Structure of PDB 2z8s Chain B

Receptor sequence

>2z8sB (length=583) Species: 1423 (Bacillus subtilis)

AARQMEALNRGLVAVKTDGGIFVSWRFLGTENASVLFNVYRDGQKLNAAP
VKTTNYVDKNGSAGSTYTVRAVVNGTEQPASEKASVWAQPYHSVPLDKPA
GGTTPKGESYTYSANDASVGDVDGDGQYELILKWDPSNSKDNSQDGYTGD
VLIDAYKLDGTKLWRINLGKNIRAGAHYTQFMVYDLDGDGKAEVAMKTAD
GTKDGTGKVIGNANADYRNEQGRVLSGPEYLTVFQGSTGKELVTANFEPA
RGNVSDWGDSYGNRVDRFLAGIAYLDGQRPSLIMTRGYYAKTMLVAYNFR
DGKLSKLWTLDSSKSGNEAFAGQGNHNLSIADVDGDGKDEIIFGSMAVDH
DGKGMYSTGLGHGDALHTGDLDPGRPGLEVFQVHEDKNAKYGLSFRDAAT
GKILWGVYAGKDVGRGMAADIDPRYPGQEVWANGSLYSAKGVKIGSGVPS
STNFGIWWDGDLLREQLDSNRIDKWDYQNGVSKNMLTASGAAANNGTKAT
PTLQADLLGDWREEVVWRTEDSSALRIYTTTIPTEHRLYTLMHDPVYRLG
IAWQNIAYNQPPHTSFFLGDGMAEQPKPNMYTP

3D structure

• PDB: 2z8s A Novel Structural Fold in Polysaccharide Lyases: BACILLUS SUBTILIS FAMILY 11 RHAMNOGALACTURONAN LYASE YesW WITH AN EIGHT-BLADED -PROPELLER
• Chain: B
• Resolution: 2.5 Å

Enzymatic activity

• Enzyme Commision number: 4.2.2.23: rhamnogalacturonan endolyase.

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	ADA	B	R452 T534 K535	R415 T497 K498
BS02	CA	B	H363 H399 D401 E422	H326 H362 D364 E385
BS03	CA	B	D153 N592 I593 A594 N596	D116 N555 I556 A557 N559
BS04	CA	B	D496 D498 L500 E502	D459 D461 L463 E465
BS05	CA	B	D457 D459 Y462 G464 E466	D420 D422 Y425 G427 E429
BS06	CA	B	D369 D371 D373 K375 E377	D332 D334 D336 K338 E340
BS07	CA	B	D407 D409 R412 G414 E416	D370 D372 R375 G377 E379
BS08	CA	B	D543 L545 G546 D547 R549 E551	D506 L508 G509 D510 R512 E514
BS09	CA	B	D222 D224 D226 K228 E230	D185 D187 D189 K191 E193
BS10	CA	B	D158 D160 D162 Q164 E166	D121 D123 D125 Q127 E129
BS11	CA	B	D371 D373 E377 D386 H387	D334 D336 E340 D349 H350

Gene Ontology

Molecular Function

• GO:0016829 lyase activity
• GO:0046872 metal ion binding
• GO:0102210 rhamnogalacturonan endolyase activity

Biological Process

• GO:0071555 cell wall organization

Cellular Component

• GO:0005576 extracellular region

External links

• PDB: RCSB:2z8s, PDBe:2z8s, PDBj:2z8s
• PDBsum: 2z8s
• PubMed: 17947240
• UniProt: O31526|YESW_BACSU Rhamnogalacturonan endolyase YesW (Gene Name=yesW)