Structure of PDB 3dyo Chain D

Receptor sequence
>3dyoD (length=1011) Species: 83333 (Escherichia coli K-12) [Search protein sequence]
RRDWENPGVTQLNRLAAHPPFASWRNSEEARTDRPSQQLRSLNGEWRFAW
FPAPEAVPESWLECDLPEADTVVVPSNWQMHGYDAPIYTNVTYPITVNPP
FVPTENPTGCYSLTFNVDESWLQEGQTRIIFDGVNSAFHLWCNGRWVGYG
QDSRLPSEFDLSAFLRAGENRLAVMVLRWSDGSYLEDQDMWRMSGIFRDV
SLLHKPTTQISDFHVATRFNDDFSRAVLEAEVQMCGELRDYLRVTVSLWQ
GETQVASGTAPFGGEIIDERGGYADRVTLRLNVENPKLWSAEIPNLYRAV
VELHTADGTLIEAEACDVGFREVRIENGLLLLNGKPLLIRGVNRHEHHPL
HGQVMDEQTMVQDILLMKQNNFNAVRCSHYPNHPLWYTLCDRYGLYVVDE
ANIETNGMVPMNRLTDDPRWLPAMSERVTRMVQRDRNHPSVIIWSLGNES
GHGANHDALYRWIKSVDPSRPVQYEGGGADTTATDIICPMYARVDEDQPF
PAVPKWSIKKWLSLPGETRPLILCEYAHAMGNSLGGFAKYWQAFRQYPRL
QGGFVWDWVDQSLIKYDENGNPWSAYGGDFGDTPNDRQFCMNGLVFADRT
PHPALTEAKHQQQFFQFRLSGQTIEVTSEYLFRHSDNELLHWMVALDGKP
LASGEVPLDVAPQGKQLIELPELPQPESAGQLWLTVRVVQPNATAWSEAG
HISAWQQWRLAENLSVTLPAASHAIPHLTTSEMDFCIELGNKRWQFNRQS
GFLSQMWIGDKKQLLTPLRDQFTRAPLDNDIGVSEATRIDPNAWVERWKA
AGHYQAEAALLQCTADTLADAVLITTAHAWQHQGKTLFISRKTYRIDGSG
QMAITVDVEVASDTPHPARIGLNCQLAQVAERVNWLGLGPQENYPDRLTA
ACFDRWDLPLSDMYTPYVFPSENGLRCGTRELNYGPHQWRGDFQFNISRY
SQQQLMETSHRHLLHAEEGTWLNIDGFHMGIGGDDSWSPSVSAEFQLSAG
RYHYQLVWCQK
3D structure
PDB3dyo Direct and indirect roles of His-418 in metal binding and in the activity of beta-galactosidase (E. coli).
ChainD
Resolution1.8 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) D201 H357 H391 E416 N418 E461 Y503 E537 N597 F601 N604
Catalytic site (residue number reindexed from 1) D189 H345 H379 E404 N406 E449 Y491 E525 N585 F589 N592
Enzyme Commision number 3.2.1.23: beta-galactosidase.
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 IPT D D507 E508 D495 E496 MOAD: Ki=5mM
PDBbind-CN: -logKd/Ki=2.30,Ki=5.0mM
BindingDB: Ki=7.6e+4nM
BS02 MG D E416 N418 E461 E404 N406 E449
BS03 MG D D15 N18 V21 Q163 D193 D3 N6 V9 Q151 D181
BS04 IPT D R230 F231 N232 A238 V239 R218 F219 N220 A226 V227 MOAD: Ki=5mM
PDBbind-CN: -logKd/Ki=2.30,Ki=5.0mM
BindingDB: Ki=7.6e+4nM
BS05 IPT D N102 D201 E461 H540 N604 W999 N90 D189 E449 H528 N592 W987 MOAD: Ki=5mM
PDBbind-CN: -logKd/Ki=2.30,Ki=5.0mM
BindingDB: Ki=7.6e+4nM
BS06 IPT D E304 R645 D648 Q702 W708 E292 R633 D636 Q690 W696 MOAD: Ki=5mM
PDBbind-CN: -logKd/Ki=2.30,Ki=5.0mM
BindingDB: Ki=7.6e+4nM
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003824 catalytic activity
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
GO:0004565 beta-galactosidase activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0030246 carbohydrate binding
GO:0031420 alkali metal ion binding
GO:0042802 identical protein binding
GO:0046872 metal ion binding
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0005990 lactose catabolic process
GO:0009056 catabolic process
Cellular Component
GO:0009341 beta-galactosidase complex

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3dyo, PDBe:3dyo, PDBj:3dyo
PDBsum3dyo
PubMed19472413
UniProtP00722|BGAL_ECOLI Beta-galactosidase (Gene Name=lacZ)

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