2XQR | pdb_00002xqr

Crystal structure of plant cell wall invertase in complex with a specific protein inhibitor

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d2xqrb_	All alpha proteins	Bromodomain-like	Plant invertase/pectin methylesterase inhibitor	Plant invertase/pectin methylesterase inhibitor	automated matches	COMMON TOBACCO (Nicotiana tabacum ) [TaxId: 4097 ],	SCOPe (2.08)
D	d2xqrd_	All alpha proteins	Bromodomain-like	Plant invertase/pectin methylesterase inhibitor	Plant invertase/pectin methylesterase inhibitor	automated matches	COMMON TOBACCO (Nicotiana tabacum ) [TaxId: 4097 ],	SCOPe (2.08)
F	d2xqrf_	All alpha proteins	Bromodomain-like	Plant invertase/pectin methylesterase inhibitor	Plant invertase/pectin methylesterase inhibitor	automated matches	COMMON TOBACCO (Nicotiana tabacum ) [TaxId: 4097 ],	SCOPe (2.08)
H	d2xqrh_	All alpha proteins	Bromodomain-like	Plant invertase/pectin methylesterase inhibitor	Plant invertase/pectin methylesterase inhibitor	automated matches	COMMON TOBACCO (Nicotiana tabacum ) [TaxId: 4097 ],	SCOPe (2.08)
J	d2xqrj_	All alpha proteins	Bromodomain-like	Plant invertase/pectin methylesterase inhibitor	Plant invertase/pectin methylesterase inhibitor	automated matches	COMMON TOBACCO (Nicotiana tabacum ) [TaxId: 4097 ],	SCOPe (2.08)
L	d2xqrl_	All alpha proteins	Bromodomain-like	Plant invertase/pectin methylesterase inhibitor	Plant invertase/pectin methylesterase inhibitor	automated matches	COMMON TOBACCO (Nicotiana tabacum ) [TaxId: 4097 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8105326	3000120	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Furanosidase-like	8105327	3000845	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8105326	3000120	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Furanosidase-like	8105327	3000845	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8105326	3000120	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Furanosidase-like	8105327	3000845	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Furanosidase-like	8105327	3000845	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8105326	3000120	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Furanosidase-like	8105327	3000845	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8105326	3000120	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Furanosidase-like	8105327	3000845	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8105326	3000120	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Plant invertase/pectin methylesterase inhibitor	8038935	3000860	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Plant invertase/pectin methylesterase inhibitor	8038935	3000860	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Plant invertase/pectin methylesterase inhibitor	8038935	3000860	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Plant invertase/pectin methylesterase inhibitor	8038935	3000860	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Plant invertase/pectin methylesterase inhibitor	8038935	3000860	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Plant invertase/pectin methylesterase inhibitor	8038935	3000860	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	Glyco_hydro_32C	e2xqrA2	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: Glyco_hydro_32C	ECOD (1.6)
A	Glyco_hydro_130	e2xqrA1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 5-bladed	F: Glyco_hydro_130	ECOD (1.6)
C	Glyco_hydro_32C	e2xqrC1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: Glyco_hydro_32C	ECOD (1.6)
C	Glyco_hydro_130	e2xqrC2	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 5-bladed	F: Glyco_hydro_130	ECOD (1.6)
E	Glyco_hydro_32C	e2xqrE1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: Glyco_hydro_32C	ECOD (1.6)
E	Glyco_hydro_130	e2xqrE2	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 5-bladed	F: Glyco_hydro_130	ECOD (1.6)
G	Glyco_hydro_32C	e2xqrG1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: Glyco_hydro_32C	ECOD (1.6)
G	Glyco_hydro_130	e2xqrG2	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 5-bladed	F: Glyco_hydro_130	ECOD (1.6)
I	Glyco_hydro_32C	e2xqrI1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: Glyco_hydro_32C	ECOD (1.6)
I	Glyco_hydro_130	e2xqrI2	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 5-bladed	F: Glyco_hydro_130	ECOD (1.6)
K	Glyco_hydro_32C	e2xqrK1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: Glyco_hydro_32C	ECOD (1.6)
K	Glyco_hydro_130	e2xqrK2	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 5-bladed	F: Glyco_hydro_130	ECOD (1.6)
B	PMEI	e2xqrB1	A: alpha bundles	X: Bromodomain-like	H: Plant invertase/pectin methylesterase inhibitor (From Topology)	T: Plant invertase/pectin methylesterase inhibitor	F: PMEI	ECOD (1.6)
D	PMEI	e2xqrD1	A: alpha bundles	X: Bromodomain-like	H: Plant invertase/pectin methylesterase inhibitor (From Topology)	T: Plant invertase/pectin methylesterase inhibitor	F: PMEI	ECOD (1.6)
F	PMEI	e2xqrF1	A: alpha bundles	X: Bromodomain-like	H: Plant invertase/pectin methylesterase inhibitor (From Topology)	T: Plant invertase/pectin methylesterase inhibitor	F: PMEI	ECOD (1.6)
H	PMEI	e2xqrH1	A: alpha bundles	X: Bromodomain-like	H: Plant invertase/pectin methylesterase inhibitor (From Topology)	T: Plant invertase/pectin methylesterase inhibitor	F: PMEI	ECOD (1.6)
J	PMEI	e2xqrJ1	A: alpha bundles	X: Bromodomain-like	H: Plant invertase/pectin methylesterase inhibitor (From Topology)	T: Plant invertase/pectin methylesterase inhibitor	F: PMEI	ECOD (1.6)
L	PMEI	e2xqrL1	A: alpha bundles	X: Bromodomain-like	H: Plant invertase/pectin methylesterase inhibitor (From Topology)	T: Plant invertase/pectin methylesterase inhibitor	F: PMEI	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.115.10.20	Mainly Beta	5 Propeller	Tachylectin-2	Chain A	CATH (4.3.0)
