Structure of PDB 3dsv Chain B

Receptor sequence

>3dsvB (length=324) Species: 10116 (Rattus norvegicus)

QKDVTIKSDAPDTLLLEKHADYIASYGSDYEYCMSEYLRMSGVYWGLTVM
DLMGQLHRMNKEEILVFIKSCQHECGGVSASIGHDPHLLYTLSAVQILTL
YDSIHVINVDKVVAYVQSLQKEDGSFAGDIWGEIDTRFSFCAVATLALLG
KLDAINVEKAIEFVLSCMNFDGGFGCRPGSESHAGQIYCCTGFLAITSQL
HQVNSDLLGWWLCERQLPSGGLNGRPEKLPDVCYSWWVLASLKIIGRLHW
IDREKLRSFILACQDEETGGFADRPGDMVDPFHTLFGIAGLSLLGEEQIK
PVSPVFCMPEEVLQRVNVQPELVS

3D structure

• PDB: 3dsv Structures of RabGGTase-substrate/product complexes provide insights into the evolution of protein prenylation
• Chain: B
• Resolution: 2.1 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): H190 R232 K235 D238 C240 Y241 D280 D287 H290
• Catalytic site (residue number reindexed from 1): H183 R225 K228 D231 C233 Y234 D273 D280 H283
• Enzyme Commision number: 2.5.1.60: protein geranylgeranyltransferase type II.

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	ZN	B	D238 C240 H290	D231 C233 H283
BS02	CA	B	H64 M66	H57 M59
BS03	GER	B	G192 C196 W244 F293	G185 C189 W237 F286

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0004659 prenyltransferase activity
• GO:0004661 protein geranylgeranyltransferase activity
• GO:0004663 Rab geranylgeranyltransferase activity
• GO:0005515 protein binding
• GO:0008270 zinc ion binding
• GO:0008318 protein prenyltransferase activity
• GO:0019840 isoprenoid binding
• GO:0031267 small GTPase binding
• GO:0046872 metal ion binding

Biological Process

• GO:0018344 protein geranylgeranylation

Cellular Component

• GO:0005968 Rab-protein geranylgeranyltransferase complex

External links

• PDB: RCSB:3dsv, PDBe:3dsv, PDBj:3dsv
• PDBsum: 3dsv
• PubMed: 18756270
• UniProt: Q08603|PGTB2_RAT Geranylgeranyl transferase type-2 subunit beta (Gene Name=Rabggtb)