Structure of PDB 4whr Chain D

Receptor sequence

>4whrD (length=237) Species: 303 (Pseudomonas putida)

PAQDNSRFVIRDRNWHPKALTPDYKTSIARSPRQALVSIPQSISETTGPN
FSHLGFGAHDHDLLLNFNNGGLPIGERIIVAGRVVDQYGKPVPNTLVEMW
QANAGGRYRHKNDRYLAPLDPNFGGVGRCLTDSDGYYSFRTIKPGPYPWR
NGPNDWRPAHIHFGISGPSIATKLITQLYFEGDPLIPMCPIVKSIANPEA
VQQLIAKLDMNNANPMDCLAYRFDIVLRGQRKTHFEN

3D structure

• PDB: 4whr Crystal structures of alkylperoxo and anhydride intermediates in an intradiol ring-cleaving dioxygenase.
• Chain: D
• Resolution: 1.58 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): Y408 Y447 R457 H460 H462
• Catalytic site (residue number reindexed from 1): Y108 Y147 R157 H160 H162
• 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	D	Y408 Y447 H460 H462	Y108 Y147 H160 H162
BS02	3N8	D	R307 Q341 R531 E536	R7 Q41 R231 E236
BS03	3N8	D	L416 A417	L116 A117
BS04	3N8	D	S338 I339 P340	S38 I39 P40
BS05	3N8	D	K493 I495 A496 V501	K193 I195 A196 V201

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:4whr, PDBe:4whr, PDBj:4whr
• PDBsum: 4whr
• PubMed: 25548185
• UniProt: P00437|PCXB_PSEPU Protocatechuate 3,4-dioxygenase beta chain (Gene Name=pcaH)