NDMB_PSEPU
ID NDMB_PSEPU Reviewed; 355 AA.
AC H9N290;
DT 29-MAY-2013, integrated into UniProtKB/Swiss-Prot.
DT 13-JUN-2012, sequence version 1.
DT 03-AUG-2022, entry version 34.
DE RecName: Full=Methylxanthine N3-demethylase NdmB;
DE EC=1.14.13.179;
DE AltName: Full=3-methylxanthine demethylase;
GN Name=ndmB;
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 N3-demethylation of theobromine to produce 7-
CC methylxanthine and formaldehyde. Also catalyzes the N3-demethylation of
CC 3-methylxanthine, caffeine, and theophylline to xanthine, paraxanthine,
CC and 1-methylxanthine, respectively. NADH is the preferred substrate.
CC {ECO:0000269|PubMed:20966097, ECO:0000269|PubMed:22328667}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H(+) + NADH + O2 + theobromine = 7-methylxanthine +
CC formaldehyde + H2O + NAD(+); Xref=Rhea:RHEA:30319, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:15379, ChEBI:CHEBI:16842,
CC ChEBI:CHEBI:28946, ChEBI:CHEBI:48991, ChEBI:CHEBI:57540,
CC ChEBI:CHEBI:57945; EC=1.14.13.179;
CC Evidence={ECO:0000269|PubMed:22328667};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H(+) + NADPH + O2 + theobromine = 7-methylxanthine +
CC formaldehyde + H2O + NADP(+); Xref=Rhea:RHEA:36287,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:15379,
CC ChEBI:CHEBI:16842, ChEBI:CHEBI:28946, ChEBI:CHEBI:48991,
CC ChEBI:CHEBI:57783, ChEBI:CHEBI:58349; EC=1.14.13.179;
CC Evidence={ECO:0000269|PubMed:22328667};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=3-methylxanthine + H(+) + NADH + O2 = formaldehyde + H2O +
CC NAD(+) + xanthine; Xref=Rhea:RHEA:30447, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:15379, ChEBI:CHEBI:16842,
CC ChEBI:CHEBI:17712, ChEBI:CHEBI:57540, ChEBI:CHEBI:57945,
CC ChEBI:CHEBI:62208; EC=1.14.13.179;
CC Evidence={ECO:0000269|PubMed:22328667};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=3-methylxanthine + H(+) + NADPH + O2 = formaldehyde + H2O +
CC NADP(+) + xanthine; Xref=Rhea:RHEA:36291, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:15379, ChEBI:CHEBI:16842,
CC ChEBI:CHEBI:17712, ChEBI:CHEBI:57783, ChEBI:CHEBI:58349,
CC ChEBI:CHEBI:62208; EC=1.14.13.179;
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=22 uM for 3-methylxanthine (at pH 7.5 and 30 degrees Celsius)
CC {ECO:0000269|PubMed:20966097, ECO:0000269|PubMed:22328667};
CC KM=25 uM for theobromine (at pH 7.5 and 30 degrees Celsius)
CC {ECO:0000269|PubMed:20966097, ECO:0000269|PubMed:22328667};
CC KM=42 uM for caffeine (at pH 7.5 and 30 degrees Celsius)
CC {ECO:0000269|PubMed:20966097, ECO:0000269|PubMed:22328667};
CC KM=170 uM for theophylline (at pH 7.5 and 30 degrees Celsius)
CC {ECO:0000269|PubMed:20966097, ECO:0000269|PubMed:22328667};
CC Note=kcat is 46 min(-1) for theobromine (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};
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DR EMBL; JQ061128; AFD03117.1; -; Genomic_DNA.
DR RefSeq; WP_046819639.1; NZ_JTEN01000129.1.
DR PDB; 6ICL; X-ray; 2.10 A; A=1-355.
DR PDBsum; 6ICL; -.
DR AlphaFoldDB; H9N290; -.
DR SASBDB; H9N290; -.
DR SMR; H9N290; -.
DR KEGG; ag:AFD03117; -.
DR BioCyc; MetaCyc:MON-17180; -.
