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UniProtKB - H9N289 (NDMA_PSEPU)

Entry version 23 (16 Oct 2019)
Sequence version 1 (13 Jun 2012)
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Protein

Methylxanthine N1-demethylase NdmA

Gene

ndmA

Organism
Pseudomonas putida (Arthrobacter siderocapsulatus)
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Involved in the caffeine degradation, which is the essential first step for assimilating the carbon and nitrogen in caffeine. Catalyzes the N1-demethylation of caffeine to produce theobromine and formaldehyde. Also catalyzes the N1-demethylation of theophylline, paraxanthine, and 1-methylxanthine to 3-methylxanthine, 7-methylxanthine, and xanthine, respectively. NADH is the preferred substrate.2 Publications

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the ‘Function’ section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

[2Fe-2S] clusterPROSITE-ProRule annotation2 PublicationsNote: Binds 1 [2Fe-2S] cluster per subunit.PROSITE-ProRule annotation2 Publications

<p>This subsection of the ‘Function’ section describes biophysical and chemical properties, such as maximal absorption, kinetic parameters, pH dependence, redox potentials and temperature dependence.<p><a href='/help/biophysicochemical_properties' target='_top'>More...</a></p>Kineticsi

Kcat is 190 (min-1) for caffeine (at pH 7.5 and 30 degrees Celsius).
  1. KM=9.1 µM for theophylline (at pH 7.5 and 30 degrees Celsius)2 Publications
  2. KM=37 µM for caffeine (at pH 7.5 and 30 degrees Celsius)2 Publications
  3. KM=53 µM for paraxanthine (at pH 7.5 and 30 degrees Celsius)2 Publications
  4. KM=270 µM for 1-methylxanthine (at pH 7.5 and 30 degrees Celsius)2 Publications

    pH dependencei

    Optimum pH is 7.5.2 Publications

    Temperature dependencei

    Optimum temperature is 30 degrees Celsius.2 Publications

    <p>This subsection of the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section describes the metabolic pathway(s) associated with a protein.<p><a href='/help/pathway' target='_top'>More...</a></p>Pathwayi: Alkaloid degradation

    This protein is involved in Alkaloid degradation.
    View all proteins of this organism that are known to be involved in Alkaloid degradation.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the ‘Description’ field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi62Iron-sulfur (2Fe-2S)PROSITE-ProRule annotation1
    Metal bindingi64Iron-sulfur (2Fe-2S); via pros nitrogenPROSITE-ProRule annotation1
    Metal bindingi81Iron-sulfur (2Fe-2S)PROSITE-ProRule annotation1
    Metal bindingi84Iron-sulfur (2Fe-2S); via pros nitrogenPROSITE-ProRule annotation1

    <p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

    Complete GO annotation on QuickGO ...

    GO - Biological processi

    Complete GO annotation on QuickGO ...

    <p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

    Molecular functionOxidoreductase
    Biological processAlkaloid metabolism
    Ligand2Fe-2S, Iron, Iron-sulfur, Metal-binding, NAD

    Enzyme and pathway databases

    BioCyc Collection of Pathway/Genome Databases

    More...    BioCyci    		MetaCyc:MONOMER-17179

    BRENDA Comprehensive Enzyme Information System

    More...    BRENDAi    		1.14.13.178 5092

    <p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
    Recommended name:
    Methylxanthine N1-demethylase NdmA (EC:1.14.13.178)
    Alternative name(s):
    1-methylxanthine demethylase
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
    Name:ndmA
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiPseudomonas putida (Arthrobacter siderocapsulatus)
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri303 [NCBI]
    <p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiBacteria › Proteobacteria › Gammaproteobacteria › Pseudomonadales › Pseudomonadaceae › Pseudomonas ›

    <p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00004223701 – 351Methylxanthine N1-demethylase NdmAAdd BLAST351

    <p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

    3D structure databases

    SWISS-MODEL Repository - a database of annotated 3D protein structure models

    More...    SMRi    		H9N289

    Database of comparative protein structure models

    More...    ModBasei    		Search...

    Protein Data Bank in Europe - Knowledge Base

    More...    PDBe-KBi    		Search...

