2BVC

Crystal structure of Mycobacterium tuberculosis glutamine synthetase in complex with a transition state mimic

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	d2bvca1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Glutamine synthetase, N-terminal domain	automated matches	automated matches	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)
A	d2bvca2	Alpha and beta proteins (a+b)	Glutamine synthetase/guanido kinase	Glutamine synthetase/guanido kinase	automated matches	automated matches	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)
F	d2bvcf1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Glutamine synthetase, N-terminal domain	automated matches	automated matches	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)
F	d2bvcf2	Alpha and beta proteins (a+b)	Glutamine synthetase/guanido kinase	Glutamine synthetase/guanido kinase	automated matches	automated matches	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)
B	d2bvcb1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Glutamine synthetase, N-terminal domain	automated matches	automated matches	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)
B	d2bvcb2	Alpha and beta proteins (a+b)	Glutamine synthetase/guanido kinase	Glutamine synthetase/guanido kinase	automated matches	automated matches	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)
C	d2bvcc1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Glutamine synthetase, N-terminal domain	automated matches	automated matches	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)
C	d2bvcc2	Alpha and beta proteins (a+b)	Glutamine synthetase/guanido kinase	Glutamine synthetase/guanido kinase	automated matches	automated matches	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)
D	d2bvcd1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Glutamine synthetase, N-terminal domain	automated matches	automated matches	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)
D	d2bvcd2	Alpha and beta proteins (a+b)	Glutamine synthetase/guanido kinase	Glutamine synthetase/guanido kinase	automated matches	automated matches	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)
E	d2bvce1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Glutamine synthetase, N-terminal domain	automated matches	automated matches	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)
E	d2bvce2	Alpha and beta proteins (a+b)	Glutamine synthetase/guanido kinase	Glutamine synthetase/guanido kinase	automated matches	automated matches	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Glutamine synthetase, N-terminal domain	8026290	4001002	SCOP2 (2022-06-29)
A	SCOP2 Family	Glutamine synthetase catalytic domain	8026292	4002006	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	GS N-terminal domain-like	8038669	3000408	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Glutamine synthetase/guanido kinase	8038671	3000676	SCOP2 (2022-06-29)
F	SCOP2B Superfamily	Glutamine synthetase/guanido kinase	8038671	3000676	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	GS N-terminal domain-like	8038669	3000408	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Glutamine synthetase/guanido kinase	8038671	3000676	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	GS N-terminal domain-like	8038669	3000408	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	GS N-terminal domain-like	8038669	3000408	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Glutamine synthetase/guanido kinase	8038671	3000676	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Glutamine synthetase/guanido kinase	8038671	3000676	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	GS N-terminal domain-like	8038669	3000408	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	GS N-terminal domain-like	8038669	3000408	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Glutamine synthetase/guanido kinase	8038671	3000676	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	Gln-synt_N	e2bvcA2	A: beta barrels	X: Ribosomal protein L25-like	H: Glutamine synthetase, N-terminal domain (From Topology)	T: Glutamine synthetase, N-terminal domain	F: Gln-synt_N	ECOD (1.6)
A	Gln-synt_C	e2bvcA1	A: a+b two layers	X: Glutamine synthetase-like	H: Glutamine synthetase/guanido kinase (From Topology)	T: Glutamine synthetase/guanido kinase	F: Gln-synt_C	ECOD (1.6)
F	Gln-synt_N	e2bvcF2	A: beta barrels	X: Ribosomal protein L25-like	H: Glutamine synthetase, N-terminal domain (From Topology)	T: Glutamine synthetase, N-terminal domain	F: Gln-synt_N	ECOD (1.6)
F	Gln-synt_C	e2bvcF1	A: a+b two layers	X: Glutamine synthetase-like	H: Glutamine synthetase/guanido kinase (From Topology)	T: Glutamine synthetase/guanido kinase	F: Gln-synt_C	ECOD (1.6)
B	Gln-synt_N	e2bvcB2	A: beta barrels	X: Ribosomal protein L25-like	H: Glutamine synthetase, N-terminal domain (From Topology)	T: Glutamine synthetase, N-terminal domain	F: Gln-synt_N	ECOD (1.6)
B	Gln-synt_C	e2bvcB1	A: a+b two layers	X: Glutamine synthetase-like	H: Glutamine synthetase/guanido kinase (From Topology)	T: Glutamine synthetase/guanido kinase	F: Gln-synt_C	ECOD (1.6)
C	Gln-synt_N	e2bvcC2	A: beta barrels	X: Ribosomal protein L25-like	H: Glutamine synthetase, N-terminal domain (From Topology)	T: Glutamine synthetase, N-terminal domain	F: Gln-synt_N	ECOD (1.6)
C	Gln-synt_C	e2bvcC1	A: a+b two layers	X: Glutamine synthetase-like	H: Glutamine synthetase/guanido kinase (From Topology)	T: Glutamine synthetase/guanido kinase	F: Gln-synt_C	ECOD (1.6)
D	Gln-synt_N	e2bvcD2	A: beta barrels	X: Ribosomal protein L25-like	H: Glutamine synthetase, N-terminal domain (From Topology)	T: Glutamine synthetase, N-terminal domain	F: Gln-synt_N	ECOD (1.6)
D	Gln-synt_C	e2bvcD1	A: a+b two layers	X: Glutamine synthetase-like	H: Glutamine synthetase/guanido kinase (From Topology)	T: Glutamine synthetase/guanido kinase	F: Gln-synt_C	ECOD (1.6)
E	Gln-synt_N	e2bvcE2	A: beta barrels	X: Ribosomal protein L25-like	H: Glutamine synthetase, N-terminal domain (From Topology)	T: Glutamine synthetase, N-terminal domain	F: Gln-synt_N	ECOD (1.6)
E	Gln-synt_C	e2bvcE1	A: a+b two layers	X: Glutamine synthetase-like	H: Glutamine synthetase/guanido kinase (From Topology)	T: Glutamine synthetase/guanido kinase	F: Gln-synt_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.20.70	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Glutamine synthetase, N-terminal domain	CATH (4.3.0)
A	3.30.590.10	Alpha Beta	2-Layer Sandwich	Creatine Kinase	Chain A, domain 2	CATH (4.3.0)
F	3.10.20.70	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Glutamine synthetase, N-terminal domain	CATH (4.3.0)
F	3.30.590.10	Alpha Beta	2-Layer Sandwich	Creatine Kinase	Chain A, domain 2	CATH (4.3.0)
B	3.10.20.70	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Glutamine synthetase, N-terminal domain	CATH (4.3.0)
B	3.30.590.10	Alpha Beta	2-Layer Sandwich	Creatine Kinase	Chain A, domain 2	CATH (4.3.0)
C	3.10.20.70	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Glutamine synthetase, N-terminal domain	CATH (4.3.0)
C	3.30.590.10	Alpha Beta	2-Layer Sandwich	Creatine Kinase	Chain A, domain 2	CATH (4.3.0)
D	3.10.20.70	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Glutamine synthetase, N-terminal domain	CATH (4.3.0)
D	3.30.590.10	Alpha Beta	2-Layer Sandwich	Creatine Kinase	Chain A, domain 2	CATH (4.3.0)
E	3.10.20.70	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Glutamine synthetase, N-terminal domain	CATH (4.3.0)
E	3.30.590.10	Alpha Beta	2-Layer Sandwich	Creatine Kinase	Chain A, domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF00120	Glutamine synthetase, catalytic domain (Gln-synt_C)	Glutamine synthetase, catalytic domain	-	Domain
A, B, C, D, E A, B, C, D, E, F	PF03951	Glutamine synthetase, beta-Grasp domain (Gln-synt_N)	Glutamine synthetase, beta-Grasp domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	GLUTAMINE SYNTHETASE 1	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding anion binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding protein binding enzyme binding zymogen binding fibronectin binding acid-ammonia (or amide) ligase activity ammonia ligase activity glutamine synthetase activity catalytic activity ligase activity, forming carbon-nitrogen bonds ligase activity	response to nutrient levels cellular homeostasis chemical homeostasis response to stimulus homeostatic process intracellular nitrogen homeostasis nitrogen utilization intracellular chemical homeostasis regulation of protein maturation positive regulation of protein maturation regulation of cellular process positive regulation of protein metabolic process positive regulation of biological process positive regulation of macromolecule biosynthetic process response to nutrient levels cellular homeostasis chemical homeostasis response to stimulus homeostatic process intracellular nitrogen homeostasis nitrogen utilization intracellular chemical homeostasis regulation of protein maturation positive regulation of protein maturation regulation of cellular process positive regulation of protein metabolic process positive regulation of biological process positive regulation of macromolecule biosynthetic process positive regulation of protein processing protein maturation regulation of primary metabolic process positive regulation of metabolic process positive regulation of plasminogen activation regulation of proteolysis positive regulation of biosynthetic process proteolysis regulation of plasminogen activation positive regulation of macromolecule metabolic process protein metabolic process plasminogen activation positive regulation of cellular process zymogen activation regulation of biosynthetic process regulation of biological process regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression positive regulation of proteolysis regulation of protein processing protein processing metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of metabolic process cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly protein homooligomerization cellular component organization or biogenesis glutamine family amino acid biosynthetic process oxoacid metabolic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process glutamine family amino acid metabolic process small molecule metabolic process glutamine metabolic process small molecule biosynthetic process carboxylic acid metabolic process L-amino acid biosynthetic process L-amino acid metabolic process proteinogenic amino acid metabolic process amino acid biosynthetic process proteinogenic amino acid biosynthetic process glutamine biosynthetic process alpha-amino acid biosynthetic process	cellular anatomical structure membrane extracellular region intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane external encapsulating structure cell wall peptidoglycan-based cell wall

