NIRN_PSEAE
ID NIRN_PSEAE Reviewed; 493 AA.
AC Q9I609; P95418;
DT 02-JUN-2021, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2001, sequence version 1.
DT 03-AUG-2022, entry version 113.
DE RecName: Full=Dihydro-heme d1 dehydrogenase {ECO:0000303|PubMed:31173777};
DE EC=1.3.-.- {ECO:0000269|PubMed:25204657};
DE Flags: Precursor;
GN Name=nirN {ECO:0000303|PubMed:8982003};
GN OrderedLocusNames=PA0509 {ECO:0000312|EMBL:AAG03898.1};
OS Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM
OS 14847 / LMG 12228 / 1C / PRS 101 / PAO1).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
OC Pseudomonadaceae; Pseudomonas.
OX NCBI_TaxID=208964;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, PATHWAY, AND DISRUPTION
RP PHENOTYPE.
RC STRAIN=ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C /
RC PRS 101 / PAO1;
RX PubMed=8982003; DOI=10.1128/jb.179.1.235-242.1997;
RA Kawasaki S., Arai H., Kodama T., Igarashi Y.;
RT "Gene cluster for dissimilatory nitrite reductase (nir) from Pseudomonas
RT aeruginosa: sequencing and identification of a locus for heme d1
RT biosynthesis.";
RL J. Bacteriol. 179:235-242(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C /
RC PRS 101 / PAO1;
RX PubMed=10984043; DOI=10.1038/35023079;
RA Stover C.K., Pham X.-Q.T., Erwin A.L., Mizoguchi S.D., Warrener P.,
RA Hickey M.J., Brinkman F.S.L., Hufnagle W.O., Kowalik D.J., Lagrou M.,
RA Garber R.L., Goltry L., Tolentino E., Westbrock-Wadman S., Yuan Y.,
RA Brody L.L., Coulter S.N., Folger K.R., Kas A., Larbig K., Lim R.M.,
RA Smith K.A., Spencer D.H., Wong G.K.-S., Wu Z., Paulsen I.T., Reizer J.,
RA Saier M.H. Jr., Hancock R.E.W., Lory S., Olson M.V.;
RT "Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic
RT pathogen.";
RL Nature 406:959-964(2000).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, PATHWAY, AND DISRUPTION PHENOTYPE.
RC STRAIN=ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C /
RC PRS 101 / PAO1;
RX PubMed=25204657; DOI=10.1074/jbc.m114.603886;
RA Adamczack J., Hoffmann M., Papke U., Haufschildt K., Nicke T., Broering M.,
RA Sezer M., Weimar R., Kuhlmann U., Hildebrandt P., Layer G.;
RT "NirN protein from Pseudomonas aeruginosa is a novel electron-bifurcating
RT dehydrogenase catalyzing the last step of heme d1 biosynthesis.";
RL J. Biol. Chem. 289:30753-30762(2014).
RN [4] {ECO:0007744|PDB:6RTD, ECO:0007744|PDB:6RTE}
RP X-RAY CRYSTALLOGRAPHY (1.94 ANGSTROMS) OF 21-493 IN COMPLEXES WITH HEME C
RP AND HEME D1, COFACTOR, SUBUNIT, DOMAIN, AND MUTAGENESIS OF HIS-165;
RP HIS-341; HIS-435 AND TYR-479.
RC STRAIN=ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C /
RC PRS 101 / PAO1;
RX PubMed=31173777; DOI=10.1016/j.jmb.2019.05.046;
RA Klunemann T., Preuss A., Adamczack J., Rosa L.F.M., Harnisch F., Layer G.,
RA Blankenfeldt W.;
RT "Crystal structure of dihydro-heme d1 dehydrogenase NirN from Pseudomonas
RT aeruginosa reveals amino acid residues essential for catalysis.";
RL J. Mol. Biol. 431:3246-3260(2019).
CC -!- FUNCTION: Involved in heme d1 biosynthesis (PubMed:8982003,
CC PubMed:25204657). Catalyzes the introduction of a double bond into the
CC propionate side chain of pyrrole ring D of dihydro-heme d1, therefore
CC converting dihydro-heme d1 to heme d1 (PubMed:25204657).
CC {ECO:0000269|PubMed:25204657, ECO:0000269|PubMed:8982003}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=A + dihydro-heme d1 = AH2 + heme d1; Xref=Rhea:RHEA:56524,
CC ChEBI:CHEBI:13193, ChEBI:CHEBI:17499, ChEBI:CHEBI:60549,
CC ChEBI:CHEBI:140498; Evidence={ECO:0000269|PubMed:25204657};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:56525;
CC Evidence={ECO:0000269|PubMed:25204657};
CC -!- COFACTOR:
CC Name=heme c; Xref=ChEBI:CHEBI:61717;
CC Evidence={ECO:0000269|PubMed:25204657, ECO:0000269|PubMed:31173777};
CC -!- PATHWAY: Porphyrin-containing compound metabolism.
