NDMA_PSEPU
ID NDMA_PSEPU Reviewed; 351 AA.
AC H9N289;
DT 29-MAY-2013, integrated into UniProtKB/Swiss-Prot.
DT 13-JUN-2012, sequence version 1.
DT 03-AUG-2022, entry version 32.
DE RecName: Full=Methylxanthine N1-demethylase NdmA;
DE EC=1.14.13.178;
DE AltName: Full=1-methylxanthine demethylase;
GN Name=ndmA;
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, CATALYTIC ACTIVITY,
RP BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE SPECIFICITY, 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 PROTEIN SEQUENCE OF 1-25, FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES,
RP COFACTOR, AND SUBSTRATE SPECIFICITY.
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 N1-demethylation of caffeine to produce theobromine and
CC formaldehyde. Also catalyzes the N1-demethylation of theophylline,
CC paraxanthine, and 1-methylxanthine to 3-methylxanthine, 7-
CC methylxanthine, and xanthine, respectively. NADH is the preferred
CC substrate. {ECO:0000269|PubMed:20966097, ECO:0000269|PubMed:22328667}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=caffeine + H(+) + NADH + O2 = formaldehyde + H2O + NAD(+) +
CC theobromine; Xref=Rhea:RHEA:36267, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:15379, ChEBI:CHEBI:16842,
CC ChEBI:CHEBI:27732, ChEBI:CHEBI:28946, ChEBI:CHEBI:57540,
CC ChEBI:CHEBI:57945; EC=1.14.13.178;
CC Evidence={ECO:0000269|PubMed:22328667};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=caffeine + H(+) + NADPH + O2 = formaldehyde + H2O + NADP(+) +
CC theobromine; Xref=Rhea:RHEA:36271, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:15379, ChEBI:CHEBI:16842,
CC ChEBI:CHEBI:27732, ChEBI:CHEBI:28946, ChEBI:CHEBI:57783,
CC ChEBI:CHEBI:58349; EC=1.14.13.178;
CC Evidence={ECO:0000269|PubMed:22328667};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H(+) + NADH + O2 + theophylline = 3-methylxanthine +
CC formaldehyde + H2O + NAD(+); Xref=Rhea:RHEA:36279, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:15379, ChEBI:CHEBI:16842,
CC ChEBI:CHEBI:28177, ChEBI:CHEBI:57540, ChEBI:CHEBI:57945,
CC ChEBI:CHEBI:62208; EC=1.14.13.178;
CC Evidence={ECO:0000269|PubMed:22328667};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H(+) + NADPH + O2 + theophylline = 3-methylxanthine +
CC formaldehyde + H2O + NADP(+); Xref=Rhea:RHEA:36275,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:15379,
CC ChEBI:CHEBI:16842, ChEBI:CHEBI:28177, ChEBI:CHEBI:57783,
CC ChEBI:CHEBI:58349, ChEBI:CHEBI:62208; EC=1.14.13.178;
CC Evidence={ECO:0000269|PubMed:22328667};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=1,7-dimethylxanthine + H(+) + NADH + O2 = 7-methylxanthine +
CC formaldehyde + H2O + NAD(+); Xref=Rhea:RHEA:30315, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:15379, ChEBI:CHEBI:16842,
CC ChEBI:CHEBI:25858, ChEBI:CHEBI:48991, ChEBI:CHEBI:57540,
