1ZM2 | pdb_00001zm2

Structure of ADP-ribosylated eEF2 in complex with catalytic fragment of ETA

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
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)
F	d1zm2f_	Alpha and beta proteins (a+b)	ADP-ribosylation	ADP-ribosylation	ADP-ribosylating toxins	Exotoxin A, C-terminal domain	(Pseudomonas aeruginosa ) [TaxId: 287 ],	SCOPe (2.08)
D	d1zm2d_	Alpha and beta proteins (a+b)	ADP-ribosylation	ADP-ribosylation	ADP-ribosylating toxins	Exotoxin A, C-terminal domain	(Pseudomonas aeruginosa ) [TaxId: 287 ],	SCOPe (2.08)
B	d1zm2b_	Alpha and beta proteins (a+b)	ADP-ribosylation	ADP-ribosylation	ADP-ribosylating toxins	Exotoxin A, C-terminal domain	(Pseudomonas aeruginosa ) [TaxId: 287 ],	SCOPe (2.08)
E	d1zm2e1	All beta proteins	Reductase/isomerase/elongation factor common domain	Translation proteins	automated matches	automated matches	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
E	d1zm2e2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	automated matches	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
E	d1zm2e3	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	automated matches	automated matches	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
E	d1zm2e4	Alpha and beta proteins (a+b)	Ferredoxin-like	EF-G C-terminal domain-like	automated matches	automated matches	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
C	d1zm2c1	All beta proteins	Reductase/isomerase/elongation factor common domain	Translation proteins	automated matches	automated matches	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
C	d1zm2c2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	automated matches	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
C	d1zm2c3	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	automated matches	automated matches	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
C	d1zm2c4	Alpha and beta proteins (a+b)	Ferredoxin-like	EF-G C-terminal domain-like	automated matches	automated matches	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d1zm2a1	All beta proteins	Reductase/isomerase/elongation factor common domain	Translation proteins	automated matches	automated matches	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d1zm2a2	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	automated matches	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d1zm2a3	Alpha and beta proteins (a+b)	Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	automated matches	automated matches	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d1zm2a4	Alpha and beta proteins (a+b)	Ferredoxin-like	EF-G C-terminal domain-like	automated matches	automated matches	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	ADP-ribosylation	8036646	3001208	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	ADP-ribosylation	8036646	3001208	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	ADP-ribosylation	8036646	3001208	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ras-like P-loop GTPases	8043945	3002022	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	EF-G C-terminal domain-like	8043948	3001287	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8043947	3000100	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	EF-G C-terminal domain-like	8043949	3001287	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	EF-Tu post-G domain-like	8043943	3002024	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8043947	3000100	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	EF-G C-terminal domain-like	8043949	3001287	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	EF-Tu post-G domain-like	8043943	3002024	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ras-like P-loop GTPases	8043945	3002022	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	EF-G C-terminal domain-like	8043948	3001287	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	EF-G C-terminal domain-like	8043949	3001287	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ras-like P-loop GTPases	8043945	3002022	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	EF-Tu post-G domain-like	8043943	3002024	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	EF-G C-terminal domain-like	8043948	3001287	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8043947	3000100	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F	e1zm2F1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: CBAH	F:	ECOD (20:10:01)
D	e1zm2D1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: CBAH	F:	ECOD (20:10:01)
B	e1zm2B1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: CBAH	F:	ECOD (20:10:01)
E	e1zm2E1	A: Cloacin translocation domain	X: Cloacin translocation domain	H: Cloacin translocation domain	T: Trypsin	F:	ECOD (20:10:01)
E	e1zm2E2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Fer4,DUF3470	F:	ECOD (20:10:01)
E	e1zm2E4	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: DUF3197	F:	ECOD (20:10:01)