CC {ECO:0000269|PubMed:25204657, ECO:0000305|PubMed:8982003}.
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:31173777}.
CC -!- SUBCELLULAR LOCATION: Periplasm {ECO:0000305|PubMed:25204657}.
CC -!- DOMAIN: Consists of an N-terminal domain that binds the heme c
CC cofactor, followed by a long linker segment, and a C-terminal region
CC that exhibits an eight-bladed heme d1-binding beta-propeller domain.
CC {ECO:0000269|PubMed:31173777}.
CC -!- DISRUPTION PHENOTYPE: The mutant exhibits decreased dissimilatory
CC nitrite reductase (NIR) activity (PubMed:8982003). In the absence of
CC this gene, the formation of the acrylic double bond of heme d1 does not
CC take place and dihydro-heme d1 is inserted into the nitrite reductase
CC NirS (PubMed:25204657). {ECO:0000269|PubMed:25204657,
CC ECO:0000269|PubMed:8982003}.
CC -!- SIMILARITY: Belongs to the cytochrome c family. {ECO:0000305}.
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DR EMBL; D84475; BAA12683.1; -; Genomic_DNA.
DR EMBL; AE004091; AAG03898.1; -; Genomic_DNA.
DR PIR; A83581; A83581.
DR RefSeq; NP_249200.1; NC_002516.2.
DR RefSeq; WP_003113244.1; NZ_QZGE01000010.1.
DR PDB; 6RTD; X-ray; 2.36 A; A/B=21-493.
DR PDB; 6RTE; X-ray; 1.94 A; A/B=21-493.
DR PDBsum; 6RTD; -.
DR PDBsum; 6RTE; -.
DR AlphaFoldDB; Q9I609; -.
DR SMR; Q9I609; -.
DR STRING; 287.DR97_3477; -.
DR PaxDb; Q9I609; -.
DR PRIDE; Q9I609; -.
DR EnsemblBacteria; AAG03898; AAG03898; PA0509.
DR GeneID; 878428; -.
DR KEGG; pae:PA0509; -.
DR PATRIC; fig|208964.12.peg.539; -.
DR PseudoCAP; PA0509; -.
DR HOGENOM; CLU_025262_1_0_6; -.
DR InParanoid; Q9I609; -.
DR OMA; LHGGPKF; -.
DR PhylomeDB; Q9I609; -.
DR BioCyc; PAER208964:G1FZ6-514-MON; -.
DR Proteomes; UP000002438; Chromosome.
DR GO; GO:0042597; C:periplasmic space; IEA:UniProtKB-SubCell.
DR GO; GO:0009055; F:electron transfer activity; IEA:InterPro.
DR GO; GO:0020037; F:heme binding; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006783; P:heme biosynthetic process; IDA:PseudoCAP.
DR Gene3D; 1.10.760.10; -; 1.
DR Gene3D; 2.140.10.20; -; 1.
DR InterPro; IPR009056; Cyt_c-like_dom.
DR InterPro; IPR036909; Cyt_c-like_dom_sf.
DR InterPro; IPR003143; Cyt_cd1_C_sf.
DR InterPro; IPR011048; Haem_d1_sf.
DR Pfam; PF13442; Cytochrome_CBB3; 1.
DR SUPFAM; SSF46626; SSF46626; 1.
DR SUPFAM; SSF51004; SSF51004; 1.
DR PROSITE; PS51007; CYTC; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Heme; Iron; Metal-binding; Oxidoreductase; Periplasm;
KW Reference proteome; Signal.