CC ChEBI:CHEBI:57945; EC=1.14.13.178;
CC Evidence={ECO:0000269|PubMed:22328667};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=1,7-dimethylxanthine + H(+) + NADPH + O2 = 7-methylxanthine +
CC formaldehyde + H2O + NADP(+); Xref=Rhea:RHEA:36283,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:15379,
CC ChEBI:CHEBI:16842, ChEBI:CHEBI:25858, ChEBI:CHEBI:48991,
CC ChEBI:CHEBI:57783, ChEBI:CHEBI:58349; EC=1.14.13.178;
CC Evidence={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:20966097, ECO:0000269|PubMed:22328667};
CC Note=Binds 1 [2Fe-2S] cluster per subunit. {ECO:0000255|PROSITE-
CC ProRule:PRU00628, ECO:0000269|PubMed:20966097,
CC ECO:0000269|PubMed:22328667};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=9.1 uM for theophylline (at pH 7.5 and 30 degrees Celsius)
CC {ECO:0000269|PubMed:20966097, ECO:0000269|PubMed:22328667};
CC KM=37 uM for caffeine (at pH 7.5 and 30 degrees Celsius)
CC {ECO:0000269|PubMed:20966097, ECO:0000269|PubMed:22328667};
CC KM=53 uM for paraxanthine (at pH 7.5 and 30 degrees Celsius)
CC {ECO:0000269|PubMed:20966097, ECO:0000269|PubMed:22328667};
CC KM=270 uM for 1-methylxanthine (at pH 7.5 and 30 degrees Celsius)
CC {ECO:0000269|PubMed:20966097, ECO:0000269|PubMed:22328667};
CC Note=kcat is 190 min(-1) for caffeine (at pH 7.5 and 30 degrees
CC Celsius).;
CC pH dependence:
CC Optimum pH is 7.5. {ECO:0000269|PubMed:20966097,
CC ECO:0000269|PubMed:22328667};
CC Temperature dependence:
CC Optimum temperature is 30 degrees Celsius.
CC {ECO:0000269|PubMed:20966097, ECO:0000269|PubMed:22328667};
CC -!- PATHWAY: Alkaloid degradation.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; JQ061127; AFD03116.1; -; Genomic_DNA.
DR PDB; 6ICK; X-ray; 1.95 A; A/B/C=1-351.
DR PDB; 6ICM; X-ray; 2.96 A; A/B/C=1-351.
DR PDB; 6ICN; X-ray; 1.65 A; A/B/C=1-351.
DR PDB; 6ICO; X-ray; 1.85 A; A/B/C=1-351.
DR PDB; 6ICP; X-ray; 2.20 A; A/B/C=1-351.
DR PDB; 6ICQ; X-ray; 1.90 A; A/B/C=1-351.
DR PDBsum; 6ICK; -.
DR PDBsum; 6ICM; -.
DR PDBsum; 6ICN; -.
DR PDBsum; 6ICO; -.
DR PDBsum; 6ICP; -.
DR PDBsum; 6ICQ; -.
DR AlphaFoldDB; H9N289; -.
DR SASBDB; H9N289; -.
DR SMR; H9N289; -.
DR KEGG; ag:AFD03116; -.
DR BioCyc; MetaCyc:MON-17179; -.
DR BRENDA; 1.14.13.128; 5092.
DR BRENDA; 1.14.13.178; 5092.
DR GO; GO:0051537; F:2 iron, 2 sulfur cluster binding; IDA:UniProtKB.
DR GO; GO:0032451; F:demethylase activity; 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 Gene3D; 2.102.10.10; -; 1.
DR InterPro; IPR017941; Rieske_2Fe-2S.
DR InterPro; IPR036922; Rieske_2Fe-2S_sf.
DR InterPro; IPR044043; VanA_C_cat.
DR Pfam; PF00355; Rieske; 1.
DR Pfam; PF19112; VanA_C; 1.
DR SUPFAM; SSF50022; SSF50022; 1.
DR PROSITE; PS51296; RIESKE; 1.
PE 1: Evidence at protein level;
KW 2Fe-2S; 3D-structure; Alkaloid metabolism; Direct protein sequencing; Iron;
KW Iron-sulfur; Metal-binding; NAD; Oxidoreductase.
