NDMD_PSEPU
ID NDMD_PSEPU Reviewed; 588 AA.
AC H9N291;
DT 29-MAY-2013, integrated into UniProtKB/Swiss-Prot.
DT 13-JUN-2012, sequence version 1.
DT 03-AUG-2022, entry version 35.
DE RecName: Full=Oxidoreductase NdmD;
DE EC=1.-.-.-;
GN Name=ndmD;
OS Pseudomonas putida (Arthrobacter siderocapsulatus).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
OC Pseudomonadaceae; Pseudomonas.
OX NCBI_TaxID=303;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, AND COFACTOR.
RC STRAIN=CBB5;
RX PubMed=22328667; DOI=10.1128/jb.06637-11;
RA Summers R.M., Louie T.M., Yu C.L., Gakhar L., Louie K.C., Subramanian M.;
RT "Novel, highly specific N-demethylases enable bacteria to live on caffeine
RT and related purine alkaloids.";
RL J. Bacteriol. 194:2041-2049(2012).
RN [2]
RP FUNCTION.
RC STRAIN=CBB5;
RX PubMed=20966097; DOI=10.1099/mic.0.043612-0;
RA Summers R.M., Louie T.M., Yu C.L., Subramanian M.;
RT "Characterization of a broad-specificity non-haem iron N-demethylase from
RT Pseudomonas putida CBB5 capable of utilizing several purine alkaloids as
RT sole carbon and nitrogen source.";
RL Microbiology 157:583-592(2011).
CC -!- FUNCTION: Involved in the caffeine degradation, which is the essential
CC first step for assimilating the carbon and nitrogen in caffeine.
CC Catalyzes the oxidation of NADH and transfers electrons to NdmA and
CC NdmB, which catalyze the N-demethylation reactions.
CC {ECO:0000269|PubMed:20966097, ECO:0000269|PubMed:22328667}.
CC -!- COFACTOR:
CC Name=[2Fe-2S] cluster; Xref=ChEBI:CHEBI:190135;
CC Evidence={ECO:0000255|PROSITE-ProRule:PRU00628,
CC ECO:0000269|PubMed:22328667};
CC Note=Binds 1 [2Fe-2S] cluster per subunit. {ECO:0000255|PROSITE-
CC ProRule:PRU00628, ECO:0000269|PubMed:22328667};
CC -!- MISCELLANEOUS: It is probably a fusion between a ferredoxin and a
CC reductase into a single ORF which encodes a functional reductase that
CC is specifically coupled to NdmA and NdmB.
CC {ECO:0000305|PubMed:22328667}.
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DR EMBL; JQ061130; AFD03119.1; -; Genomic_DNA.
DR PDB; 6ICM; X-ray; 2.96 A; D=502-588.
DR PDBsum; 6ICM; -.
DR AlphaFoldDB; H9N291; -.
DR SMR; H9N291; -.
DR BioCyc; MetaCyc:MON-17177; -.
DR GO; GO:0051537; F:2 iron, 2 sulfur cluster binding; IDA:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0016491; F:oxidoreductase activity; IEA:UniProtKB-KW.
DR GO; GO:0009822; P:alkaloid catabolic process; IDA:UniProtKB.
DR CDD; cd00207; fer2; 1.
DR Gene3D; 2.102.10.10; -; 1.
DR Gene3D; 3.10.20.30; -; 1.
DR Gene3D; 3.40.50.80; -; 1.
DR InterPro; IPR036010; 2Fe-2S_ferredoxin-like_sf.
DR InterPro; IPR001041; 2Fe-2S_ferredoxin-type.
DR InterPro; IPR006058; 2Fe2S_fd_BS.
DR InterPro; IPR012675; Beta-grasp_dom_sf.
DR InterPro; IPR017927; FAD-bd_FR_type.
DR InterPro; IPR039261; FNR_nucleotide-bd.
DR InterPro; IPR000951; Ph_dOase_redase.
DR InterPro; IPR017938; Riboflavin_synthase-like_b-brl.
DR InterPro; IPR017941; Rieske_2Fe-2S.
DR InterPro; IPR036922; Rieske_2Fe-2S_sf.
