1P7T

Structure of Escherichia coli malate synthase G:pyruvate:acetyl-Coenzyme A abortive ternary complex at 1.95 angstrom 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
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1p7ta_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Malate synthase G	Malate synthase G	Malate synthase G	(Escherichia coli str. K-12 substr. W3110 ) [TaxId: 316407 ],	SCOPe (2.08)
B	d1p7tb_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Malate synthase G	Malate synthase G	Malate synthase G	(Escherichia coli str. K-12 substr. W3110 ) [TaxId: 316407 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Malate synthase G	8044290	3000549	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Malate synthase G	8044290	3000549	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	Malate_synthase	e1p7tA1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Malate_synthase	ECOD (1.6)
B	Malate_synthase	e1p7tB1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Malate_synthase	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.20.20.360	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Malate synthase, domain 3	CATH (4.3.0)
A	2.170.170.11	Mainly Beta	Beta Complex	Malate synthase G - maily-beta sub-domain	Malate synthase G - maily-beta sub-domain	CATH (4.3.0)
A	1.20.1220.12	Mainly Alpha	Up-down Bundle	Malate Synthase G	Chain: A	CATH (4.3.0)
B	3.20.20.360	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Malate synthase, domain 3	CATH (4.3.0)
B	2.170.170.11	Mainly Beta	Beta Complex	Malate synthase G - maily-beta sub-domain	Malate synthase G - maily-beta sub-domain	CATH (4.3.0)
B	1.20.1220.12	Mainly Alpha	Up-down Bundle	Malate Synthase G	Chain: A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01274	Malate synthase, TIM barrel domain (MS_TIM-barrel)	Malate synthase, TIM barrel domain	Malate synthase (MS) catalyses the aldol condensation of glyoxylate with acetyl-CoA to form malate as part of the second step of the glyoxylate bypass and an alternative to the tricarboxylic acid cycle in bacteria, fungi and plants. There have been i ...	Malate synthase (MS) catalyses the aldol condensation of glyoxylate with acetyl-CoA to form malate as part of the second step of the glyoxylate bypass and an alternative to the tricarboxylic acid cycle in bacteria, fungi and plants. There have been identified two isoforms, A and G (MSA and MSG, respectively) that differ in size and is attributed to an inserted alpha/beta domain in MSG that may have regulatory function [1,2]. In malate synthases, the TIM beta/alpha-barrel fold and the C-terminal domain are well conserved and the cleft between them forms the active site [1,2,3,4]. MSA and MSG consist of an N-terminal alpha-helical clasp domain, a central TIM barrel domain and a C-terminal helical plug domain. This is the TIM barrel domain of malate synthases.	Domain
A	PF20659	Malate synthase, C-terminal (MS_C)	Malate synthase, C-terminal	Malate synthase (MS) catalyses the aldol condensation of glyoxylate with acetyl-CoA to form malate as part of the second step of the glyoxylate bypass and an alternative to the tricarboxylic acid cycle in bacteria, fungi and plants. There have been i ...	Malate synthase (MS) catalyses the aldol condensation of glyoxylate with acetyl-CoA to form malate as part of the second step of the glyoxylate bypass and an alternative to the tricarboxylic acid cycle in bacteria, fungi and plants. There have been identified two isoforms, A and G (MSA and MSG, respectively) that differ in size and is attributed to an inserted alpha/beta domain in MSG that may have regulatory function [1,2]. In malate synthases, the TIM beta/alpha-barrel fold and the C-terminal helical domain are well conserved and the cleft between them forms the active site [1,2,3,4]. This entry represents the C-terminal domain which consists of a five-helix 'plug' connected to the barrel by an extended loop and caps the active site.	Domain
