Structure of PDB 1pvy Chain A

Receptor sequence

>1pvyA (length=219) Species: 2190 (Methanocaldococcus jannaschii)

NNVEKAIEALKKGEIILVYDSDEREGETDMVVASQFITPEHIRIMRKDAG
GLICTALHPDICNKLGIPFMVDILEFASQKFKVLRELYPNDIPYDEKSSF
SITINHRKTFTGITDNDRAFTIKKLAELVKEGRFNDFGKEFRSPGSVTLL
RAAEGLVKNRQGHTEMTVALAELANLVPITTICEMMGDDGNAMSKNETKR
YAEKHNLIYLSGEEIINYY

3D structure

• PDB: 1pvy Structure of 3,4-Dihydroxy-2-butanone 4-Phosphate Synthase from Methanococcus jannaschii in Complex with Divalent Metal Ions and the Substrate Ribulose 5-Phosphate: IMPLICATIONS FOR THE CATALYTIC MECHANISM
• Chain: A
• Resolution: 1.7 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): E26 D30 C55 Y95 F101 N106 S147 H164 E185
• Catalytic site (residue number reindexed from 1): E25 D29 C54 Y94 F100 N105 S146 H163 E184
• Enzyme Commision number: 4.1.99.12: 3,4-dihydroxy-2-butanone-4-phosphate 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	5RP	A	R25 E26 D30 C55 L151 R161 G163 H164 T165 I183 E185	R24 E25 D29 C54 L150 R160 G162 H163 T164 I182 E184
BS02	ZN	A	E26 H164	E25 H163
BS03	CA	A	E26 Y95	E25 Y94
BS04	CA	A	D96 E97	D95 E96
BS05	CA	A	E204 N207	E203 N206

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0003824 catalytic activity
• GO:0008686 3,4-dihydroxy-2-butanone-4-phosphate synthase activity
• GO:0016829 lyase activity
• GO:0030145 manganese ion binding
• GO:0046872 metal ion binding

Biological Process

• GO:0009231 riboflavin biosynthetic process

Cellular Component

• GO:0005829 cytosol

External links

• PDB: RCSB:1pvy, PDBe:1pvy, PDBj:1pvy
• PDBsum: 1pvy
• PubMed: 12904291
• UniProt: Q60364|RIBB_METJA 3,4-dihydroxy-2-butanone 4-phosphate synthase (Gene Name=ribB)