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P20906

- MDLC_PSEPU

UniProt

P20906 - MDLC_PSEPU

Protein

Benzoylformate decarboxylase

Gene

mdlC

Organism
Pseudomonas putida (Arthrobacter siderocapsulatus)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 98 (01 Oct 2014)
      Sequence version 2 (15 Dec 1998)
      Previous versions | rss
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    Functioni

    Catalytic activityi

    Benzoylformate = benzaldehyde + CO2.

    Cofactori

    Binds 1 calcium ion per subunit.
    Binds 1 thiamine pyrophosphate per subunit.
    Binds 1 magnesium ion per dimer.

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi117 – 1171Magnesium; via carbonyl oxygen
    Metal bindingi118 – 1181Magnesium; via carbonyl oxygen
    Metal bindingi120 – 1201Magnesium
    Metal bindingi428 – 4281Calcium
    Metal bindingi455 – 4551Calcium
    Metal bindingi457 – 4571Calcium

    GO - Molecular functioni

    1. benzoylformate decarboxylase activity Source: UniProtKB-EC
    2. magnesium ion binding Source: InterPro
    3. thiamine pyrophosphate binding Source: InterPro

    GO - Biological processi

    1. mandelate catabolic process Source: UniProtKB-UniPathway

    Keywords - Molecular functioni

    Decarboxylase, Lyase

    Keywords - Biological processi

    Aromatic hydrocarbons catabolism, Mandelate pathway

    Keywords - Ligandi

    Calcium, Magnesium, Metal-binding, Thiamine pyrophosphate

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-2461.
    SABIO-RKP20906.
    UniPathwayiUPA00873; UER00854.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Benzoylformate decarboxylase (EC:4.1.1.7)
    Short name:
    BFD
    Short name:
    BFDC
    Gene namesi
    Name:mdlC
    OrganismiPseudomonas putida (Arthrobacter siderocapsulatus)
    Taxonomic identifieri303 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 528528Benzoylformate decarboxylasePRO_0000090820Add
    BLAST

    Interactioni

    Subunit structurei

    Homotetramer.

    Structurei

    Secondary structure

    1
    528
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi4 – 1411
    Beta strandi19 – 224
    Helixi26 – 283
    Helixi29 – 324
    Beta strandi40 – 434
    Helixi47 – 6115
    Beta strandi65 – 706
    Helixi71 – 777
    Helixi79 – 879
    Beta strandi92 – 987
    Helixi101 – 1044
    Turni105 – 1073
    Helixi115 – 1173
    Turni118 – 1214
    Beta strandi124 – 1274
    Helixi132 – 1343
    Helixi135 – 14713
    Beta strandi148 – 1503
    Beta strandi154 – 1596
    Helixi160 – 1623
    Helixi169 – 1746
    Beta strandi183 – 1853
    Helixi187 – 19913
    Beta strandi204 – 2074
    Helixi209 – 2135
    Helixi217 – 22711
    Beta strandi231 – 2333
    Beta strandi249 – 2524
    Helixi257 – 2648
    Beta strandi268 – 2758
    Beta strandi294 – 3007
    Helixi302 – 3076
    Beta strandi309 – 3168
    Helixi318 – 32811
    Beta strandi350 – 3534
    Helixi355 – 36511
    Beta strandi371 – 3755
    Helixi377 – 3793
    Helixi380 – 3867
    Beta strandi391 – 3933
    Beta strandi395 – 3973
    Beta strandi403 – 4053
    Helixi406 – 41611
    Beta strandi422 – 4276
    Helixi428 – 4314
    Turni432 – 4343
    Helixi435 – 4373
    Helixi438 – 4447
    Beta strandi449 – 4546
    Helixi459 – 46810
    Helixi483 – 4908
    Beta strandi493 – 4997
    Helixi500 – 51112
    Beta strandi517 – 5237