FT SIGNAL 1..18
FT /evidence="ECO:0000255"
FT CHAIN 19..493
FT /note="Dihydro-heme d1 dehydrogenase"
FT /id="PRO_5004327132"
FT DOMAIN 19..96
FT /note="Cytochrome c"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00433"
FT REGION 114..468
FT /note="D1-heme domain"
FT /evidence="ECO:0000305|PubMed:31173777"
FT BINDING 31
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /note="covalent"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00433,
FT ECO:0000269|PubMed:31173777, ECO:0007744|PDB:6RTD,
FT ECO:0007744|PDB:6RTE"
FT BINDING 34
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /note="covalent"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00433,
FT ECO:0000269|PubMed:31173777, ECO:0007744|PDB:6RTD,
FT ECO:0007744|PDB:6RTE"
FT BINDING 35
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00433,
FT ECO:0000269|PubMed:31173777, ECO:0007744|PDB:6RTD,
FT ECO:0007744|PDB:6RTE"
FT BINDING 68
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /evidence="ECO:0000269|PubMed:31173777,
FT ECO:0007744|PDB:6RTD, ECO:0007744|PDB:6RTE"
FT BINDING 73
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT /evidence="ECO:0000269|PubMed:31173777,
FT ECO:0007744|PDB:6RTD, ECO:0007744|PDB:6RTE"
FT BINDING 165
FT /ligand="heme d1"
FT /ligand_id="ChEBI:CHEBI:60549"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="proximal binding residue"
FT /evidence="ECO:0000269|PubMed:31173777,
FT ECO:0007744|PDB:6RTD"
FT BINDING 167
FT /ligand="heme d1"
FT /ligand_id="ChEBI:CHEBI:60549"
FT /evidence="ECO:0000269|PubMed:31173777,
FT ECO:0007744|PDB:6RTD"
FT BINDING 169
FT /ligand="heme d1"
FT /ligand_id="ChEBI:CHEBI:60549"
FT /evidence="ECO:0000269|PubMed:31173777,
FT ECO:0007744|PDB:6RTD"
FT BINDING 182
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /evidence="ECO:0000269|PubMed:31173777,
FT ECO:0007744|PDB:6RTE"
FT BINDING 182
FT /ligand="heme d1"
FT /ligand_id="ChEBI:CHEBI:60549"
FT /evidence="ECO:0000269|PubMed:31173777,
FT ECO:0007744|PDB:6RTD"
FT BINDING 207
FT /ligand="heme d1"
FT /ligand_id="ChEBI:CHEBI:60549"
FT /evidence="ECO:0000269|PubMed:31173777,
FT ECO:0007744|PDB:6RTD"
FT BINDING 208
FT /ligand="heme d1"
FT /ligand_id="ChEBI:CHEBI:60549"
FT /evidence="ECO:0000269|PubMed:31173777,
FT ECO:0007744|PDB:6RTD"
FT BINDING 341
FT /ligand="heme d1"
FT /ligand_id="ChEBI:CHEBI:60549"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="distal binding residue"
FT /evidence="ECO:0000269|PubMed:31173777,
FT ECO:0007744|PDB:6RTD"
FT BINDING 390
FT /ligand="heme d1"
FT /ligand_id="ChEBI:CHEBI:60549"
FT /evidence="ECO:0000269|PubMed:31173777,
FT ECO:0007744|PDB:6RTD"
FT BINDING 435
FT /ligand="heme d1"
FT /ligand_id="ChEBI:CHEBI:60549"
FT /evidence="ECO:0000269|PubMed:31173777,
FT ECO:0007744|PDB:6RTD"
FT MUTAGEN 165
FT /note="H->A,Q: Abolishes heme d1 binding. Loss of
FT activity."
FT /evidence="ECO:0000269|PubMed:31173777"
FT MUTAGEN 341
FT /note="H->A,Q: Still able to bind heme d1 but lacks
FT catalytic activity."
FT /evidence="ECO:0000269|PubMed:31173777"
FT MUTAGEN 435
FT /note="H->A: Decreases both heme d1 binding and turnover."
FT /evidence="ECO:0000269|PubMed:31173777"
FT MUTAGEN 435
FT /note="H->Q: Does not affect heme d1 binding but decreases
FT catalytic activity."
FT /evidence="ECO:0000269|PubMed:31173777"
FT MUTAGEN 479
FT /note="Y->F: Still able to bind heme d1 but lacks catalytic
FT activity."
