MDLC_PSEPU
ID MDLC_PSEPU Reviewed; 528 AA.
AC P20906;
DT 01-FEB-1991, integrated into UniProtKB/Swiss-Prot.
DT 15-DEC-1998, sequence version 2.
DT 03-AUG-2022, entry version 127.
DE RecName: Full=Benzoylformate decarboxylase;
DE Short=BFD;
DE Short=BFDC;
DE EC=4.1.1.7;
GN Name=mdlC;
OS Pseudomonas putida (Arthrobacter siderocapsulatus).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
OC Pseudomonadaceae; Pseudomonas.
OX NCBI_TaxID=303;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PROTEIN SEQUENCE OF 1-19.
RC STRAIN=ATCC 12633 / DSM 291 / JCM 13063 / CCUG 12690 / LMG 2257 / NBRC
RC 14164 / NCIMB 9494 / NCTC 10936 / VKM B-2187 / Stanier 90;
RX PubMed=2271624; DOI=10.1021/bi00494a015;
RA Tsou A.Y., Ransom S.C., Gerlt J.A., Buechter D.D., Babbitt P.C.,
RA Kenyon G.L.;
RT "Mandelate pathway of Pseudomonas putida: sequence relationships involving
RT mandelate racemase, (S)-mandelate dehydrogenase, and benzoylformate
RT decarboxylase and expression of benzoylformate decarboxylase in Escherichia
RT coli.";
RL Biochemistry 29:9856-9862(1990).
RN [2]
RP CHARACTERIZATION, AND CRYSTALLIZATION.
RC STRAIN=ATCC 12633 / DSM 291 / JCM 13063 / CCUG 12690 / LMG 2257 / NBRC
RC 14164 / NCIMB 9494 / NCTC 10936 / VKM B-2187 / Stanier 90;
RX PubMed=7663351; DOI=10.1002/pro.5560040515;
RA Hasson M.S., Muscate A., Henehan G.T.M., Guidinger P.F., Petsko G.A.,
RA Ringe D., Kenyon G.L.;
RT "Purification and crystallization of benzoylformate decarboxylase.";
RL Protein Sci. 4:955-959(1995).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS), AND SEQUENCE REVISION TO C-TERMINUS.
RC STRAIN=ATCC 12633 / DSM 291 / JCM 13063 / CCUG 12690 / LMG 2257 / NBRC
RC 14164 / NCIMB 9494 / NCTC 10936 / VKM B-2187 / Stanier 90;
RX PubMed=9665697; DOI=10.1021/bi973047e;
RA Hasson M.S., Muscate A., McLeish M.J., Polovnikova L.S., Gerlt J.A.,
RA Kenyon G.L., Petsko G.A., Ringe D.;
RT "The crystal structure of benzoylformate decarboxylase at 1.6 A resolution:
RT diversity of catalytic residues in thiamin diphosphate-dependent enzymes.";
RL Biochemistry 37:9918-9930(1998).
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H(+) + phenylglyoxylate = benzaldehyde + CO2;
CC Xref=Rhea:RHEA:23368, ChEBI:CHEBI:15378, ChEBI:CHEBI:16526,
CC ChEBI:CHEBI:17169, ChEBI:CHEBI:36656; EC=4.1.1.7;
CC -!- COFACTOR:
CC Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
CC Note=Binds 1 Ca(2+) ion per subunit.;
CC -!- COFACTOR:
CC Name=thiamine diphosphate; Xref=ChEBI:CHEBI:58937;
CC Note=Binds 1 thiamine pyrophosphate per subunit.;
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Note=Binds 1 Mg(2+) ion per dimer.;
CC -!- PATHWAY: Aromatic compound metabolism; (R)-mandelate degradation;
CC benzoate from (R)-mandelate: step 3/4.
CC -!- SUBUNIT: Homotetramer.
CC -!- SIMILARITY: Belongs to the TPP enzyme family. {ECO:0000305}.
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DR EMBL; AY143338; AAC15502.1; -; Genomic_DNA.
DR PIR; C44767; C44767.
DR RefSeq; WP_016501746.1; NZ_UGUX01000003.1.
DR PDB; 1BFD; X-ray; 1.60 A; A=1-528.
DR PDB; 1MCZ; X-ray; 2.80 A; A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P=1-528.
DR PDB; 1PI3; X-ray; 1.20 A; A=1-528.
DR PDB; 1PO7; X-ray; 1.20 A; A=1-528.
DR PDB; 1Q6Z; X-ray; 1.00 A; A=1-528.
DR PDB; 1YNO; X-ray; 1.22 A; A=2-528.