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1BFDX-ray1.60A1-528[»]
    1MCZX-ray2.80A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P1-528[»]
    1PI3X-ray1.20A1-528[»]
    1PO7X-ray1.20A1-528[»]
    1Q6ZX-ray1.00A1-528[»]
    1YNOX-ray1.22A2-528[»]
    2FN3X-ray1.00A1-528[»]
    2FWNX-ray1.40A1-528[»]
    2V3WX-ray2.20A/B/C/D1-528[»]
    3F6BX-ray1.34X2-526[»]
    3F6EX-ray1.34X2-526[»]
    3FSJX-ray1.37X1-528[»]
    3FZNX-ray1.62A/B/C/D1-528[»]
    4GG1X-ray1.07A1-528[»]
    4GM0X-ray1.07A1-528[»]
    4GM1X-ray1.26A1-528[»]
    4GM4X-ray1.28A1-528[»]
    4GP9X-ray1.07A1-528[»]
    4GPEX-ray1.39A1-528[»]
    4JD5X-ray1.33A1-528[»]
    4JU8X-ray1.25A1-528[»]
    4JU9X-ray1.12A1-528[»]
    4JUAX-ray1.15A1-528[»]
    4JUBX-ray1.90A/B/C/D1-528[»]
    4JUCX-ray2.30A/B/C/D1-528[»]
    4JUDX-ray1.65X1-528[»]
    4JUFX-ray2.15A/B/C/D2-528[»]
    4K9KX-ray1.30A2-525[»]
    4K9LX-ray1.65A2-526[»]
    4K9MX-ray1.15A2-525[»]
    4K9NX-ray1.70A/B/C/D2-525[»]
    4K9OX-ray1.89A/B/C/D2-528[»]
    4K9PX-ray2.24A/B/C/D2-528[»]
    ProteinModelPortaliP20906.
    SMRiP20906. Positions 2-525.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP20906.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni377 – 46084Thiamine pyrophosphate bindingAdd
    BLAST

    Sequence similaritiesi

    Belongs to the TPP enzyme family.Curated

    Family and domain databases

    Gene3Di3.40.50.1220. 1 hit.
    3.40.50.970. 2 hits.
    InterProiIPR029035. DHS-like_NAD/FAD-binding_dom.
    IPR029061. THDP-binding.
    IPR012000. Thiamin_PyroP_enz_cen_dom.
    IPR012001. Thiamin_PyroP_enz_TPP-bd_dom.
    IPR000399. TPP-bd_CS.
    IPR011766. TPP_enzyme-bd_C.
    [Graphical view]
    PfamiPF02775. TPP_enzyme_C. 1 hit.
    PF00205. TPP_enzyme_M. 1 hit.
    PF02776. TPP_enzyme_N. 1 hit.
    [Graphical view]
    SUPFAMiSSF52467. SSF52467. 1 hit.
    SSF52518. SSF52518. 2 hits.
    PROSITEiPS00187. TPP_ENZYMES. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P20906-1 [UniParc]FASTAAdd to Basket

    « Hide

    MASVHGTTYE LLRRQGIDTV FGNPGSNELP FLKDFPEDFR YILALQEACV    50
    VGIADGYAQA SRKPAFINLH SAAGTGNAMG ALSNAWNSHS PLIVTAGQQT 100
    RAMIGVEALL TNVDAANLPR PLVKWSYEPA SAAEVPHAMS RAIHMASMAP 150
    QGPVYLSVPY DDWDKDADPQ SHHLFDRHVS SSVRLNDQDL DILVKALNSA 200
    SNPAIVLGPD VDAANANADC VMLAERLKAP VWVAPSAPRC PFPTRHPCFR 250
    GLMPAGIAAI SQLLEGHDVV LVIGAPVFRY HQYDPGQYLK PGTRLISVTC 300
    DPLEAARAPM GDAIVADIGA MASALANLVE ESSRQLPTAA PEPAKVDQDA 350
    GRLHPETVFD TLNDMAPENA IYLNESTSTT AQMWQRLNMR NPGSYYFCAA 400
    GGLGFALPAA IGVQLAEPER QVIAVIGDGS ANYSISALWT AAQYNIPTIF 450
    VIMNNGTYGA LRWFAGVLEA ENVPGLDVPG IDFRALAKGY GVQALKADNL 500
    EQLKGSLQEA LSAKGPVLIE VSTVSPVK 528
    Length:528
    Mass (Da):56,355
    Last modified:December 15, 1998 - v2
    Checksum:iDDB7BC03AD866CC1
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AY143338 Genomic DNA. Translation: AAC15502.1.
    PIRiC44767.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AY143338 Genomic DNA. Translation: AAC15502.1 .
    PIRi C44767.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1BFD X-ray 1.60 A 1-528 [» ]
    1MCZ X-ray 2.80 A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P 1-528 [» ]
    1PI3 X-ray 1.20 A 1-528 [» ]
    1PO7 X-ray 1.20 A 1-528 [» ]
    1Q6Z X-ray 1.00 A 1-528 [» ]
    1YNO X-ray 1.22 A 2-528 [» ]
    2FN3 X-ray 1.00 A 1-528 [» ]
    2FWN X-ray 1.40 A 1-528 [» ]
    2V3W X-ray 2.20 A/B/C/D 1-528 [» ]
    3F6B X-ray 1.34 X 2-526 [» ]
    3F6E X-ray 1.34 X 2-526 [» ]
    3FSJ X-ray 1.37 X 1-528 [» ]
    3FZN X-ray 1.62 A/B/C/D 1-528 [» ]
    4GG1 X-ray 1.07 A 1-528 [» ]
    4GM0 X-ray 1.07 A 1-528 [» ]
    4GM1 X-ray 1.26 A 1-528 [» ]
    4GM4 X-ray 1.28 A 1-528 [» ]
    4GP9 X-ray 1.07 A 1-528 [» ]
    4GPE X-ray 1.39 A 1-528 [» ]
    4JD5 X-ray 1.33 A 1-528 [» ]
    4JU8 X-ray 1.25 A 1-528 [» ]
    4JU9 X-ray 1.12 A 1-528 [» ]
    4JUA X-ray 1.15 A 1-528 [» ]
    4JUB X-ray 1.90 A/B/C/D 1-528 [» ]
    4JUC X-ray 2.30 A/B/C/D 1-528 [» ]
    4JUD X-ray 1.65 X 1-528 [» ]
    4JUF X-ray 2.15 A/B/C/D 2-528 [» ]
    4K9K X-ray 1.30 A 2-525 [» ]
    4K9L X-ray 1.65 A 2-526 [» ]
    4K9M X-ray 1.15 A 2-525 [» ]
    4K9N X-ray 1.70 A/B/C/D 2-525 [» ]
    4K9O X-ray 1.89 A/B/C/D 2-528 [» ]
    4K9P X-ray 2.24 A/B/C/D 2-528 [» ]
    ProteinModelPortali P20906.
    SMRi P20906. Positions 2-525.
    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Enzyme and pathway databases

