5YNE

Crystal structure of Pullulanase from Klebsiella pneumoniae complex at 10 mM alpha-cyclodextrin

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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)
A	d5ynea2	All beta proteins	Immunoglobulin-like beta-sandwich	E set domains	automated matches	automated matches	(Klebsiella pneumoniae ) [TaxId: 573 ],	SCOPe (2.08)
A	d5ynea1	All beta proteins	Prealbumin-like	Starch-binding domain-like	automated matches	automated matches	(Klebsiella pneumoniae ) [TaxId: 573 ],	SCOPe (2.08)
A	d5ynea5	All beta proteins	Glycosyl hydrolase domain	Glycosyl hydrolase domain	automated matches	automated matches	(Klebsiella pneumoniae ) [TaxId: 573 ],	SCOPe (2.08)
A	d5ynea4	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	(Trans)glycosidases	Amylase, catalytic domain	automated matches	(Klebsiella pneumoniae ) [TaxId: 573 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	pullul_strch_1st	e5yneA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: pullul_strch_1st	ECOD (1.6)
A	CBM_48	e5yneA3	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: CBM_48	ECOD (1.6)
A	PUD_1	e5yneA5	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Prealbumin-like	F: PUD_1	ECOD (1.6)
A	DUF3372	e5yneA2	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: Glycosyl hydrolase domain (From Topology)	T: Glycosyl hydrolase domain	F: DUF3372	ECOD (1.6)
A	pullul_strch_2nd	e5yneA4	A: alpha arrays	X: SP0561-like (From Topology)	H: SP0561-like (From Topology)	T: SP0561-like	F: pullul_strch_2nd	ECOD (1.6)
A	Alpha-amylase	e5yneA6	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Alpha-amylase	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.40.1110	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
A	2.60.40.1130	Mainly Beta	Sandwich	Immunoglobulin-like	Rab geranylgeranyltransferase alpha-subunit, insert domain	CATH (4.3.0)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A	3.20.20.80	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Glycosidases	CATH (4.3.0)
A	2.60.40.1180	Mainly Beta	Sandwich	Immunoglobulin-like	Golgi alpha-mannosidase II	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF18494	Pullulanase Ins domain (Pullulanase_Ins)	Pullulanase Ins domain	Pullulanases (pullulan 6-glucanohydrolase, EC 3.2.1.41) are debranching enzymes that are able to hydrolyze the alpha-1,6-glycosidic linkage in pullulan, starch, amylopectin, and related oligosaccharides. Type I pullulanases specifically cleave the al ...	Pullulanases (pullulan 6-glucanohydrolase, EC 3.2.1.41) are debranching enzymes that are able to hydrolyze the alpha-1,6-glycosidic linkage in pullulan, starch, amylopectin, and related oligosaccharides. Type I pullulanases specifically cleave the alpha-1,6-glycosidic linkages in pullulan and branched oligosaccharides to produce maltotriose and linear oligosaccharides, respectively [1]. Structural analysis of Klebsiella lipoprotein pullulanase (PulA) illustrates that the catalytic core is composed of two major regions: the TIM-barrel domain A and beta-sandwich fold domain C. PulA contains an extra domain, a highly mobile Ins subdomain of unknown function which is inserted into the catalytic TIM-barrel domain A of Klebsiella pullulanases. The Ins subdomain is rich in helical and loop secondary structure. A disulfide bond between Cys491 and Cys506 and two Ca2+ ions presumably stabilizes this domain.This insertion is also found in pullulanases from other Gram-negative genera that have a functional T2SS, such as Vibrio, Aeromonas, and Photorhabdus. Functional analysis indicate that this domain is required for PulA secretion via the T2SS [2].	Domain
A	PF02922	Carbohydrate-binding module 48 (Isoamylase N-terminal domain) (CBM_48)	Carbohydrate-binding module 48 (Isoamylase N-terminal domain)	This domain is found in a range of enzymes that act on branched substrates - isoamylase, pullulanase and branching enzyme. This family also contains the beta subunit of 5' AMP activated kinase.	Domain
A	PF11852	Alpha-1,6-glucosidases, pullulanase-type, C-terminal (Pullul_strch_C)	Alpha-1,6-glucosidases, pullulanase-type, C-terminal	-	Family
A	PF03714	Bacterial pullanase-associated domain (PUD)	Bacterial pullanase-associated domain	Domain is found in pullanase - carbohydrate de-branching - proteins. It is found both to the N or the C terminii of of the alpha-amylase active site region. This domain contains several conserved aromatic residues that are suggestive of a carbohydrat ...	Domain is found in pullanase - carbohydrate de-branching - proteins. It is found both to the N or the C terminii of of the alpha-amylase active site region. This domain contains several conserved aromatic residues that are suggestive of a carbohydrate binding function.	Domain
A	PF17967	Pullulanase N2 domain (Pullulanase_N2)	Pullulanase N2 domain	This domain is found close to the N-terminus of the Klebsiella starch debranching pullulanase enzyme [1]. The structure of the domain is a beta sandwich fold.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	PulA protein	binding carbohydrate binding pullulanase activity hydrolase activity, acting on glycosyl bonds hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity catalytic activity cation binding ion binding metal ion binding small molecule binding	carbohydrate metabolic process primary metabolic process metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR013784	Carbohydrate-binding-like fold	Homologous Superfamily
A	IPR024561	Alpha-1,6-glucosidases, pullulanase-type, C-terminal	Domain
A	IPR040671	Pullulanase, N2 domain	Domain
A	IPR017853	Glycoside hydrolase superfamily	Homologous Superfamily
A	IPR011839	Alpha-1,6-glucosidases, pullulanase-type	Domain
A	IPR041111	Pullulanase, Ins domain	Domain
A	IPR006047	Glycosyl hydrolase, family 13, catalytic domain	Domain
A	IPR005323	Pullulanase, carbohydrate-binding module 41	Domain
A	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A	IPR014756	Immunoglobulin E-set	Homologous Superfamily
A	IPR013780	Glycosyl hydrolase, all-beta	Homologous Superfamily
A	IPR004193	Glycoside hydrolase, family 13, N-terminal	Domain

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.