Structure of PDB 6d9m Chain A

Receptor sequence

>6d9mA (length=326) Species: 10665,269799

MNIFEMLRIDQGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAI
GRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALI
NMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVI
TTFRTGTWDAYGSYIDELTGLFNYRYLDISLDREIKRADRFGSTVSMIFI
DLDFFKGVNDTHGHLVGSQVLNEMGMLLKKSVREVDIVIRYGGDEFTVML
VETGEKGAATVAERIRRSIEGHTFLAAEGFNIRLTASLGYACYPADTQSK
LELLELADKAMYQGKEQGKNCVFRAT

3D structure

• PDB: 6d9m Structure and mechanism of a Hypr GGDEF enzyme that activates cGAMP signaling to control extracellular metal respiration.
• Chain: A
• Resolution: 1.35 Å

Enzymatic activity

• Enzyme Commision number: 3.2.1.17: lysozyme.

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	GTP	A	V69 R70 D73 T90 V98 R101	V232 R233 D236 T253 V261 R264
BS02	GTP	A	N-19 R-15 I16 D19 R20 K23 R24 R27	N144 R148 I179 D182 R183 K186 R187 R190
BS03	GMP	A	F42 K43 N46 H51 G54 S55 G80	F205 K206 N209 H214 G217 S218 G243
BS04	POP	A	D38 L39 D40 F41 F42 K43 K152 K156	D201 L202 D203 F204 F205 K206 K315 K319
BS05	MG	A	D38 L39 D81	D201 L202 D244

Gene Ontology

Molecular Function

• GO:0003796 lysozyme activity
• GO:0016798 hydrolase activity, acting on glycosyl bonds

Biological Process

• GO:0009253 peptidoglycan catabolic process
• GO:0016998 cell wall macromolecule catabolic process
• GO:0031640 killing of cells of another organism
• GO:0042742 defense response to bacterium
• GO:0044659 viral release from host cell by cytolysis

Cellular Component

• GO:0030430 host cell cytoplasm

External links

• PDB: RCSB:6d9m, PDBe:6d9m, PDBj:6d9m
• PDBsum: 6d9m
• PubMed: 30964001
• UniProt: P00720|ENLYS_BPT4 Endolysin (Gene Name=E);
  Q39UD1