FT /evidence="ECO:0000269|PubMed:31173777"
FT CONFLICT 214
FT /note="D -> H (in Ref. 1; BAA12683)"
FT /evidence="ECO:0000305"
FT HELIX 22..30
FT /evidence="ECO:0007829|PDB:6RTE"
FT HELIX 32..35
FT /evidence="ECO:0007829|PDB:6RTE"
FT HELIX 37..39
FT /evidence="ECO:0007829|PDB:6RTE"
FT STRAND 42..44
FT /evidence="ECO:0007829|PDB:6RTE"
FT HELIX 50..52
FT /evidence="ECO:0007829|PDB:6RTE"
FT HELIX 57..66
FT /evidence="ECO:0007829|PDB:6RTE"
FT TURN 77..79
FT /evidence="ECO:0007829|PDB:6RTE"
FT HELIX 82..93
FT /evidence="ECO:0007829|PDB:6RTE"
FT HELIX 104..110
FT /evidence="ECO:0007829|PDB:6RTE"
FT HELIX 117..119
FT /evidence="ECO:0007829|PDB:6RTE"
FT STRAND 125..128
FT /evidence="ECO:0007829|PDB:6RTE"
FT HELIX 130..132
FT /evidence="ECO:0007829|PDB:6RTE"
FT STRAND 134..138
FT /evidence="ECO:0007829|PDB:6RTE"
FT TURN 139..142
FT /evidence="ECO:0007829|PDB:6RTE"
FT STRAND 143..148
FT /evidence="ECO:0007829|PDB:6RTE"
FT TURN 149..152
FT /evidence="ECO:0007829|PDB:6RTE"
FT STRAND 153..159
FT /evidence="ECO:0007829|PDB:6RTE"
FT STRAND 161..170
FT /evidence="ECO:0007829|PDB:6RTE"
FT STRAND 174..181
FT /evidence="ECO:0007829|PDB:6RTE"
FT STRAND 184..190
FT /evidence="ECO:0007829|PDB:6RTE"
FT TURN 191..194
FT /evidence="ECO:0007829|PDB:6RTE"
FT STRAND 195..201
FT /evidence="ECO:0007829|PDB:6RTE"
FT STRAND 204..211
FT /evidence="ECO:0007829|PDB:6RTE"
FT STRAND 217..224
FT /evidence="ECO:0007829|PDB:6RTE"
FT STRAND 227..232
FT /evidence="ECO:0007829|PDB:6RTE"
FT TURN 233..235
FT /evidence="ECO:0007829|PDB:6RTE"
FT STRAND 238..243
FT /evidence="ECO:0007829|PDB:6RTE"
FT STRAND 254..260
FT /evidence="ECO:0007829|PDB:6RTE"
FT HELIX 261..263
FT /evidence="ECO:0007829|PDB:6RTE"
FT STRAND 265..280
FT /evidence="ECO:0007829|PDB:6RTE"
FT STRAND 290..293
FT /evidence="ECO:0007829|PDB:6RTE"
FT STRAND 298..303
FT /evidence="ECO:0007829|PDB:6RTE"
FT STRAND 307..314
FT /evidence="ECO:0007829|PDB:6RTE"
FT STRAND 320..324
FT /evidence="ECO:0007829|PDB:6RTE"
FT TURN 325..327
FT /evidence="ECO:0007829|PDB:6RTE"
FT STRAND 330..334
FT /evidence="ECO:0007829|PDB:6RTE"
FT HELIX 342..344
FT /evidence="ECO:0007829|PDB:6RTE"
FT STRAND 346..358
FT /evidence="ECO:0007829|PDB:6RTE"
FT STRAND 360..370
FT /evidence="ECO:0007829|PDB:6RTE"
FT TURN 371..374
FT /evidence="ECO:0007829|PDB:6RTE"
FT STRAND 375..381
FT /evidence="ECO:0007829|PDB:6RTE"
FT STRAND 396..401
FT /evidence="ECO:0007829|PDB:6RTE"
FT STRAND 405..407
FT /evidence="ECO:0007829|PDB:6RTE"
FT STRAND 411..415
FT /evidence="ECO:0007829|PDB:6RTE"
FT TURN 416..418
FT /evidence="ECO:0007829|PDB:6RTE"
FT STRAND 420..425
FT /evidence="ECO:0007829|PDB:6RTE"
FT STRAND 433..438
FT /evidence="ECO:0007829|PDB:6RTE"
FT STRAND 442..449
FT /evidence="ECO:0007829|PDB:6RTE"
FT STRAND 454..460
FT /evidence="ECO:0007829|PDB:6RTE"
FT TURN 461..463
FT /evidence="ECO:0007829|PDB:6RTE"
FT STRAND 466..480
FT /evidence="ECO:0007829|PDB:6RTE"
FT HELIX 481..485
FT /evidence="ECO:0007829|PDB:6RTE"
SQ SEQUENCE 493 AA; 53978 MW; 8E11E64DF8B637A4 CRC64;
MRLIGLALGL LLGALAQAGE APGEALYRQH CQACHGAGRL GGSGPTLLPE SLSRLKPAQA
REVILHGRPA TQMAGFAGQL DDAAADALVA YLYQAPPREP QWSAEDIRAS QVQPHPLATL
PSRPRFEADP LNLFVVVESG DHHVTILDGD RFEPIARFPS RYALHGGPKF SPDGRLVYFA
SRDGWVTLYD LYNLKVVAEV RAGLNTRNLA VSDDGRWVLV GNYLPGNLVL LDARDLSLVQ
VIPAADAQGQ ASRVSAVYTA PPRHSFVVAL KDVHELWELP YANGKPVAPK RLAVADYLDD
FSFSPDYRYL LGSSRQARGG EVIELDSGAR VASIPLSGMP HLGSGIYWKR DGRWVFATPN
ISRGVISVID LQNWKPLKEI VTDGPGFFMR SHADSPYAWT DTFLGKKHDE ILLIDKQTLE
IAHRLRPSPG KVAGHVEFTR DGRYALLSVW DRDGALVVYD AHSLEEVKRL PMNKPSGKYN
VGNKIGYAEG TSH
