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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.

Pathwayi: (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)DescriptionActionsGraphical viewLength
Metal bindingi117Magnesium; via carbonyl oxygen1
Metal bindingi118Magnesium; via carbonyl oxygen1
Metal bindingi120Magnesium1
Metal bindingi428Calcium1
Metal bindingi455Calcium1
Metal bindingi457Calcium1

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)DescriptionActionsGraphical viewLength
ChainiPRO_00000908201 – 528Benzoylformate decarboxylaseAdd BLAST528

Interactioni

Subunit structurei

Homotetramer.

Structurei

Secondary structure

1528
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi4 – 14Combined sources11
Beta strandi19 – 22Combined sources4
Helixi26 – 28Combined sources3
Helixi29 – 32Combined sources4
Beta strandi40 – 43Combined sources4
Helixi47 – 61Combined sources15
Beta strandi65 – 70Combined sources6
Helixi71 – 77Combined sources7
Helixi79 – 87Combined sources9
Beta strandi92 – 98Combined sources7
Helixi101 – 104Combined sources4
Turni105 – 107Combined sources3
Helixi115 – 117Combined sources3
Turni118 – 121Combined sources4
Beta strandi124 – 127Combined sources4
Helixi132 – 134Combined sources3
Helixi135 – 147Combined sources13
Beta strandi148 – 150Combined sources3
Beta strandi154 – 159Combined sources6
Helixi160 – 162Combined sources3
Helixi169 – 174Combined sources6
Beta strandi183 – 185Combined sources3
Helixi187 – 199Combined sources13
Beta strandi204 – 207Combined sources4
Helixi209 – 213Combined sources5
Helixi217 – 227Combined sources11
Beta strandi231 – 233Combined sources3
Beta strandi249 – 252Combined sources4
Helixi257 – 264Combined sources8
Beta strandi268 – 275Combined sources8
Beta strandi294 – 300Combined sources7
Helixi302 – 307Combined sources6
Beta strandi309 – 316Combined sources8
Helixi318 – 328Combined sources11
Beta strandi350 – 353Combined sources4
Helixi355 – 365Combined sources11
Beta strandi371 – 375Combined sources5
Helixi377 – 379Combined sources3
Helixi380 – 386Combined sources7
Beta strandi391 – 393Combined sources3
Beta strandi395 – 397Combined sources3
Beta strandi403 – 405Combined sources3
Helixi406 – 416Combined sources11
Beta strandi422 – 427Combined sources6
Helixi428 – 431Combined sources4
Turni432 – 434Combined sources3
Helixi435 – 437Combined sources3
Helixi438 – 444Combined sources7
Beta strandi449 – 454Combined sources6
Helixi459 – 468Combined sources10
Helixi483 – 490Combined sources8
Beta strandi493 – 499Combined sources7
Helixi500 – 511Combined sources12
Beta strandi517 – 523Combined sources7

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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[»]
5DEIX-ray1.30A/B/C/D2-525[»]
5DGDX-ray1.13A2-525[»]
5DGTX-ray1.08A2-525[»]
ProteinModelPortaliP20906.
SMRiP20906.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP20906.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni377 – 460Thiamine pyrophosphate bindingAdd BLAST84

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
PDB 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[»]
5DEIX-ray1.30A/B/C/D2-525[»]
5DGDX-ray1.13A2-525[»]
5DGTX-ray1.08A2-525[»]
ProteinModelPortaliP20906.
SMRiP20906.
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...

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: November 2, 2016
This is version 109 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

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 one 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.