1E9Y | pdb_00001e9y

Crystal structure of Helicobacter pylori urease in complex with acetohydroxamic acid


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
BSCOP2 Familyalpha-Subunit of urease 8023200 4003022 SCOP2 (2022-06-29)
BSCOP2 Familyalpha-subunit of urease, catalytic domain 8023204 4003208 SCOP2 (2022-06-29)
BSCOP2 SuperfamilyComposite domain of metallo-dependent hydrolases 8035580 3000176 SCOP2 (2022-06-29)
BSCOP2 SuperfamilyMetallo-dependent hydrolases 8035584 3000428 SCOP2 (2022-06-29)
ASCOP2 FamilyUrease, beta-subunit 8023195 4002967 SCOP2 (2022-06-29)
ASCOP2 FamilyUrease, gamma-subunit 8023198 4000909 SCOP2 (2022-06-29)
ASCOP2 SuperfamilyUrease, beta-subunit 8035575 3001949 SCOP2 (2022-06-29)
ASCOP2 SuperfamilyUrease, gamma-subunit 8035578 3001945 SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
BNagA_Ne1e9yB1 A: a/b three-layered sandwichesX: Phage tail fiber protein trimerization domainH: beta-Prism IT: beta-Prism IF: NagA_NECOD (v294.1)
BDUF711e1e9yB2 A: a/b three-layered sandwichesX: HTHH: HTHT: winged helix domainF: DUF711ECOD (v294.1)
AAlpha-L-AF_Ce1e9yA1 A: a/b three-layered sandwichesX: Phage tail fiber protein trimerization domainH: beta-Prism IT: beta-Prism IF: Alpha-L-AF_CECOD (v294.1)
AIMS_Ce1e9yA2 A: a/b three-layered sandwichesX: ETN0001 domain-likeH: Rpp14/Pop5-likeT: Rpp14/Pop5-likeF: IMS_CECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
B2.30.40.10 Mainly Beta Roll Urease, subunit C domain 1CATH (4.3.0)
B3.20.20.140 Alpha Beta Alpha-Beta Barrel TIM Barrel Metal-dependent hydrolasesCATH (4.3.0)
A2.10.150.10 Mainly Beta Ribbon Urease, subunit B Urease, beta subunitCATH (4.3.0)
A3.30.280.10 Alpha Beta 2-Layer Sandwich Urease subunit ACATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
PF00449Urease alpha-subunit, N-terminal domain (Urease_alpha)Urease alpha-subunit, N-terminal domainThe N-terminal domain is a composite domain and plays a major trimer stabilising role by contacting the catalytic domain of the symmetry related alpha-subunit. Domain
PF01979Amidohydrolase family (Amidohydro_1)Amidohydrolase familyThis family of enzymes are a a large metal dependent hydrolase superfamily [1]. The family includes Adenine deaminase EC:3.5.4.2 that hydrolyses adenine to form hypoxanthine and ammonia. Adenine deaminases reaction is important for adenine utilisatio ...This family of enzymes are a a large metal dependent hydrolase superfamily [1]. The family includes Adenine deaminase EC:3.5.4.2 that hydrolyses adenine to form hypoxanthine and ammonia. Adenine deaminases reaction is important for adenine utilisation as a purine and also as a nitrogen source [2]. This family also includes dihydroorotase and N-acetylglucosamine-6-phosphate deacetylases, EC:3.5.1.25 These enzymes catalyse the reaction N-acetyl-D-glucosamine 6-phosphate + H2O <=> D-glucosamine 6-phosphate + acetate. This family includes the catalytic domain of urease alpha subunit [3]. Dihydroorotases (EC:3.5.2.3) are also included [4-5].
Domain
PF00699Urease beta subunit (Urease_beta)Urease beta subunitThis subunit is known as alpha in Heliobacter. Domain
PF00547Urease, gamma subunit (Urease_gamma)Urease, gamma subunitUrease is a nickel-binding enzyme that catalyses the hydrolysis of urea to carbon dioxide and ammonia. Domain