A	PF20656	Malate synthase, N-terminal domain (MS_N)	Malate synthase, N-terminal domain	Malate synthase (MS) catalyses the aldol condensation of glyoxylate with acetyl-CoA to form malate as part of the second step of the glyoxylate bypass and an alternative to the tricarboxylic acid cycle in bacteria, fungi and plants. There have been i ...	Malate synthase (MS) catalyses the aldol condensation of glyoxylate with acetyl-CoA to form malate as part of the second step of the glyoxylate bypass and an alternative to the tricarboxylic acid cycle in bacteria, fungi and plants. There have been identified two isoforms, A and G (MSA and MSG, respectively) that differ in size and is attributed to an inserted alpha/beta domain in MSG that may have regulatory function [1,2]. They consist of an N-terminal alpha-helical claps, a central TIM barrel and a C-terminal alpha-helical plug. This entry represents the N-terminal clasp that wraps around one side of the TIM barrel and buttressed it [1,2,3,4].	Domain
B	PF20658	Malate synthase G, alpha-beta insertion domain (MSG_insertion)	Malate synthase G, alpha-beta insertion domain	Malate synthase (MS) catalyses the aldol condensation of glyoxylate with acetyl-CoA to form malate as part of the second step of the glyoxylate bypass and an alternative to the tricarboxylic acid cycle in bacteria, fungi and plants. There have been i ...	Malate synthase (MS) catalyses the aldol condensation of glyoxylate with acetyl-CoA to form malate as part of the second step of the glyoxylate bypass and an alternative to the tricarboxylic acid cycle in bacteria, fungi and plants. There have been identified two isoforms, A and G (MSA and MSG, respectively) that differ in size and is attributed to an inserted alpha/beta domain in MSG that may have regulatory function [1,2,3,4]. Members of the isoform G family are only found in bacteria. This entry represents the alpha/beta insertion domain from MSG, which buttressed one side of the TIM-barrel domain [1].	Domain
B	PF01274	Malate synthase, TIM barrel domain (MS_TIM-barrel)	Malate synthase, TIM barrel domain	Malate synthase (MS) catalyses the aldol condensation of glyoxylate with acetyl-CoA to form malate as part of the second step of the glyoxylate bypass and an alternative to the tricarboxylic acid cycle in bacteria, fungi and plants. There have been i ...	Malate synthase (MS) catalyses the aldol condensation of glyoxylate with acetyl-CoA to form malate as part of the second step of the glyoxylate bypass and an alternative to the tricarboxylic acid cycle in bacteria, fungi and plants. There have been identified two isoforms, A and G (MSA and MSG, respectively) that differ in size and is attributed to an inserted alpha/beta domain in MSG that may have regulatory function [1,2]. In malate synthases, the TIM beta/alpha-barrel fold and the C-terminal domain are well conserved and the cleft between them forms the active site [1,2,3,4]. MSA and MSG consist of an N-terminal alpha-helical clasp domain, a central TIM barrel domain and a C-terminal helical plug domain. This is the TIM barrel domain of malate synthases.	Domain
B	PF20659	Malate synthase, C-terminal (MS_C)	Malate synthase, C-terminal	Malate synthase (MS) catalyses the aldol condensation of glyoxylate with acetyl-CoA to form malate as part of the second step of the glyoxylate bypass and an alternative to the tricarboxylic acid cycle in bacteria, fungi and plants. There have been i ...	Malate synthase (MS) catalyses the aldol condensation of glyoxylate with acetyl-CoA to form malate as part of the second step of the glyoxylate bypass and an alternative to the tricarboxylic acid cycle in bacteria, fungi and plants. There have been identified two isoforms, A and G (MSA and MSG, respectively) that differ in size and is attributed to an inserted alpha/beta domain in MSG that may have regulatory function [1,2]. In malate synthases, the TIM beta/alpha-barrel fold and the C-terminal helical domain are well conserved and the cleft between them forms the active site [1,2,3,4]. This entry represents the C-terminal domain which consists of a five-helix 'plug' connected to the barrel by an extended loop and caps the active site.	Domain
