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Protein

Benzoylformate decarboxylase

Gene

mdlC

Organism
Pseudomonas putida (Arthrobacter siderocapsulatus)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalytic activityi

Benzoylformate = benzaldehyde + CO2.

Cofactori

Protein has several cofactor binding sites:
  • Ca2+Note: Binds 1 Ca2+ ion per subunit.
  • thiamine diphosphateNote: Binds 1 thiamine pyrophosphate per subunit.
  • Mg2+Note: Binds 1 Mg2+ ion per dimer.

Pathway:i(R)-mandelate degradation

This protein is involved in step 3 of the subpathway that synthesizes benzoate from (R)-mandelate.
Proteins known to be involved in the 4 steps of the subpathway in this organism are:
  1. Mandelate racemase (mdlA)
  2. (S)-mandelate dehydrogenase (mdlB)
  3. Benzoylformate decarboxylase (mdlC)
  4. NAD(P)-dependent benzaldehyde dehydrogenase (mdlD)
This subpathway is part of the pathway (R)-mandelate degradation, which is itself part of Aromatic compound metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes benzoate from (R)-mandelate, the pathway (R)-mandelate degradation and in Aromatic compound metabolism.

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

GO - Biological processi

Complete GO annotation...

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.
BRENDAi4.1.1.7. 5092.
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 – 1411Combined sources
Beta strandi19 – 224Combined sources
Helixi26 – 283Combined sources
Helixi29 – 324Combined sources
Beta strandi40 – 434Combined sources
Helixi47 – 6115Combined sources
Beta strandi65 – 706Combined sources
Helixi71 – 777Combined sources
Helixi79 – 879Combined sources
Beta strandi92 – 987Combined sources
Helixi101 – 1044Combined sources
Turni105 – 1073Combined sources
Helixi115 – 1173Combined sources
Turni118 – 1214Combined sources
Beta strandi124 – 1274Combined sources
Helixi132 – 1343Combined sources
Helixi135 – 14713Combined sources
Beta strandi148 – 1503Combined sources
Beta strandi154 – 1596Combined sources
Helixi160 – 1623Combined sources
Helixi169 – 1746Combined sources
Beta strandi183 – 1853Combined sources
Helixi187 – 19913Combined sources
Beta strandi204 – 2074Combined sources
Helixi209 – 2135Combined sources
Helixi217 – 22711Combined sources
Beta strandi231 – 2333Combined sources
Beta strandi249 – 2524Combined sources
Helixi257 – 2648Combined sources
Beta strandi268 – 2758Combined sources
Beta strandi294 – 3007Combined sources
Helixi302 – 3076Combined sources
Beta strandi309 – 3168Combined sources
Helixi318 – 32811Combined sources
Beta strandi350 – 3534Combined sources
Helixi355 – 36511Combined sources
Beta strandi371 – 3755Combined sources
Helixi377 – 3793Combined sources
Helixi380 – 3867Combined sources
Beta strandi391 – 3933Combined sources
Beta strandi395 – 3973Combined sources
Beta strandi403 – 4053Combined sources
Helixi406 – 41611Combined sources
Beta strandi422 – 4276Combined sources
Helixi428 – 4314Combined sources
Turni432 – 4343Combined sources
Helixi435 – 4373Combined sources
Helixi438 – 4447Combined sources
Beta strandi449 – 4546Combined sources
Helixi459 – 46810Combined sources
Helixi483 – 4908Combined sources
Beta strandi493 – 4997Combined sources
Helixi500 – 51112Combined sources
Beta strandi517 – 5237Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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[»]
4MPJX-ray1.50A1-528[»]
4MPPX-ray1.50A1-528[»]
4MPRX-ray1.40A1-528[»]
4MQ5X-ray1.50A1-528[»]
4MZXX-ray1.56A1-528[»]
4QELX-ray1.43A1-528[»]
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

        10         20         30         40         50
MASVHGTTYE LLRRQGIDTV FGNPGSNELP FLKDFPEDFR YILALQEACV
60 70 80 90 100
VGIADGYAQA SRKPAFINLH SAAGTGNAMG ALSNAWNSHS PLIVTAGQQT
110 120 130 140 150
RAMIGVEALL TNVDAANLPR PLVKWSYEPA SAAEVPHAMS RAIHMASMAP
160 170 180 190 200
QGPVYLSVPY DDWDKDADPQ SHHLFDRHVS SSVRLNDQDL DILVKALNSA
210 220 230 240 250
SNPAIVLGPD VDAANANADC VMLAERLKAP VWVAPSAPRC PFPTRHPCFR
260 270 280 290 300
GLMPAGIAAI SQLLEGHDVV LVIGAPVFRY HQYDPGQYLK PGTRLISVTC
310 320 330 340 350
DPLEAARAPM GDAIVADIGA MASALANLVE ESSRQLPTAA PEPAKVDQDA
360 370 380 390 400
GRLHPETVFD TLNDMAPENA IYLNESTSTT AQMWQRLNMR NPGSYYFCAA
410 420 430 440 450
GGLGFALPAA IGVQLAEPER QVIAVIGDGS ANYSISALWT AAQYNIPTIF
460 470 480 490 500
VIMNNGTYGA LRWFAGVLEA ENVPGLDVPG IDFRALAKGY GVQALKADNL
510 520
EQLKGSLQEA LSAKGPVLIE VSTVSPVK
Length:528
Mass (Da):56,355
Last modified:December 15, 1998 - v2
Checksum:iDDB7BC03AD866CC1
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY143338 Genomic DNA. Translation: AAC15502.1.
PIRiC44767.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY143338 Genomic DNA. Translation: AAC15502.1.
PIRiC44767.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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[»]
4MPJX-ray1.50A1-528[»]
4MPPX-ray1.50A1-528[»]
4MPRX-ray1.40A1-528[»]
4MQ5X-ray1.50A1-528[»]
4MZXX-ray1.56A1-528[»]
4QELX-ray1.43A1-528[»]
ProteinModelPortaliP20906.
SMRiP20906. Positions 2-525.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Enzyme and pathway databases

UniPathwayiUPA00873; UER00854.
BioCyciMetaCyc:MONOMER-2461.
BRENDAi4.1.1.7. 5092.
SABIO-RKP20906.

Miscellaneous databases

EvolutionaryTraceiP20906.

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]
ProtoNetiSearch...

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: July 22, 2015
This is version 103 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.