E	e1zm2E5	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: GBP	F:	ECOD (20:10:01)
C	e1zm2C1	A: Cloacin translocation domain	X: Cloacin translocation domain	H: Cloacin translocation domain	T: Trypsin	F:	ECOD (20:10:01)
C	e1zm2C2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Fer4,DUF3470	F:	ECOD (20:10:01)
C	e1zm2C4	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: DUF3197	F:	ECOD (20:10:01)
C	e1zm2C5	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: GBP	F:	ECOD (20:10:01)
A	e1zm2A1	A: Cloacin translocation domain	X: Cloacin translocation domain	H: Cloacin translocation domain	T: Trypsin	F:	ECOD (20:10:01)
A	e1zm2A2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Fer4,DUF3470	F:	ECOD (20:10:01)
A	e1zm2A4	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: DUF3197	F:	ECOD (20:10:01)
A	e1zm2A5	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: GBP	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.90.175.10	Alpha Beta	Alpha-Beta Complex	Diphtheria Toxin	domain 1	CATH (4.3.0)
D	3.90.175.10	Alpha Beta	Alpha-Beta Complex	Diphtheria Toxin	domain 1	CATH (4.3.0)
B	3.90.175.10	Alpha Beta	Alpha-Beta Complex	Diphtheria Toxin	domain 1	CATH (4.3.0)
E	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
E	3.90.1430.10	Alpha Beta	Alpha-Beta Complex	Yeast translation eEF2 (G' domain)	Yeast translation eEF2 (G' domain)	CATH (4.3.0)
E	2.40.30.10	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
E	3.30.70.870	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Elongation Factor G (Translational Gtpase), domain 3	CATH (4.3.0)
E	3.30.230.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)
E	3.30.70.240	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
C	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C	3.90.1430.10	Alpha Beta	Alpha-Beta Complex	Yeast translation eEF2 (G' domain)	Yeast translation eEF2 (G' domain)	CATH (4.3.0)
C	2.40.30.10	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
C	3.30.70.870	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Elongation Factor G (Translational Gtpase), domain 3	CATH (4.3.0)
C	3.30.230.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)
C	3.30.70.240	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A	3.90.1430.10	Alpha Beta	Alpha-Beta Complex	Yeast translation eEF2 (G' domain)	Yeast translation eEF2 (G' domain)	CATH (4.3.0)
A	2.40.30.10	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
A	3.30.70.870	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Elongation Factor G (Translational Gtpase), domain 3	CATH (4.3.0)
A	3.30.230.10	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)
A	3.30.70.240	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D, F	PF09009	Exotoxin A catalytic (Exotox-A_cataly)	Exotoxin A catalytic	Members of this family, which are found in prokaryotic exotoxin A, catalyse the transfer of ADP ribose from nicotinamide adenine dinucleotide (NAD) to elongation factor-2 in eukaryotic cells, with subsequent inhibition of protein synthesis [1].	Domain
A, C, E	PF00679	Elongation factor G C-terminus (EFG_C)	Elongation factor G C-terminus	This domain includes the carboxyl terminal regions of Elongation factor G, elongation factor 2 and some tetracycline resistance proteins and adopt a ferredoxin-like fold.	Domain
A, C, E	PF00009	Elongation factor Tu GTP binding domain (GTP_EFTU)	Elongation factor Tu GTP binding domain	This domain contains a P-loop motif, also found in several other families such as Pfam:PF00071, Pfam:PF00025 and Pfam:PF00063. Elongation factor Tu consists of three structural domains, this plus two C-terminal beta barrel domains.	Domain
A, C, E	PF14492	Elongation Factor G, domain III (EFG_III)	Elongation Factor G, domain III	This domain is found in Elongation Factor G. It shares a similar structure with domain V (Pfam:PF00679). Structural studies in drosophila indicate this is domain 3 [1].	Domain
A, C, E	PF03144	Elongation factor Tu domain 2 (GTP_EFTU_D2)	Elongation factor Tu domain 2	Elongation factor Tu consists of three structural domains, this is the second domain. This domain adopts a beta barrel structure. This the second domain is involved in binding to charged tRNA [1]. This domain is also found in other proteins such as e ...	Elongation factor Tu consists of three structural domains, this is the second domain. This domain adopts a beta barrel structure. This the second domain is involved in binding to charged tRNA [1]. This domain is also found in other proteins such as elongation factor G and translation initiation factor IF-2. This domain is structurally related to Pfam:PF03143, and in fact has weak sequence matches to this domain.	Domain
