Structure of PDB 1ypn Chain A

Receptor sequence
>1ypnA (length=294) Species: 562 (Escherichia coli) [Search protein sequence]
DNVLRIATRQSPLALWQAHYVKDKLMASHPGLVVELVPMVTRGDVGQGLF
VKELEVALLENRADIAVHSMKDVPVEFPQGLGLVTICEREDPRDAFVSNN
YDSLDALPAGSIVGTSSLRRQCQLAERRPDLIIRSLRGNVGTRLSKLDNG
EYDAIILAVAGLKRLGLESRIRAALPPEISLPAVGQGAVGIECRLDDSRT
RELLAALNHHETALRVTAERAMNTRLEGGCQVPIGSYAELIDGEIWLRAL
VGAPDGSQIIRGERRGAPQDAEQMGISLAEELLNNGAREILAEV
3D structure
PDB1ypn Time-Resolved Protein Crystal Diffraction: Determination by the Laue Method of the Behaviour of the Enzyme Hydroxymethylbilane Synthase (Lys59Gln Mutant) as It is Loaded with Substrate in the Crystal
ChainA
Resolution2.3 Å
3D
structure
Catalytic site residues are labeled in the structure
[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]
Enzymatic activity
Catalytic site (original residue number in PDB) K83 D84 R131 R132 R149 R155 C242
Catalytic site (residue number reindexed from 1) K71 D72 R119 R120 R137 R143 C230
Enzyme Commision number 2.5.1.61: hydroxymethylbilane synthase.
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 DPM A S81 K83 D84 T127 S128 S129 R131 R132 R155 L169 A170 C242 S69 K71 D72 T115 S116 S117 R119 R120 R143 L157 A158 C230
Gene Ontology
Molecular Function
GO:0004418 hydroxymethylbilane synthase activity
GO:0016740 transferase activity
Biological Process
GO:0006779 porphyrin-containing compound biosynthetic process
GO:0006782 protoporphyrinogen IX biosynthetic process
GO:0006783 heme biosynthetic process
GO:0018160 peptidyl-pyrromethane cofactor linkage
GO:0033014 tetrapyrrole biosynthetic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:1ypn, PDBe:1ypn, PDBj:1ypn
PDBsum1ypn
PubMed
UniProtP06983|HEM3_ECOLI Porphobilinogen deaminase (Gene Name=hemC)

[Back to BioLiP]