DR BRENDA; 1.14.13.179; 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..355
FT /note="Methylxanthine N3-demethylase NdmB"
FT /id="PRO_0000422371"
FT DOMAIN 19..131
FT /note="Rieske"
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 66
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00628"
FT BINDING 87
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00628"
FT BINDING 90
FT /ligand="[2Fe-2S] cluster"
FT /ligand_id="ChEBI:CHEBI:190135"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00628"
FT HELIX 13..17
FT /evidence="ECO:0007829|PDB:6ICL"
FT STRAND 18..24
FT /evidence="ECO:0007829|PDB:6ICL"
FT HELIX 25..30
FT /evidence="ECO:0007829|PDB:6ICL"
FT STRAND 39..43
FT /evidence="ECO:0007829|PDB:6ICL"
FT STRAND 46..53
FT /evidence="ECO:0007829|PDB:6ICL"
FT STRAND 56..63
FT /evidence="ECO:0007829|PDB:6ICL"
FT TURN 65..67
FT /evidence="ECO:0007829|PDB:6ICL"
FT HELIX 71..73
FT /evidence="ECO:0007829|PDB:6ICL"
FT STRAND 74..79
FT /evidence="ECO:0007829|PDB:6ICL"
FT STRAND 82..86
FT /evidence="ECO:0007829|PDB:6ICL"
FT TURN 88..90
FT /evidence="ECO:0007829|PDB:6ICL"
FT STRAND 98..102
FT /evidence="ECO:0007829|PDB:6ICL"
FT STRAND 119..125
FT /evidence="ECO:0007829|PDB:6ICL"
FT STRAND 128..133
FT /evidence="ECO:0007829|PDB:6ICL"
FT STRAND 153..157
FT /evidence="ECO:0007829|PDB:6ICL"
FT STRAND 161..165
FT /evidence="ECO:0007829|PDB:6ICL"
FT HELIX 167..174
FT /evidence="ECO:0007829|PDB:6ICL"
FT HELIX 180..183
FT /evidence="ECO:0007829|PDB:6ICL"
FT TURN 185..187
FT /evidence="ECO:0007829|PDB:6ICL"
FT TURN 191..194
FT /evidence="ECO:0007829|PDB:6ICL"
FT STRAND 201..204
FT /evidence="ECO:0007829|PDB:6ICL"
FT STRAND 207..212
FT /evidence="ECO:0007829|PDB:6ICL"
FT STRAND 228..235
FT /evidence="ECO:0007829|PDB:6ICL"
FT TURN 236..238
FT /evidence="ECO:0007829|PDB:6ICL"
FT STRAND 239..249
FT /evidence="ECO:0007829|PDB:6ICL"
FT STRAND 252..263
FT /evidence="ECO:0007829|PDB:6ICL"
FT STRAND 266..276
FT /evidence="ECO:0007829|PDB:6ICL"
FT HELIX 282..301
FT /evidence="ECO:0007829|PDB:6ICL"
FT STRAND 304..307
FT /evidence="ECO:0007829|PDB:6ICL"
FT HELIX 316..318
FT /evidence="ECO:0007829|PDB:6ICL"
FT HELIX 319..337
FT /evidence="ECO:0007829|PDB:6ICL"
FT HELIX 339..347
FT /evidence="ECO:0007829|PDB:6ICL"
SQ SEQUENCE 355 AA; 40888 MW; BE4E9C202F31EB5A CRC64;
MKEQLKPLLE DKTYLRHFWH PVCTLNEFER ANASGHGPMG VTLLGEKLVL ARLNSKIIAA
ADRCAHRSAQ LSIGRVCSNA GKDYLECPYH GWRYDEAGAC QLIPACPDKS ISPRAKISSF
DCEVKYDIVW VRLDNSFDCT QIPYLSDFDN PDMQVIVADS YIWETVAERR WENFTDFSHF
AFVHPGTLYD PFFASHPTVY VNRVDGELQF KLAPPREMKG IPPEAPMGDF TYRCTMPYSV
NLEIKLWKDD SRFVLWTTAS PVDNKSCRNF MIIVREKDNQ PDHMHLAFQK RVLDEDQPVI
ESQWPLEIQT SEVSVATDKI SVQFRKWHKE LSLSAVEGRE AFRDSVLTNV IEEEQ
