Structure of PDB 2ybq Chain A

Receptor sequence

>2ybqA (length=242) Species: 208964 (Pseudomonas aeruginosa PAO1)

VDFPAGSVALVGAGPGDPGLLTLRAWALLQQAEVVVYDRLVARELIALLP
ESCQRIYVGPQEEINELLVRLARQQRRVVRLKGGDPFIFGRGAEELERLL
EAGVDCQVVPGVTAASGCSTYAGIPLTHRDLAQSCTFVTGHLQLDLDWAG
LARGKQTLVFYMGLGNLAEIAARLVEHGLASDTPAALVSQGTQAGQQVTR
GALAELPALARRYQLKPPTLIVVGQVVALFAERAMAHPSYLG

3D structure

• PDB: 2ybq Crystal Structure of the Heme D1 Biosynthesis Enzyme Nire in Complex with its Substrate Reveals New Insights Into the Catalytic Mechanism of S-Adenosyl-L-Methionine-Dependent Uroporphyrinogen III Methyltransferases.
• Chain: A
• Resolution: 2.0 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): D50 M186
• Catalytic site (residue number reindexed from 1): D38 M162
• Enzyme Commision number: 2.1.1.107: uroporphyrinogen-III C-methyltransferase.

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	SAH	A	L52 G103 G104 D105 I108 F109 T133 A134 C138 Y185 M186 G215 P242 T243 L244	L40 G83 G84 D85 I88 F89 T113 A114 C118 Y161 M162 G191 P218 T219 L220
BS02	UP2	A	R51 L52 F109 R111 H161 L162 Q163 M186 L188 G189 P241	R39 L40 F89 R91 H141 L142 Q143 M162 L164 G165 P217

Gene Ontology

Molecular Function

• GO:0004851 uroporphyrin-III C-methyltransferase activity
• GO:0008168 methyltransferase activity

Biological Process

• GO:0006779 porphyrin-containing compound biosynthetic process
• GO:0009236 cobalamin biosynthetic process
• GO:0019354 siroheme biosynthetic process
• GO:0032259 methylation

External links

• PDB: RCSB:2ybq, PDBe:2ybq, PDBj:2ybq
• PDBsum: 2ybq
• PubMed: 21632530
• UniProt: P95417