    <p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the <a href="http://www.uniprot.org/help/family_and_domains_section">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini17 – 125RieskePROSITE-ProRule annotationAdd BLAST109

    Phylogenomic databases

    KEGG Orthology (KO)

    More...    KOi    		K21722

    Family and domain databases

    Gene3D Structural and Functional Annotation of Protein Families

    More...    Gene3Di    		2.102.10.10, 1 hit

    Integrated resource of protein families, domains and functional sites

    More...    InterProi    		View protein in InterPro
    IPR017941 Rieske_2Fe-2S
    IPR036922 Rieske_2Fe-2S_sf

    Pfam protein domain database

    More...    Pfami    		View protein in Pfam
    PF00355 Rieske, 1 hit

    Superfamily database of structural and functional annotation

    More...    SUPFAMi    		SSF50022 SSF50022, 1 hit

    PROSITE; a protein domain and family database

    More...    PROSITEi    		View protein in PROSITE
    PS51296 RIESKE, 1 hit

    <p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

    <p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

    H9N289-1 [UniParc]FASTAAdd to basket
    « Hide
            10         20         30         40         50
    MEQAIINDER EYLRHFWHPV CTVTELEKAH PSSLGPLAVK LLNEQLVVAK 
            60         70         80         90        100
    LGDEYVAMRD RCAHRSAKLS LGTVSGNRLQ CPYHGWQYDT HGACQLVPAC 
           110        120        130        140        150
    PNSPIPNKAK VDRFDCEERY GLIWIRLDSS FDCTEIPYFS AANDPRLRIV 
           160        170        180        190        200
    IQEPYWWDAT AERRWENFTD FSHFAFIHPG TLFDPNNAEP PIVPMDRFNG 
           210        220        230        240        250
    QFRFVYDTPE DMAVPNQAPI GSFSYTCSMP FAINLEVSKY SSSSLHVLFN 
           260        270        280        290        300
    VSCPVDSHTT KNFLIFAREQ SDDSDYLHIA FNDLVFAEDK PVIESQWPKD 
           310        320        330        340        350
    APADEVSVVA DKVSIQYRKW LRELKEAHKE GSQAFRSALL DPVIESDRSY 

    I
    Length:351
    Mass (Da):40,203
    Last modified:June 13, 2012 - v1
    <p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:iA2CA80A8ABAB4A99
    GO

    Sequence databases

    Select the link destinations:

    EMBL nucleotide sequence database

    More...    EMBLi

    GenBank nucleotide sequence database

    More...    GenBanki

    DNA Data Bank of Japan; a nucleotide sequence database

    More...    DDBJi
    Links Updated
    		JQ061127 Genomic DNA Translation: AFD03116.1

    Genome annotation databases

    KEGG: Kyoto Encyclopedia of Genes and Genomes

    More...    KEGGi    		ag:AFD03116

    <p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

    <p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    		JQ061127 Genomic DNA Translation: AFD03116.1

    3D structure databases

    Select the link destinations:

    Protein Data Bank Europe

    More...    PDBei

    Protein Data Bank RCSB

    More...    RCSB PDBi

    Protein Data Bank Japan

    More...    PDBji
    Links Updated
    		PDB entryMethodResolution (Å)ChainPositionsPDBsum
    6ICKX-ray1.95A/B/C1-351[»]
    6ICMX-ray2.96A/B/C1-351[»]
    6ICNX-ray1.65A/B/C1-351[»]
    6ICOX-ray1.85A/B/C1-351[»]
    6ICPX-ray2.20A/B/C1-351[»]
    6ICQX-ray1.90A/B/C1-351[»]
    SMRiH9N289
    ModBaseiSearch...
    PDBe-KBiSearch...

    Genome annotation databases

    KEGGiag:AFD03116

    Phylogenomic databases

    KOiK21722

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-17179
    BRENDAi1.14.13.178 5092

    Family and domain databases

    Gene3Di2.102.10.10, 1 hit
    InterProiView protein in InterPro
    IPR017941 Rieske_2Fe-2S
    IPR036922 Rieske_2Fe-2S_sf
    PfamiView protein in Pfam
    PF00355 Rieske, 1 hit
    SUPFAMiSSF50022 SSF50022, 1 hit
    PROSITEiView protein in PROSITE
    PS51296 RIESKE, 1 hit

    ProtoNet; Automatic hierarchical classification of proteins

    More...    ProtoNeti    		Search...

    MobiDB: a database of protein disorder and mobility annotations

    More...    MobiDBi    		Search...

    <p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

    <p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiNDMA_PSEPU
    <p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: H9N289
    <p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 29, 2013
    Last sequence update: June 13, 2012
    Last modified: October 16, 2019
    This is version 23 of the entry and version 1 of the sequence. See complete history.
    <p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    <p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

    Keywords - Technical termi

    3D-structure, Direct protein sequencing

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
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