DR PDB; 2FN3; X-ray; 1.00 A; A=1-528.
DR PDB; 2FWN; X-ray; 1.40 A; A=1-528.
DR PDB; 2V3W; X-ray; 2.20 A; A/B/C/D=1-528.
DR PDB; 3F6B; X-ray; 1.34 A; X=2-526.
DR PDB; 3F6E; X-ray; 1.34 A; X=2-526.
DR PDB; 3FSJ; X-ray; 1.37 A; X=1-528.
DR PDB; 3FZN; X-ray; 1.62 A; A/B/C/D=1-528.
DR PDB; 4GG1; X-ray; 1.07 A; A=1-528.
DR PDB; 4GM0; X-ray; 1.07 A; A=1-528.
DR PDB; 4GM1; X-ray; 1.26 A; A=1-528.
DR PDB; 4GM4; X-ray; 1.28 A; A=1-528.
DR PDB; 4GP9; X-ray; 1.07 A; A=1-528.
DR PDB; 4GPE; X-ray; 1.39 A; A=1-528.
DR PDB; 4JD5; X-ray; 1.33 A; A=1-528.
DR PDB; 4JU8; X-ray; 1.25 A; A=1-528.
DR PDB; 4JU9; X-ray; 1.12 A; A=1-528.
DR PDB; 4JUA; X-ray; 1.15 A; A=1-528.
DR PDB; 4JUB; X-ray; 1.90 A; A/B/C/D=1-528.
DR PDB; 4JUC; X-ray; 2.30 A; A/B/C/D=1-528.
DR PDB; 4JUD; X-ray; 1.65 A; X=1-528.
DR PDB; 4JUF; X-ray; 2.15 A; A/B/C/D=2-528.
DR PDB; 4K9K; X-ray; 1.30 A; A=2-525.
DR PDB; 4K9L; X-ray; 1.65 A; A=2-526.
DR PDB; 4K9M; X-ray; 1.15 A; A=2-525.
DR PDB; 4K9N; X-ray; 1.70 A; A/B/C/D=2-525.
DR PDB; 4K9O; X-ray; 1.89 A; A/B/C/D=2-528.
DR PDB; 4K9P; X-ray; 2.24 A; A/B/C/D=2-528.
DR PDB; 4MPJ; X-ray; 1.50 A; A=1-528.
DR PDB; 4MPP; X-ray; 1.50 A; A=1-528.
DR PDB; 4MPR; X-ray; 1.40 A; A=1-528.
DR PDB; 4MQ5; X-ray; 1.50 A; A=1-528.
DR PDB; 4MZX; X-ray; 1.56 A; A=1-528.
DR PDB; 4QEL; X-ray; 1.43 A; A=1-528.
DR PDB; 5DEI; X-ray; 1.30 A; A/B/C/D=2-525.
DR PDB; 5DGD; X-ray; 1.13 A; A=2-525.
DR PDB; 5DGT; X-ray; 1.08 A; A=2-525.
DR PDB; 6M2Y; X-ray; 2.10 A; A=1-528.
DR PDB; 6M2Z; X-ray; 2.35 A; A=1-528.
DR PDBsum; 1BFD; -.
DR PDBsum; 1MCZ; -.
DR PDBsum; 1PI3; -.
DR PDBsum; 1PO7; -.
DR PDBsum; 1Q6Z; -.
DR PDBsum; 1YNO; -.
DR PDBsum; 2FN3; -.
DR PDBsum; 2FWN; -.
DR PDBsum; 2V3W; -.
DR PDBsum; 3F6B; -.
DR PDBsum; 3F6E; -.
DR PDBsum; 3FSJ; -.
DR PDBsum; 3FZN; -.
DR PDBsum; 4GG1; -.
DR PDBsum; 4GM0; -.
DR PDBsum; 4GM1; -.
DR PDBsum; 4GM4; -.
DR PDBsum; 4GP9; -.
DR PDBsum; 4GPE; -.
DR PDBsum; 4JD5; -.
DR PDBsum; 4JU8; -.
DR PDBsum; 4JU9; -.
DR PDBsum; 4JUA; -.
DR PDBsum; 4JUB; -.
DR PDBsum; 4JUC; -.
DR PDBsum; 4JUD; -.
DR PDBsum; 4JUF; -.
DR PDBsum; 4K9K; -.
DR PDBsum; 4K9L; -.
DR PDBsum; 4K9M; -.
DR PDBsum; 4K9N; -.
DR PDBsum; 4K9O; -.
DR PDBsum; 4K9P; -.
DR PDBsum; 4MPJ; -.
DR PDBsum; 4MPP; -.
DR PDBsum; 4MPR; -.