A, C, E	PF03764	Elongation factor G, domain IV (EFG_IV)	Elongation factor G, domain IV	This domain is found in elongation factor G, elongation factor 2 and some tetracycline resistance proteins and adopts a ribosomal protein S5 domain 2-like fold.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F	Exotoxin A	transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups pentosyltransferase activity glycosyltransferase activity NAD+-diphthamide ADP-ribosyltransferase activity toxin activity	biological process involved in interspecies interaction between organisms cellular process disruption of cell in another organism disruption of anatomical structure in another organism symbiont-mediated killing of host cell killing of cells of another organism cell killing biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated perturbation of host cellular process symbiont-mediated perturbation of host process symbiont-mediated perturbation of host gene expression modulation of process of another organism symbiont-mediated suppression of host translation elongation	-
A, C, E	Elongation factor 2	translation factor activity translation elongation factor activity RNA binding binding rRNA binding nucleic acid binding ribonucleoprotein complex binding protein-containing complex binding ribosome binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding translation factor activity translation elongation factor activity RNA binding binding rRNA binding nucleic acid binding ribonucleoprotein complex binding protein-containing complex binding ribosome binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding protein binding protein-folding chaperone binding pyrophosphatase activity GTPase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity identical protein binding	regulation of cellular process positive regulation of protein metabolic process positive regulation of biological process positive regulation of translation protein biosynthetic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression positive regulation of metabolic process regulation of translational elongation positive regulation of biosynthetic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of cellular process regulation of cellular process positive regulation of protein metabolic process positive regulation of biological process positive regulation of translation protein biosynthetic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression positive regulation of metabolic process regulation of translational elongation positive regulation of biosynthetic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of cellular process 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 translation macromolecule biosynthetic process regulation of gene expression positive regulation of translational elongation biosynthetic process positive regulation of gene expression regulation of translation translational elongation regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process maintenance of translational fidelity	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex ribonucleoprotein complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F	IPR036478	Exotoxin A, middle domain superfamily	Homologous Superfamily
B, D, F	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
B, D, F	IPR015099	Exotoxin A catalytic domain	Domain
B, D, F	IPR015185	Exotoxin A, binding	Domain
B, D, F	IPR015186	Exotoxin A, middle domain	Domain
A, C, E	IPR005225	Small GTP-binding domain	Domain
A, C, E	IPR005517	Translation elongation factor EFG/EF2, domain IV	Domain
A, C, E	IPR000795	Translational (tr)-type GTP-binding domain	Domain
A, C, E	IPR000640	Elongation factor EFG, domain V-like	Domain
A, C, E	IPR031157	Tr-type G domain, conserved site	Conserved Site
A, C, E	IPR035647	EF-G domain III/V-like	Homologous Superfamily
A, C, E	IPR041095	Elongation Factor G, domain II	Domain
A, C, E	IPR004161	Translation elongation factor EFTu-like, domain 2	Domain
A, C, E	IPR009000	Translation protein, beta-barrel domain superfamily	Homologous Superfamily
A, C, E	IPR020568	Ribosomal protein uS5 domain 2-type superfamily	Homologous Superfamily
A, C, E	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, C, E	IPR014721	Small ribosomal subunit protein uS5 domain 2-type fold, subgroup	Homologous Superfamily

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, C, E	DDE	Parent Component: HIS RESID: AA0040 PSI-MOD : 2'-[3-carboxamido-3-(trimethylammonio)propyl]-L-histidine MOD:00049

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

Chains	Enzyme Name	Description	Catalytic Residues
F	NAD+---diphthamide ADP-ribosyltransferase M-CSA #769	Exotoxin A (ETA) from Pseudomonas aeruginosa is an NAD+-diphthamide ADP-ribosyltransferase from the enzyme family of mono-ADP-ribosyltransferases. It catalyses the ADP-ribosylation of eukaryotic elongation factor 2 (eEF2). Inactivation of eEF2 then results in cessation of protein synthesis and eventual cellular death.	Defined by 1 residue: GLU:F-155 [auth F-553] \| Explore in 3D: M-CSA Motif Definition At least 2 residues must be present to support Structure Motif searching. EC: 2.4.2 (PDB Primary Data) EC: 2.4.2.36 (UniProt)