Structure of PDB 3pck Chain M

Receptor sequence

>3pckM (length=233) Species: 303 (Pseudomonas putida)

PAQDNSRFVIRDRNWHPKALTPDYKTSIARSPRQALVSIPQSISETTGPN
FSHLGFGAHDHDLLLNFGLPIGERIIVAGRVVDQYGKPVPNTLVEMWQAN
AGGRYRHKNDRYLAPLDPNFGGVGRCLTDSDGYYSFRTIKPGPYPWRNGP
NDWRPAHIHFGISGPSIATKLITQLYFEGDPLIPMCPIVKSIANPEAVQQ
LIAKLDMNNANPMDCLAYRFDIVLRGQRKTHFE

3D structure

• PDB: 3pck Crystal structures of substrate and substrate analog complexes of protocatechuate 3,4-dioxygenase: endogenous Fe3+ ligand displacement in response to substrate binding.
• Chain: M
• Resolution: 2.13 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): Y408 Y447 R457 H460 H462
• Catalytic site (residue number reindexed from 1): Y105 Y144 R154 H157 H159
• Enzyme Commision number: 1.13.11.3: protocatechuate 3,4-dioxygenase.

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	FE	M	Y408 H460 H462	Y105 H157 H159
BS02	NNO	M	Y324 Y408 W449 R457 H460 H462 I491	Y24 Y105 W146 R154 H157 H159 I188	MOAD: Kd=0.2uM PDBbind-CN: -logKd/Ki=6.70,Kd=0.2uM

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0005506 iron ion binding
• GO:0008199 ferric iron binding
• GO:0016702 oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
• GO:0018578 protocatechuate 3,4-dioxygenase activity
• GO:0046872 metal ion binding
• GO:0051213 dioxygenase activity

Biological Process

• GO:0009056 catabolic process
• GO:0019619 3,4-dihydroxybenzoate catabolic process
• GO:0042952 beta-ketoadipate pathway

External links

• PDB: RCSB:3pck, PDBe:3pck, PDBj:3pck
• PDBsum: 3pck
• PubMed: 9254600
• UniProt: P00437|PCXB_PSEPU Protocatechuate 3,4-dioxygenase beta chain (Gene Name=pcaH)