DR PDBsum; 4MQ5; -.
DR PDBsum; 4MZX; -.
DR PDBsum; 4QEL; -.
DR PDBsum; 5DEI; -.
DR PDBsum; 5DGD; -.
DR PDBsum; 5DGT; -.
DR PDBsum; 6M2Y; -.
DR PDBsum; 6M2Z; -.
DR AlphaFoldDB; P20906; -.
DR SMR; P20906; -.
DR DrugBank; DB02280; (R)-Mandelic acid.
DR DrugBank; DB01987; Cocarboxylase.
DR GeneID; 45526286; -.
DR BioCyc; MetaCyc:MON-2461; -.
DR BRENDA; 4.1.1.7; 5092.
DR SABIO-RK; P20906; -.
DR UniPathway; UPA00873; UER00854.
DR EvolutionaryTrace; P20906; -.
DR GO; GO:0050695; F:benzoylformate decarboxylase activity; IEA:UniProtKB-EC.
DR GO; GO:0000287; F:magnesium ion binding; IEA:InterPro.
DR GO; GO:0030976; F:thiamine pyrophosphate binding; IEA:InterPro.
DR GO; GO:0019596; P:mandelate catabolic process; IEA:UniProtKB-UniPathway.
DR InterPro; IPR029035; DHS-like_NAD/FAD-binding_dom.
DR InterPro; IPR029061; THDP-binding.
DR InterPro; IPR012000; Thiamin_PyroP_enz_cen_dom.
DR InterPro; IPR012001; Thiamin_PyroP_enz_TPP-bd_dom.
DR InterPro; IPR000399; TPP-bd_CS.
DR InterPro; IPR045229; TPP_enz.
DR InterPro; IPR011766; TPP_enzyme-bd_C.
DR PANTHER; PTHR18968; PTHR18968; 1.
DR Pfam; PF02775; TPP_enzyme_C; 1.
DR Pfam; PF00205; TPP_enzyme_M; 1.
DR Pfam; PF02776; TPP_enzyme_N; 1.
DR SUPFAM; SSF52467; SSF52467; 1.
DR SUPFAM; SSF52518; SSF52518; 2.
DR PROSITE; PS00187; TPP_ENZYMES; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Aromatic hydrocarbons catabolism; Calcium; Decarboxylase;
KW Direct protein sequencing; Lyase; Magnesium; Mandelate pathway;
KW Metal-binding; Thiamine pyrophosphate.
FT CHAIN 1..528
FT /note="Benzoylformate decarboxylase"
FT /id="PRO_0000090820"
FT REGION 377..460
FT /note="Thiamine pyrophosphate binding"
FT BINDING 117
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT BINDING 118
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT BINDING 120
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT BINDING 428
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT BINDING 455
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT BINDING 457
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT HELIX 4..14
FT /evidence="ECO:0007829|PDB:1Q6Z"
FT STRAND 19..22
FT /evidence="ECO:0007829|PDB:1Q6Z"
FT HELIX 26..28
FT /evidence="ECO:0007829|PDB:1Q6Z"
FT HELIX 29..32
FT /evidence="ECO:0007829|PDB:1Q6Z"
FT STRAND 40..43
FT /evidence="ECO:0007829|PDB:1Q6Z"
FT HELIX 47..61
FT /evidence="ECO:0007829|PDB:1Q6Z"
FT STRAND 65..70
FT /evidence="ECO:0007829|PDB:1Q6Z"
FT HELIX 71..77
FT /evidence="ECO:0007829|PDB:1Q6Z"
FT HELIX 79..87
FT /evidence="ECO:0007829|PDB:1Q6Z"
FT STRAND 92..98
FT /evidence="ECO:0007829|PDB:1Q6Z"
FT HELIX 101..104
FT /evidence="ECO:0007829|PDB:1Q6Z"
FT TURN 105..107
FT /evidence="ECO:0007829|PDB:1Q6Z"
FT HELIX 115..117
FT /evidence="ECO:0007829|PDB:1Q6Z"
FT TURN 118..121
FT /evidence="ECO:0007829|PDB:2FN3"
FT STRAND 124..127