B	PF20656	Malate synthase, N-terminal domain (MS_N)	Malate synthase, N-terminal domain	Malate synthase (MS) catalyses the aldol condensation of glyoxylate with acetyl-CoA to form malate as part of the second step of the glyoxylate bypass and an alternative to the tricarboxylic acid cycle in bacteria, fungi and plants. There have been i ...	Malate synthase (MS) catalyses the aldol condensation of glyoxylate with acetyl-CoA to form malate as part of the second step of the glyoxylate bypass and an alternative to the tricarboxylic acid cycle in bacteria, fungi and plants. There have been identified two isoforms, A and G (MSA and MSG, respectively) that differ in size and is attributed to an inserted alpha/beta domain in MSG that may have regulatory function [1,2]. They consist of an N-terminal alpha-helical claps, a central TIM barrel and a C-terminal alpha-helical plug. This entry represents the N-terminal clasp that wraps around one side of the TIM barrel and buttressed it [1,2,3,4].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Malate synthase G	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding acyltransferase activity acyltransferase activity, acyl groups converted into alkyl on transfer transferase activity malate synthase activity catalytic activity	aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds primary metabolic process metabolic process cellular process generation of precursor metabolites and energy carbohydrate metabolic process glyoxylate metabolic process glyoxylate cycle oxoacid metabolic process carboxylic acid metabolic process organic acid metabolic process aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds primary metabolic process metabolic process cellular process generation of precursor metabolites and energy carbohydrate metabolic process glyoxylate metabolic process glyoxylate cycle oxoacid metabolic process carboxylic acid metabolic process organic acid metabolic process aldehyde metabolic process small molecule metabolic process monocarboxylic acid metabolic process catabolic process organic acid catabolic process cellular catabolic process monocarboxylic acid catabolic process carboxylic acid catabolic process glyoxylate catabolic process aldehyde catabolic process small molecule catabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol
B	Malate synthase G	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding acyltransferase activity acyltransferase activity, acyl groups converted into alkyl on transfer transferase activity malate synthase activity catalytic activity	aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds primary metabolic process metabolic process cellular process generation of precursor metabolites and energy carbohydrate metabolic process glyoxylate metabolic process glyoxylate cycle oxoacid metabolic process carboxylic acid metabolic process organic acid metabolic process aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds primary metabolic process metabolic process cellular process generation of precursor metabolites and energy carbohydrate metabolic process glyoxylate metabolic process glyoxylate cycle oxoacid metabolic process carboxylic acid metabolic process organic acid metabolic process aldehyde metabolic process small molecule metabolic process monocarboxylic acid metabolic process catabolic process organic acid catabolic process cellular catabolic process monocarboxylic acid catabolic process carboxylic acid catabolic process glyoxylate catabolic process aldehyde catabolic process small molecule catabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR006253	Malate synthase G	Family
A	IPR046363	Malate synthase, N-terminal and TIM-barrel domains	Homologous Superfamily
A	IPR048356	Malate synthase, N-terminal domain	Domain
A	IPR011076	Malate synthase superfamily	Homologous Superfamily
A	IPR001465	Malate synthase, TIM barrel domain	Domain
A	IPR048357	Malate synthase G, alpha-beta insertion domain	Domain
A	IPR048355	Malate synthase, C-terminal domain	Domain
A	IPR044856	Malate synthase, C-terminal superfamily	Homologous Superfamily
B	IPR006253	Malate synthase G	Family
B	IPR046363	Malate synthase, N-terminal and TIM-barrel domains	Homologous Superfamily
B	IPR048356	Malate synthase, N-terminal domain	Domain
B	IPR011076	Malate synthase superfamily	Homologous Superfamily
B	IPR001465	Malate synthase, TIM barrel domain	Domain
B	IPR048357	Malate synthase G, alpha-beta insertion domain	Domain
B	IPR048355	Malate synthase, C-terminal domain	Domain
B	IPR044856	Malate synthase, C-terminal superfamily	Homologous Superfamily

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A	CSO	Parent Component: CYS RESID: AA0205 PSI-MOD : L-cysteine sulfenic acid MOD:00210
B	CSO	Parent Component: CYS RESID: AA0205 , AA0205 PSI-MOD : L-cysteine sulfenic acid MOD:00210 , L-cysteine sulfenic acid MOD:00210

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.