3VMT | pdb_00003vmt

Crystal structure of Staphylococcus aureus membrane-bound transglycosylase in complex with a Lipid II analog

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD
Membrane Protein Annotation: mpstruc
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Lysozyme-like	8066613	3001879	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Lysozyme-like	8066613	3001879	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Transgly	e3vmtA2	A: a+b complex topology	X: Lysozyme-like (From Homology)	H: Lysozyme-like	T: Lysozyme-like	F: Transgly	ECOD (1.6)
B	Transgly	e3vmtB2	A: a+b complex topology	X: Lysozyme-like (From Homology)	H: Lysozyme-like	T: Lysozyme-like	F: Transgly	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.3810.10	Mainly Alpha	Orthogonal Bundle	Penicillin binding protein transpeptidase fold	Biosynthetic peptidoglycan transglycosylase-like	CATH (4.2.0)
B	1.10.3810.10	Mainly Alpha	Orthogonal Bundle	Penicillin binding protein transpeptidase fold	Biosynthetic peptidoglycan transglycosylase-like	CATH (4.2.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Monofunctional glycosyltransferase	peptidoglycan glycosyltransferase activity glycosyltransferase activity transferase activity hexosyltransferase activity catalytic activity	developmental process regulation of biological process regulation of developmental process biological regulation regulation of cell shape cell morphogenesis regulation of cell morphogenesis anatomical structure morphogenesis anatomical structure development regulation of biological quality regulation of anatomical structure morphogenesis carbohydrate derivative biosynthetic process peptidoglycan-based cell wall biogenesis cell wall organization or biogenesis developmental process regulation of biological process regulation of developmental process biological regulation regulation of cell shape cell morphogenesis regulation of cell morphogenesis anatomical structure morphogenesis anatomical structure development regulation of biological quality regulation of anatomical structure morphogenesis carbohydrate derivative biosynthetic process peptidoglycan-based cell wall biogenesis cell wall organization or biogenesis glycosaminoglycan metabolic process carbohydrate derivative metabolic process macromolecule biosynthetic process cellular component biogenesis peptidoglycan biosynthetic process cell wall biogenesis biosynthetic process cell wall macromolecule biosynthetic process aminoglycan metabolic process peptidoglycan metabolic process aminoglycan biosynthetic process cellular process metabolic process glycosaminoglycan biosynthetic process cellular component organization or biogenesis macromolecule metabolic process cell wall macromolecule metabolic process cellular component organization cell wall organization external encapsulating structure organization	cell periphery cellular anatomical structure plasma membrane membrane outer membrane-bounded periplasmic space cell envelope periplasmic space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR022978	Monofunctional glycosyl transferase	Family
A, B	IPR001264	Glycosyl transferase, family 51	Domain
A, B	IPR036950	Penicillin binding protein transglycosylase domain	Homologous Superfamily
A, B	IPR050396	Glycosyltransferase 51/Transpeptidase	Family
A, B	IPR023346	Lysozyme-like domain superfamily	Homologous Superfamily

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B	OPM	Transmembrane	Bitopic proteins	Lysozyme-like	Transglycosylase of penicillin-binding proteins (Glycosyltransferase family 51)

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B	mpstruc	MONOTOPIC MEMBRANE PROTEINS	Glycosyltransferases	Monofunctional glycosyltransferase in complex with Lipid II analog

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	Peptidoglycan glycosyltransferase M-CSA #970	Bacterial peptidoglycan glycosyltransferases (PGT) catalyse the polymerization of peptidoglycan (lipid II) into linear glycan chains, which is an essential part of peptidoglycan biosynthesis. It uses lipid II precursors to synthesize glycan chains of the peptidoglycan, the polymeric layer in the cell wall of bacteria. PGT inhibition leads to bacterial cell wall lysis, making it an important topic of research.	Defined by 4 residues: GLU:A-94 [auth A-100]GLY:A-125 [auth A-131]SER:A-126 [auth A-132]GLN:A-130 [auth A-136] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 2.4 (PDB Primary Data) Search M-CSA Motif + EC 2.4 EC: 2.4.99.28 (UniProt) Search M-CSA Motif + EC 2.4.99.28

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.