FT /evidence="ECO:0007829|PDB:4K9K"
FT HELIX 132..134
FT /evidence="ECO:0007829|PDB:1Q6Z"
FT HELIX 135..147
FT /evidence="ECO:0007829|PDB:1Q6Z"
FT STRAND 148..150
FT /evidence="ECO:0007829|PDB:1Q6Z"
FT STRAND 154..159
FT /evidence="ECO:0007829|PDB:1Q6Z"
FT HELIX 160..162
FT /evidence="ECO:0007829|PDB:1Q6Z"
FT HELIX 169..174
FT /evidence="ECO:0007829|PDB:1Q6Z"
FT STRAND 183..185
FT /evidence="ECO:0007829|PDB:5DEI"
FT HELIX 187..199
FT /evidence="ECO:0007829|PDB:1Q6Z"
FT STRAND 204..207
FT /evidence="ECO:0007829|PDB:1Q6Z"
FT HELIX 209..213
FT /evidence="ECO:0007829|PDB:1Q6Z"
FT HELIX 217..227
FT /evidence="ECO:0007829|PDB:1Q6Z"
FT STRAND 231..233
FT /evidence="ECO:0007829|PDB:1Q6Z"
FT STRAND 249..252
FT /evidence="ECO:0007829|PDB:1Q6Z"
FT HELIX 257..264
FT /evidence="ECO:0007829|PDB:1Q6Z"
FT STRAND 268..275
FT /evidence="ECO:0007829|PDB:1Q6Z"
FT STRAND 294..300
FT /evidence="ECO:0007829|PDB:1Q6Z"
FT HELIX 302..307
FT /evidence="ECO:0007829|PDB:1Q6Z"
FT STRAND 309..316
FT /evidence="ECO:0007829|PDB:1Q6Z"
FT HELIX 318..328
FT /evidence="ECO:0007829|PDB:1Q6Z"
FT STRAND 350..353
FT /evidence="ECO:0007829|PDB:1Q6Z"
FT HELIX 355..365
FT /evidence="ECO:0007829|PDB:1Q6Z"
FT STRAND 371..375
FT /evidence="ECO:0007829|PDB:1Q6Z"
FT HELIX 377..379
FT /evidence="ECO:0007829|PDB:4GP9"
FT HELIX 380..386
FT /evidence="ECO:0007829|PDB:1Q6Z"
FT STRAND 391..393
FT /evidence="ECO:0007829|PDB:1Q6Z"
FT STRAND 395..397
FT /evidence="ECO:0007829|PDB:1Q6Z"
FT STRAND 403..405
FT /evidence="ECO:0007829|PDB:4GM4"
FT HELIX 406..416
FT /evidence="ECO:0007829|PDB:1Q6Z"
FT STRAND 422..427
FT /evidence="ECO:0007829|PDB:1Q6Z"
FT HELIX 428..431
FT /evidence="ECO:0007829|PDB:1Q6Z"
FT TURN 432..434
FT /evidence="ECO:0007829|PDB:1Q6Z"
FT HELIX 435..437
FT /evidence="ECO:0007829|PDB:1Q6Z"
FT HELIX 438..444
FT /evidence="ECO:0007829|PDB:1Q6Z"
FT STRAND 449..454
FT /evidence="ECO:0007829|PDB:1Q6Z"
FT HELIX 459..468
FT /evidence="ECO:0007829|PDB:1Q6Z"
FT HELIX 483..490
FT /evidence="ECO:0007829|PDB:1Q6Z"
FT STRAND 493..499
FT /evidence="ECO:0007829|PDB:1Q6Z"
FT HELIX 500..511
FT /evidence="ECO:0007829|PDB:1Q6Z"
FT STRAND 517..523
FT /evidence="ECO:0007829|PDB:1Q6Z"
SQ SEQUENCE 528 AA; 56355 MW; DDB7BC03AD866CC1 CRC64;
MASVHGTTYE LLRRQGIDTV FGNPGSNELP FLKDFPEDFR YILALQEACV VGIADGYAQA
SRKPAFINLH SAAGTGNAMG ALSNAWNSHS PLIVTAGQQT RAMIGVEALL TNVDAANLPR
PLVKWSYEPA SAAEVPHAMS RAIHMASMAP QGPVYLSVPY DDWDKDADPQ SHHLFDRHVS
SSVRLNDQDL DILVKALNSA SNPAIVLGPD VDAANANADC VMLAERLKAP VWVAPSAPRC
PFPTRHPCFR GLMPAGIAAI SQLLEGHDVV LVIGAPVFRY HQYDPGQYLK PGTRLISVTC
DPLEAARAPM GDAIVADIGA MASALANLVE ESSRQLPTAA PEPAKVDQDA GRLHPETVFD
TLNDMAPENA IYLNESTSTT AQMWQRLNMR NPGSYYFCAA GGLGFALPAA IGVQLAEPER
QVIAVIGDGS ANYSISALWT AAQYNIPTIF VIMNNGTYGA LRWFAGVLEA ENVPGLDVPG
IDFRALAKGY GVQALKADNL EQLKGSLQEA LSAKGPVLIE VSTVSPVK