    UniPathwayi UPA00873 ; UER00854 .
    BioCyci MetaCyc:MONOMER-2461.
    SABIO-RK P20906.

    Miscellaneous databases

    EvolutionaryTracei P20906.

    Family and domain databases

    Gene3Di 3.40.50.1220. 1 hit.
    3.40.50.970. 2 hits.
    InterProi IPR029035. DHS-like_NAD/FAD-binding_dom.
    IPR029061. THDP-binding.
    IPR012000. Thiamin_PyroP_enz_cen_dom.
    IPR012001. Thiamin_PyroP_enz_TPP-bd_dom.
    IPR000399. TPP-bd_CS.
    IPR011766. TPP_enzyme-bd_C.
    [Graphical view ]
    Pfami PF02775. TPP_enzyme_C. 1 hit.
    PF00205. TPP_enzyme_M. 1 hit.
    PF02776. TPP_enzyme_N. 1 hit.
    [Graphical view ]
    SUPFAMi SSF52467. SSF52467. 1 hit.
    SSF52518. SSF52518. 2 hits.
    PROSITEi PS00187. TPP_ENZYMES. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Mandelate pathway of Pseudomonas putida: sequence relationships involving mandelate racemase, (S)-mandelate dehydrogenase, and benzoylformate decarboxylase and expression of benzoylformate decarboxylase in Escherichia coli."
      Tsou A.Y., Ransom S.C., Gerlt J.A., Buechter D.D., Babbitt P.C., Kenyon G.L.
      Biochemistry 29:9856-9862(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-19.
      Strain: ATCC 12633 / DSM 291 / JCM 13063 / NCIMB 9494 / NCTC 10936 / VKM B-2187 / Stanier 90.
    2. "Purification and crystallization of benzoylformate decarboxylase."
      Hasson M.S., Muscate A., Henehan G.T.M., Guidinger P.F., Petsko G.A., Ringe D., Kenyon G.L.
      Protein Sci. 4:955-959(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: CHARACTERIZATION, CRYSTALLIZATION.
      Strain: ATCC 12633 / DSM 291 / JCM 13063 / NCIMB 9494 / NCTC 10936 / VKM B-2187 / Stanier 90.
    3. "The crystal structure of benzoylformate decarboxylase at 1.6 A resolution: diversity of catalytic residues in thiamin diphosphate-dependent enzymes."
      Hasson M.S., Muscate A., McLeish M.J., Polovnikova L.S., Gerlt J.A., Kenyon G.L., Petsko G.A., Ringe D.
      Biochemistry 37:9918-9930(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS), SEQUENCE REVISION TO C-TERMINUS.
      Strain: ATCC 12633 / DSM 291 / JCM 13063 / NCIMB 9494 / NCTC 10936 / VKM B-2187 / Stanier 90.

    Entry informationi

    Entry nameiMDLC_PSEPU
    AccessioniPrimary (citable) accession number: P20906
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1991
    Last sequence update: December 15, 1998
    Last modified: October 1, 2014
    This is version 98 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Direct protein sequencing

    Documents

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

    External Data

    Dasty 3