Structure of PDB 3rik Chain B

Receptor sequence

>3rikB (length=497) Species: 9606 (Homo sapiens) [Search protein sequence]

ARPCIPKSFGYSSVVCVCNATYCDSFDPPTFPALGTFSRYESTRSGRRME
LSMGPIQANHTGTGLLLTLQPEQKFQKVKGFGGAMTDAAALNILALSPPA
QNLLLKSYFSEEGIGYNIIRVPMASCDFSIRTYTYADTPDDFQLHNFSLP
EEDTKLKIPLIHRALQLAQRPVSLLASPWTSPTWLKTNGAVNGKGSLKGQ
PGDIYHQTWARYFVKFLDAYAEHKLQFWAVTAENEPSAGLLSGYPFQCLG
FTPEHQRDFIARDLGPTLANSTHHNVRLLMLDDQRLLLPHWAKVVLTDPE
AAKYVHGIAVHWYLDFLAPAKATLGETHRLFPNTMLFASEACVGSKFWEQ
SVRLGSWDRGMQYSHSIITNLLYHVVGWTDWNLALNPEGGPNWVRNFVDS
PIIVDITKDTFYKQPMFYHLGHFSKFIPEGSQRVGLVASQKNDLDAVALM
HPDGSAVVVVLNRSSKDVPLTIKDPAVGFLETISPGYSIHTYLWHRQ

3D structure

PDB

3rik Binding of 3,4,5,6-tetrahydroxyazepanes to the acid-beta-glucosidase active site: implications for pharmacological chaperone design for Gaucher disease

Chain

Resolution

2.48 Å

3D
structure

Catalytic site residues are labeled in the structure
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Enzymatic activity

Catalytic site (original residue number in PDB)	E235 E340 C342 N370
Catalytic site (residue number reindexed from 1)	E235 E340 C342 N370
Enzyme Commision number	2.4.1.- 3.2.1.- 3.2.1.45: glucosylceramidase. 3.2.1.46: galactosylceramidase.

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	3RI	B	D127 F128 W179 N234 E235 W312 Y313 E340 W381	D127 F128 W179 N234 E235 W312 Y313 E340 W381	MOAD: ic50=3.4mM PDBbind-CN: -logKd/Ki=2.47,IC50=3.4mM

Gene Ontology

	Molecular Function
GO:0004336	galactosylceramidase activity
GO:0004348	glucosylceramidase activity
GO:0005102	signaling receptor binding
GO:0005124	scavenger receptor binding
GO:0005515	protein binding
GO:0008422	beta-glucosidase activity
GO:0016757	glycosyltransferase activity
GO:0016787	hydrolase activity
GO:0016798	hydrolase activity, acting on glycosyl bonds
GO:0046527	glucosyltransferase activity
GO:0050295	steryl-beta-glucosidase activity

	Biological Process
GO:0006665	sphingolipid metabolic process
GO:0006678	glucosylceramide metabolic process
GO:0006680	glucosylceramide catabolic process
GO:0006914	autophagy
GO:0007005	mitochondrion organization
GO:0007040	lysosome organization
GO:0007417	central nervous system development
GO:0008203	cholesterol metabolic process
GO:0008340	determination of adult lifespan
GO:0009267	cellular response to starvation
GO:0009268	response to pH
GO:0014004	microglia differentiation
GO:0016241	regulation of macroautophagy
GO:0019882	antigen processing and presentation
GO:0019915	lipid storage
GO:0021694	cerebellar Purkinje cell layer formation
GO:0021859	pyramidal neuron differentiation
GO:0022904	respiratory electron transport chain
GO:0023021	termination of signal transduction
GO:0030259	lipid glycosylation
GO:0031175	neuron projection development
GO:0031333	negative regulation of protein-containing complex assembly
GO:0032006	regulation of TOR signaling
GO:0032436	positive regulation of proteasomal ubiquitin-dependent protein catabolic process
GO:0032715	negative regulation of interleukin-6 production
GO:0033077	T cell differentiation in thymus
GO:0033574	response to testosterone
GO:0042391	regulation of membrane potential
GO:0043161	proteasome-mediated ubiquitin-dependent protein catabolic process
GO:0043243	positive regulation of protein-containing complex disassembly
GO:0043407	negative regulation of MAP kinase activity
GO:0043524	negative regulation of neuron apoptotic process
GO:0043627	response to estrogen
GO:0046512	sphingosine biosynthetic process
GO:0046513	ceramide biosynthetic process
GO:0048469	cell maturation
GO:0048854	brain morphogenesis
GO:0048872	homeostasis of number of cells
GO:0050728	negative regulation of inflammatory response
GO:0050877	nervous system process
GO:0050905	neuromuscular process
GO:0051246	regulation of protein metabolic process
GO:0051248	negative regulation of protein metabolic process
GO:0051402	neuron apoptotic process
GO:0061436	establishment of skin barrier
GO:0061518	microglial cell proliferation
GO:0061744	motor behavior
GO:0071356	cellular response to tumor necrosis factor
GO:0071425	hematopoietic stem cell proliferation
GO:0071548	response to dexamethasone
GO:0072676	lymphocyte migration
GO:0097066	response to thyroid hormone
GO:0098773	skin epidermis development
GO:1901805	beta-glucoside catabolic process
GO:1903052	positive regulation of proteolysis involved in protein catabolic process
GO:1903061	positive regulation of protein lipidation
GO:1904457	positive regulation of neuronal action potential
GO:1905037	autophagosome organization
GO:1905165	regulation of lysosomal protein catabolic process

	Cellular Component
GO:0005615	extracellular space
GO:0005764	lysosome
GO:0005765	lysosomal membrane
GO:0005783	endoplasmic reticulum
GO:0005794	Golgi apparatus
GO:0005802	trans-Golgi network
GO:0016020	membrane
GO:0043202	lysosomal lumen
GO:0070062	extracellular exosome

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component

External links

PDB	RCSB:3rik, PDBe:3rik, PDBj:3rik
PDBsum	3rik
PubMed	22047104
UniProt	P04062\|GBA1_HUMAN Lysosomal acid glucosylceramidase (Gene Name=GBA1)

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