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR004809	Glutamine synthetase type I	Family
A, B, C, D, E A, B, C, D, E, F	IPR008146	Glutamine synthetase, catalytic domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR001637	Glutamine synthetase class-I, adenylation site	Conserved Site
A, B, C, D, E A, B, C, D, E, F	IPR027303	Glutamine synthetase, glycine-rich site	Conserved Site
A, B, C, D, E A, B, C, D, E, F	IPR027302	Glutamine synthetase, N-terminal conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F	IPR014746	Glutamine synthetase/guanido kinase, catalytic domain	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR008147	Glutamine synthetase, N-terminal domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR036651	Glutamine synthetase, N-terminal domain superfamily	Homologous Superfamily

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

Chains	Enzyme Name	Description	Catalytic Residues
A, F	glutamine synthetase (type I) M-CSA #537	Glutamine synthetase catalyses the condensation reaction of ammonium and glutamate to form glutamine, using ATP. This is observed in the early stages of infection by Mycobacterium tuberculosis as an extracellular component in the synthesis of poly(L-glutamine-L-glutamate) chains requires for cell wall formation. Therefore this enzyme is an important drug target for halting tuberculosis infection.	Defined by 9 residues: GLU:A-141 [auth A-133]GLU:A-143 [auth A-135]GLU:A-227 [auth A-219]GLU:A-235 [auth A-227]HIS:A-284 [auth A-276]ARG:A-355 [auth A-347]GLU:A-374 [auth A-366]ARG:A-376 [auth A-368]ASP:F-62 [auth F-54] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 6.3.1.2 (PDB Primary Data) Search M-CSA Motif + EC 6.3.1.2

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.