A	2.60.120.560	Mainly Beta	Sandwich	Jelly Rolls	Exo-inulinase	CATH (4.3.0)
C	2.115.10.20	Mainly Beta	5 Propeller	Tachylectin-2	Chain A	CATH (4.3.0)
C	2.60.120.560	Mainly Beta	Sandwich	Jelly Rolls	Exo-inulinase	CATH (4.3.0)
E	2.115.10.20	Mainly Beta	5 Propeller	Tachylectin-2	Chain A	CATH (4.3.0)
E	2.60.120.560	Mainly Beta	Sandwich	Jelly Rolls	Exo-inulinase	CATH (4.3.0)
G	2.115.10.20	Mainly Beta	5 Propeller	Tachylectin-2	Chain A	CATH (4.3.0)
G	2.60.120.560	Mainly Beta	Sandwich	Jelly Rolls	Exo-inulinase	CATH (4.3.0)
I	2.115.10.20	Mainly Beta	5 Propeller	Tachylectin-2	Chain A	CATH (4.3.0)
I	2.60.120.560	Mainly Beta	Sandwich	Jelly Rolls	Exo-inulinase	CATH (4.3.0)
K	2.115.10.20	Mainly Beta	5 Propeller	Tachylectin-2	Chain A	CATH (4.3.0)
K	2.60.120.560	Mainly Beta	Sandwich	Jelly Rolls	Exo-inulinase	CATH (4.3.0)
B	1.20.140.40	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (4.3.0)
D	1.20.140.40	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (4.3.0)
F	1.20.140.40	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (4.3.0)
H	1.20.140.40	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (4.3.0)
J	1.20.140.40	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (4.3.0)
L	1.20.140.40	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E, G, I A, C, E, G, I, K	PF08244	Glycosyl hydrolases family 32 C terminal (Glyco_hydro_32C)	Glycosyl hydrolases family 32 C terminal	This domain corresponds to the C terminal domain of glycosyl hydrolase family 32. It forms a beta sandwich module [1].	Domain
A, C, E, G, I A, C, E, G, I, K	PF00251	Glycosyl hydrolases family 32 N-terminal domain (Glyco_hydro_32N)	Glycosyl hydrolases family 32 N-terminal domain	-	Repeat
B, D, F, H, J B, D, F, H, J, L	PF04043	Plant invertase/pectin methylesterase inhibitor (PMEI)	Plant invertase/pectin methylesterase inhibitor	This domain inhibits pectin methylesterases (PMEs) and invertases through formation of a non-covalent 1:1 complex [1]. It has been implicated in the regulation of fruit development, carbohydrate metabolism and cell wall extension (see [2]). It may al ...	This domain inhibits pectin methylesterases (PMEs) and invertases through formation of a non-covalent 1:1 complex [1]. It has been implicated in the regulation of fruit development, carbohydrate metabolism and cell wall extension (see [2]). It may also be involved in inhibiting microbial pathogen PMEs. It has been observed that it is often expressed as a large inactive preprotein [1]. It is also found at the N-termini of PMEs predicted from DNA sequences (personal obs:C Yeats), suggesting that both PMEs and their inhibitor are expressed as a single polyprotein and subsequently processed. It has two disulphide bridges and is mainly alpha-helical [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E, G, I A, C, E, G, I, K	BETA-FRUCTOFURANOSIDASE, INSOLUBLE ISOENZYME CWINV1	hydrolase activity, acting on glycosyl bonds beta-fructofuranosidase activity hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity catalytic activity	carbohydrate metabolic process primary metabolic process metabolic process cellular process response to stimulus response to stress response to wounding defense response to fungus biological process involved in interspecies interaction between organisms response to other organism defense response response to external stimulus response to fungus response to external biotic stimulus carbohydrate metabolic process primary metabolic process metabolic process cellular process response to stimulus response to stress response to wounding defense response to fungus biological process involved in interspecies interaction between organisms response to other organism defense response response to external stimulus response to fungus response to external biotic stimulus response to biotic stimulus	cell periphery cellular anatomical structure plasma membrane membrane extracellular region apoplast
B, D, F, H, J B, D, F, H, J, L	INVERTASE INHIBITOR	enzyme regulator activity molecular function inhibitor activity molecular function regulator activity enzyme inhibitor activity	plant-type cell wall organization cellular component organization plant-type cell wall organization or biogenesis cell wall modification cell wall organization or biogenesis cell wall organization cellular process cellular component organization or biogenesis plant-type cell wall modification external encapsulating structure organization	cell periphery cellular anatomical structure external encapsulating structure plant-type cell wall cell wall

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G, I A, C, E, G, I, K	IPR023296	Glycosyl hydrolase, five-bladed beta-propeller domain superfamily	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K	IPR013189	Glycosyl hydrolase family 32, C-terminal	Domain
A, C, E, G, I A, C, E, G, I, K	IPR018053	Glycoside hydrolase, family 32, active site	Active Site
A, C, E, G, I A, C, E, G, I, K	IPR001362	Glycoside hydrolase, family 32	Family
A, C, E, G, I A, C, E, G, I, K	IPR013148	Glycosyl hydrolase family 32, N-terminal	Domain
A, C, E, G, I A, C, E, G, I, K	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K	IPR050551	Plant Fructan Metabolism Enzymes	Family
B, D, F, H, J B, D, F, H, J, L	IPR006501	Pectinesterase inhibitor domain	Domain
B, D, F, H, J B, D, F, H, J, L	IPR035513	Invertase/pectin methylesterase inhibitor domain superfamily	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L	IPR034087	Cell wall/vacuolar inhibitor of fructosidase	Family

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.