CC       {ECO:0000269|PubMed:29076625};
CC   -!- PATHWAY: Porphyrin-containing compound metabolism.
CC       {ECO:0000269|PubMed:29076625}.
CC   -!- SIMILARITY: Belongs to the radical SAM superfamily. {ECO:0000305}.
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DR   EMBL; CP000830; ABV94906.1; -; Genomic_DNA.
DR   RefSeq; WP_012179833.1; NC_009952.1.
DR   AlphaFoldDB; A8LLZ7; -.
DR   SMR; A8LLZ7; -.
DR   STRING; 398580.Dshi_3173; -.
DR   EnsemblBacteria; ABV94906; ABV94906; Dshi_3173.
DR   KEGG; dsh:Dshi_3173; -.
DR   eggNOG; COG0535; Bacteria.
DR   HOGENOM; CLU_009273_4_0_5; -.
DR   OMA; PVVIWNL; -.
DR   OrthoDB; 1172757at2; -.
DR   Proteomes; UP000006833; Chromosome.
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; Reference proteome;
KW   S-adenosyl-L-methionine.
FT   CHAIN           1..404
FT                   /note="Pre-heme d1 synthase"
FT                   /id="PRO_0000452837"
FT   DOMAIN          22..235
FT                   /note="Radical SAM core"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01266"
FT   BINDING         36
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                   ECO:0000269|PubMed:29076625"
FT   BINDING         40
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                   ECO:0000269|PubMed:29076625"
FT   BINDING         43
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                   ECO:0000269|PubMed:29076625"
FT   BINDING         340
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000305|PubMed:29076625"
FT   BINDING         343
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000305|PubMed:29076625"
FT   BINDING         349
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000305|PubMed:29076625"
FT   BINDING         371
FT                   /ligand="[4Fe-4S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:49883"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000305|PubMed:29076625"
FT   MUTAGEN         36
FT                   /note="C->A: Contains half the amount of iron and sulfide
FT                   per enzyme compared to the wild-type; when associated with
FT                   A-40 and A-43."
FT                   /evidence="ECO:0000269|PubMed:29076625"
FT   MUTAGEN         40
FT                   /note="C->A: Contains half the amount of iron and sulfide
FT                   per enzyme compared to the wild-type; when associated with
FT                   A-36 and A-43."
FT                   /evidence="ECO:0000269|PubMed:29076625"
FT   MUTAGEN         43
FT                   /note="C->A: Contains half the amount of iron and sulfide
FT                   per enzyme compared to the wild-type; when associated with
FT                   A-36 and A-40."
FT                   /evidence="ECO:0000269|PubMed:29076625"
SQ   SEQUENCE   404 AA;  44225 MW;  20A034C9F10E9CE8 CRC64;
     MFRLSHYLDQ LYHPTPPRIA RGTPKPVVIW NLTRRCNLKC KHCYTVSADV DFPGELTAAQ
     ARETLEDIGR FKVPALILSG GEPLLRDDLF ALAKRARALT RVLALSTNGT GVIGSKADRV
     AEIGFDYVGI SIDGIGATND AFRGVIGAYE QALAGVRSCK RRGIKVGLRF TITEQNESQL
     PELLKLCDDE GVDKFYLSHL VYAGRGNKNR GEDADHARTR RAMDLLIARA LESAEGRGHP
     LEIVTGNNDA DAVYFLNWAK ANFPAAQVAH LRKHLEAWGG NASGVGVANI DTQGDVHPDT
     YWSEYTVGSV KQTPFSELWT GPDPMLAELR RRPRPLKGRC GACAHQAVCG GNTRIRALQL
     TGDPWAEDPA CYLTAAETGT ATDIDRLTVR PFIGDRHDPK PAFV