1VQ1

Crystal structure of N5-glutamine methyltransferase, HemK(EC 2.1.1.-) (TM0488) from Thermotoga maritima at 2.80 A resolution

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1vq1a_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	N5-glutamine methyltransferase, HemK	automated matches	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
B	d1vq1b_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	N5-glutamine methyltransferase, HemK	automated matches	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8033643	3000118	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8033643	3000118	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	PRK09328_like	e1vq1A1	A: alpha arrays	X: SP1917-like (From Topology)	H: SP1917-like (From Topology)	T: SP1917-like	F: PRK09328_like	ECOD (1.6)
A	Methyltransf_11_2	e1vq1A2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltransf_11_2	ECOD (1.6)
B	PRK09328_like	e1vq1B1	A: alpha arrays	X: SP1917-like (From Topology)	H: SP1917-like (From Topology)	T: SP1917-like	F: PRK09328_like	ECOD (1.6)
B	Methyltransf_11_2	e1vq1B2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltransf_11_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.8.10	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
A	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
B	1.10.8.10	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)
B	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF17827	PrmC N-terminal domain (PrmC_N)	PrmC N-terminal domain	This entry corresponds to the N-terminal alpha helical domain of the HemK protein. HemK is a methyltransferase enzyme that carries out the methylation of the N5 nitrogen of the glutamine found in the conserved GGQ motif of class-1 release factors [3] ...	This entry corresponds to the N-terminal alpha helical domain of the HemK protein. HemK is a methyltransferase enzyme that carries out the methylation of the N5 nitrogen of the glutamine found in the conserved GGQ motif of class-1 release factors [3].	Domain
A, B	PF05175	Methyltransferase small domain (MTS)	Methyltransferase small domain	This domain is found in ribosomal RNA small subunit methyltransferase C (eg Swiss:P44453) as well as other methyltransferases (eg Swiss:Q53742).	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	N5-glutamine methyltransferase, HemK	transferase activity, transferring one-carbon groups transferase activity protein-(glutamine-N5) methyltransferase activity methyltransferase activity catalytic activity catalytic activity, acting on a protein N-methyltransferase activity protein methyltransferase activity protein-glutamine N-methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity binding organic cyclic compound binding nucleic acid binding	methylation metabolic process primary metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR040758	Release factor glutamine methyltransferase, N-terminal domain	Domain
A, B	IPR002052	DNA methylase, N-6 adenine-specific, conserved site	Conserved Site
A, B	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A, B	IPR004556	Methyltransferase HemK-like	Family
A, B	IPR019874	Protein-(glutamine-N5) methyltransferase, release factor-specific	Family
A, B	IPR007848	Methyltransferase small domain	Domain

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

Chains	Enzyme Name	Description	Catalytic Residues
A	peptide chain release factor N5-glutamine methyltransferase M-CSA #703	Post translational methylation of release factors on the glutamine residue of a conserved GGQ motif is required for efficient termination of protein synthesis. This methylation is performed by an N5-glutamine methyltransferase called HemK. Release factor 1 and 2 contain a conserved GGQ motif that is thought to play a role in activating or positioning the water molecule involved in hydrolysis at the peptidyl transferase active site.	Defined by 3 residues: PHE:A-112 [auth A-100]ASN:A-209 [auth A-197]PRO:A-210 [auth A-198] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 2.1.1 (PDB Primary Data) Search M-CSA Motif + EC 2.1.1

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.