DR Pfam; PF00111; Fer2; 1.
DR Pfam; PF00355; Rieske; 1.
DR PRINTS; PR00409; PHDIOXRDTASE.
DR SUPFAM; SSF50022; SSF50022; 1.
DR SUPFAM; SSF52343; SSF52343; 1.
DR SUPFAM; SSF54292; SSF54292; 1.
DR SUPFAM; SSF63380; SSF63380; 1.
DR PROSITE; PS00197; 2FE2S_FER_1; 1.
DR PROSITE; PS51085; 2FE2S_FER_2; 1.
DR PROSITE; PS51384; FAD_FR; 1.
DR PROSITE; PS51296; RIESKE; 1.
PE 1: Evidence at protein level;
KW 2Fe-2S; 3D-structure; Alkaloid metabolism; Flavoprotein; Iron; Iron-sulfur;
KW Metal-binding; Oxidoreductase.
FT CHAIN 1..588
FT /note="Oxidoreductase NdmD"
FT /id="PRO_0000422372"
FT DOMAIN 9..114
FT /note="Rieske"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00628"
FT DOMAIN 272..373
FT /note="FAD-binding FR-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00716"
FT DOMAIN 503..588
FT /note="2Fe-2S ferredoxin-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00465"
FT BINDING 50
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000250"
FT BINDING 52
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00628"
FT BINDING 69
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000250"
FT BINDING 72
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00628"
FT BINDING 537
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000250"
FT BINDING 542
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000250"
FT BINDING 545
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000250"
FT BINDING 575
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000250"
FT STRAND 504..507
FT /evidence="ECO:0007829|PDB:6ICM"
FT STRAND 514..516
FT /evidence="ECO:0007829|PDB:6ICM"
FT HELIX 522..528
FT /evidence="ECO:0007829|PDB:6ICM"
FT STRAND 536..539
FT /evidence="ECO:0007829|PDB:6ICM"
FT STRAND 547..551
FT /evidence="ECO:0007829|PDB:6ICM"
FT STRAND 559..561
FT /evidence="ECO:0007829|PDB:6ICM"
FT HELIX 563..566
FT /evidence="ECO:0007829|PDB:6ICM"
FT TURN 567..569
FT /evidence="ECO:0007829|PDB:6ICM"
FT STRAND 570..572
FT /evidence="ECO:0007829|PDB:6ICM"
FT TURN 574..576
FT /evidence="ECO:0007829|PDB:6ICM"
FT STRAND 578..586
FT /evidence="ECO:0007829|PDB:6ICM"
SQ SEQUENCE 588 AA; 65089 MW; 9D0F70759B87A0F0 CRC64;
MNKLDVNQWF PIATTEDLPK RHVFHATLLG QEMAIWRDDS GSVNAWENRC PHRGLRLTLG
ANTGNELRCQ YHGWTYESGT GGCTFVPAHR DAPPPNAARV NTFPVREKHG FIWTTLGQPP
GEPISILDDA QLVNAVKTNL HSVVIDADID GVVSVLRQNL SAFIDVFGAA SAEDLHLKSM
LQDRGILVTR SGSIAIHFYM QRSTISKCVV HAQVLTPGRP GYELQKNYSY AMNVIRRAAE
AVATDLISIT DISDQTIEKL EVVRENMTKA PPTHYICEVV TRTQETGDIN SYWLKPIGYP
LPAFSPGMHI SITTPEGSIR QYSLVNGPDE RESFIIGVKK EIQSRGGSRS MHEDVKVGTQ
LKVTLPRNGF PLVQTRKHPI LVAGGIGITP ILCMAQALDQ QGSSYEIHYF ARAFEHVPFQ
DRLTALGDRL NVHLGLGPDE TRAKLPDIME IHNAQDVDVY TCGPQPMIET VSAVALAHGI
AEESIRFEFF SKKNDVPVSD EEYEVELKKT GQIFTVSPGS TLLQACLDND VRIEASCEQG
VCGTCITPVV SGDLEHHDTY LSKKERESGK WIMPCVSRCK SKKIVLDL