FT CHAIN 1..351
FT /note="Methylxanthine N1-demethylase NdmA"
FT /id="PRO_0000422370"
FT DOMAIN 17..125
FT /note="Rieske"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00628"
FT BINDING 62
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00628"
FT BINDING 64
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00628"
FT BINDING 81
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00628"
FT BINDING 84
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00628"
FT HELIX 8..15
FT /evidence="ECO:0007829|PDB:6ICN"
FT STRAND 16..22
FT /evidence="ECO:0007829|PDB:6ICN"
FT HELIX 23..29
FT /evidence="ECO:0007829|PDB:6ICN"
FT STRAND 37..41
FT /evidence="ECO:0007829|PDB:6ICN"
FT STRAND 44..51
FT /evidence="ECO:0007829|PDB:6ICN"
FT STRAND 54..61
FT /evidence="ECO:0007829|PDB:6ICN"
FT TURN 63..65
FT /evidence="ECO:0007829|PDB:6ICN"
FT HELIX 69..71
FT /evidence="ECO:0007829|PDB:6ICN"
FT STRAND 72..75
FT /evidence="ECO:0007829|PDB:6ICN"
FT STRAND 78..80
FT /evidence="ECO:0007829|PDB:6ICN"
FT TURN 82..84
FT /evidence="ECO:0007829|PDB:6ICN"
FT STRAND 92..96
FT /evidence="ECO:0007829|PDB:6ICN"
FT STRAND 100..103
FT /evidence="ECO:0007829|PDB:6ICO"
FT STRAND 113..119
FT /evidence="ECO:0007829|PDB:6ICN"
FT STRAND 122..127
FT /evidence="ECO:0007829|PDB:6ICN"
FT TURN 140..143
FT /evidence="ECO:0007829|PDB:6ICN"
FT STRAND 148..151
FT /evidence="ECO:0007829|PDB:6ICN"
FT STRAND 155..159
FT /evidence="ECO:0007829|PDB:6ICN"
FT HELIX 161..168
FT /evidence="ECO:0007829|PDB:6ICN"
FT STRAND 171..173
FT /evidence="ECO:0007829|PDB:6ICN"
FT HELIX 174..177
FT /evidence="ECO:0007829|PDB:6ICN"
FT TURN 179..182
FT /evidence="ECO:0007829|PDB:6ICN"
FT TURN 185..187
FT /evidence="ECO:0007829|PDB:6ICQ"
FT STRAND 196..198
FT /evidence="ECO:0007829|PDB:6ICN"
FT STRAND 201..207
FT /evidence="ECO:0007829|PDB:6ICN"
FT STRAND 221..228
FT /evidence="ECO:0007829|PDB:6ICN"
FT TURN 229..231
FT /evidence="ECO:0007829|PDB:6ICN"
FT STRAND 232..239
FT /evidence="ECO:0007829|PDB:6ICN"
FT TURN 240..242
FT /evidence="ECO:0007829|PDB:6ICN"
FT STRAND 245..256
FT /evidence="ECO:0007829|PDB:6ICN"
FT STRAND 259..269
FT /evidence="ECO:0007829|PDB:6ICN"
FT HELIX 275..295
FT /evidence="ECO:0007829|PDB:6ICN"
FT STRAND 297..300
FT /evidence="ECO:0007829|PDB:6ICN"
FT HELIX 309..311
FT /evidence="ECO:0007829|PDB:6ICN"
FT HELIX 312..330
FT /evidence="ECO:0007829|PDB:6ICN"
FT HELIX 332..340
FT /evidence="ECO:0007829|PDB:6ICN"
SQ SEQUENCE 351 AA; 40203 MW; A2CA80A8ABAB4A99 CRC64;
MEQAIINDER EYLRHFWHPV CTVTELEKAH PSSLGPLAVK LLNEQLVVAK LGDEYVAMRD
RCAHRSAKLS LGTVSGNRLQ CPYHGWQYDT HGACQLVPAC PNSPIPNKAK VDRFDCEERY
GLIWIRLDSS FDCTEIPYFS AANDPRLRIV IQEPYWWDAT AERRWENFTD FSHFAFIHPG
TLFDPNNAEP PIVPMDRFNG QFRFVYDTPE DMAVPNQAPI GSFSYTCSMP FAINLEVSKY
SSSSLHVLFN VSCPVDSHTT KNFLIFAREQ SDDSDYLHIA FNDLVFAEDK PVIESQWPKD
APADEVSVVA DKVSIQYRKW LRELKEAHKE GSQAFRSALL DPVIESDRSY I
