Structure of PDB 3fzn Chain B

Receptor sequence

>3fznB (length=523) Species: 303 (Pseudomonas putida)

ASVHGTTYELLRRQGIDTVFGNPGSNELPFLKDFPEDFRYILALQEACVV
GIADGYAQASRKPAFINLHSAAGTGNAMGALSNAWNSHSPLIVTAGQQTR
AMIGVEALLTNVDAANLPRPLVKWSYEPASAAEVPHAMSRAIHMASMAPQ
GPVYLSVPYDDWDKDADPQSHHLFDRHVSSSVRLNDQDLDILVKALNSAS
NPAIVLGPDVDAANANADCVMLAERLKAPVWVAPSAPRCPFPTRHPCFRG
LMPAGIAAISQLLEGHDVVLVIGAPVFRYHQYDPGQYLKPGTRLISVTCD
PLEAARAPMGDAIVADIGAMASALANLVEESSRQLPTAAPEPAKVDQDAG
RLHPETVFDTLNDMAPENAIYLNESTSTTAQMWQRLNMRNPGSYYFCAAG
GLGFALPAAIGVQLAEPERQVIAVIGDGSANYSISALWTAAQYNIPTIFV
IMNNGTYGALRWFAGVLEAENVPGLDVPGIDFRALAKGYGVQALKADNLE
QLKGSLQEALSAKGPVLIEVSTV

3D structure

• PDB: 3fzn Structural and kinetic studies on native intermediates and an intermediate analogue in benzoylformate decarboxylase reveal a least motion mechanism with an unprecedented short-lived predecarboxylation intermediate.
• Chain: B
• Resolution: 1.62 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): N23 G25 S26 N27 E28 E47 H70 L109 L110 T111 N112 Y160 P254 H281 S376 G401 L403 D428 N455 T457 Y458 A460 L461 F464
• Catalytic site (residue number reindexed from 1): N22 G24 S25 N26 E27 E46 H69 L108 L109 T110 N111 Y159 P253 H280 S375 G400 L402 D427 N454 T456 Y457 A459 L460 F463
• Enzyme Commision number: 4.1.1.7: benzoylformate decarboxylase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	D7K	B	N23 P24 G25 S26 E47 H70	N22 P23 G24 S25 E46 H69	PDBbind-CN: -logKd/Ki=4.01,Kd=97uM
BS02	D7K	B	H281 T377 S378 G401 L403 G427 D428 G429 S430 Y433 N455 T457 Y458 G459 A460 L461 F464	H280 T376 S377 G400 L402 G426 D427 G428 S429 Y432 N454 T456 Y457 G458 A459 L460 F463	PDBbind-CN: -logKd/Ki=4.01,Kd=97uM
BS03	MG	B	D428 N455 T457	D427 N454 T456
BS04	PO4	B	Q170 H172 H173	Q169 H171 H172
BS05	PO4	B	Q287 L289 K290 P291	Q286 L288 K289 P290

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0003824 catalytic activity
• GO:0003984 acetolactate synthase activity
• GO:0016831 carboxy-lyase activity
• GO:0030976 thiamine pyrophosphate binding
• GO:0046872 metal ion binding
• GO:0050660 flavin adenine dinucleotide binding
• GO:0050695 benzoylformate decarboxylase activity

Biological Process

• GO:0009056 catabolic process
• GO:0018924 mandelate metabolic process
• GO:0019596 mandelate catabolic process
• GO:0019752 carboxylic acid metabolic process

External links

• PDB: RCSB:3fzn, PDBe:3fzn, PDBj:3fzn
• PDBsum: 3fzn
• PubMed: 19182954
• UniProt: P20906|MDLC_PSEPU Benzoylformate decarboxylase (Gene Name=mdlC)