6QSU | pdb_00006qsu

Helicobacter pylori urease with BME bound in the active site


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

ChainsDomain InfoClassFoldSuperfamilyFamilyDomainSpeciesProvenance Source (Version)
M [auth W]d6qsuw2 All beta proteins beta-clip Urease, beta-subunit Urease, beta-subunit automated matches (Helicobacter pylori ) [TaxId: 210 ], SCOPe (2.08)
M [auth W]d6qsuw1 Alpha and beta proteins (a+b) Urease, gamma-subunit Urease, gamma-subunit Urease, gamma-subunit automated matches (Helicobacter pylori ) [TaxId: 210 ], SCOPe (2.08)
L [auth U]d6qsuu2 All beta proteins beta-clip Urease, beta-subunit Urease, beta-subunit automated matches (Helicobacter pylori ) [TaxId: 210 ], SCOPe (2.08)
L [auth U]d6qsuu1 Alpha and beta proteins (a+b) Urease, gamma-subunit Urease, gamma-subunit Urease, gamma-subunit automated matches (Helicobacter pylori ) [TaxId: 210 ], SCOPe (2.08)
K [auth S]d6qsus2 All beta proteins beta-clip Urease, beta-subunit Urease, beta-subunit automated matches (Helicobacter pylori ) [TaxId: 210 ], SCOPe (2.08)
K [auth S]d6qsus1 Alpha and beta proteins (a+b) Urease, gamma-subunit Urease, gamma-subunit Urease, gamma-subunit automated matches (Helicobacter pylori ) [TaxId: 210 ], SCOPe (2.08)
J [auth Q]d6qsuq2 All beta proteins beta-clip Urease, beta-subunit Urease, beta-subunit automated matches (Helicobacter pylori ) [TaxId: 210 ], SCOPe (2.08)
J [auth Q]d6qsuq1 Alpha and beta proteins (a+b) Urease, gamma-subunit Urease, gamma-subunit Urease, gamma-subunit automated matches (Helicobacter pylori ) [TaxId: 210 ], SCOPe (2.08)
I [auth O]d6qsuo2 All beta proteins beta-clip Urease, beta-subunit Urease, beta-subunit automated matches (Helicobacter pylori ) [TaxId: 210 ], SCOPe (2.08)
I [auth O]d6qsuo1 Alpha and beta proteins (a+b) Urease, gamma-subunit Urease, gamma-subunit Urease, gamma-subunit automated matches (Helicobacter pylori ) [TaxId: 210 ], SCOPe (2.08)
H [auth M]d6qsum2 All beta proteins beta-clip Urease, beta-subunit Urease, beta-subunit automated matches (Helicobacter pylori ) [TaxId: 210 ], SCOPe (2.08)
H [auth M]d6qsum1 Alpha and beta proteins (a+b) Urease, gamma-subunit Urease, gamma-subunit Urease, gamma-subunit automated matches (Helicobacter pylori ) [TaxId: 210 ], SCOPe (2.08)
G [auth K]d6qsuk2 All beta proteins beta-clip Urease, beta-subunit Urease, beta-subunit automated matches (Helicobacter pylori ) [TaxId: 210 ], SCOPe (2.08)
G [auth K]d6qsuk1 Alpha and beta proteins (a+b) Urease, gamma-subunit Urease, gamma-subunit Urease, gamma-subunit automated matches (Helicobacter pylori ) [TaxId: 210 ], SCOPe (2.08)
F [auth I]d6qsui2 All beta proteins beta-clip Urease, beta-subunit Urease, beta-subunit automated matches (Helicobacter pylori ) [TaxId: 210 ], SCOPe (2.08)
F [auth I]d6qsui1 Alpha and beta proteins (a+b) Urease, gamma-subunit Urease, gamma-subunit Urease, gamma-subunit automated matches (Helicobacter pylori ) [TaxId: 210 ], SCOPe (2.08)
E [auth G]d6qsug2 All beta proteins beta-clip Urease, beta-subunit Urease, beta-subunit automated matches (Helicobacter pylori ) [TaxId: 210 ], SCOPe (2.08)
E [auth G]d6qsug1 Alpha and beta proteins (a+b) Urease, gamma-subunit Urease, gamma-subunit Urease, gamma-subunit automated matches (Helicobacter pylori ) [TaxId: 210 ], SCOPe (2.08)
D [auth E]d6qsue2 All beta proteins beta-clip Urease, beta-subunit Urease, beta-subunit automated matches (Helicobacter pylori ) [TaxId: 210 ], SCOPe (2.08)
D [auth E]d6qsue1 Alpha and beta proteins (a+b) Urease, gamma-subunit Urease, gamma-subunit Urease, gamma-subunit automated matches (Helicobacter pylori ) [TaxId: 210 ], SCOPe (2.08)
Cd6qsuc2 All beta proteins beta-clip Urease, beta-subunit Urease, beta-subunit automated matches (Helicobacter pylori ) [TaxId: 210 ], SCOPe (2.08)
Cd6qsuc1 Alpha and beta proteins (a+b) Urease, gamma-subunit Urease, gamma-subunit Urease, gamma-subunit automated matches (Helicobacter pylori ) [TaxId: 210 ], SCOPe (2.08)
Ad6qsua2 All beta proteins beta-clip Urease, beta-subunit Urease, beta-subunit automated matches (Helicobacter pylori ) [TaxId: 210 ], SCOPe (2.08)
Ad6qsua1 Alpha and beta proteins (a+b) Urease, gamma-subunit Urease, gamma-subunit Urease, gamma-subunit automated matches (Helicobacter pylori ) [TaxId: 210 ], SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
XSCOP2B SuperfamilyComposite domain of metallo-dependent hydrolases 8035580 3000176 SCOP2B (2022-06-29)
XSCOP2B SuperfamilyComposite domain of metallo-dependent hydrolases 8035580 3000176 SCOP2B (2022-06-29)
XSCOP2B SuperfamilyMetallo-dependent hydrolases 8035584 3000428 SCOP2B (2022-06-29)
XSCOP2B SuperfamilyMetallo-dependent hydrolases 8035584 3000428 SCOP2B (2022-06-29)
W [auth V]SCOP2B SuperfamilyComposite domain of metallo-dependent hydrolases 8035580 3000176 SCOP2B (2022-06-29)
W [auth V]SCOP2B SuperfamilyComposite domain of metallo-dependent hydrolases 8035580 3000176 SCOP2B (2022-06-29)
W [auth V]SCOP2B SuperfamilyMetallo-dependent hydrolases 8035584 3000428 SCOP2B (2022-06-29)
W [auth V]SCOP2B SuperfamilyMetallo-dependent hydrolases 8035584 3000428 SCOP2B (2022-06-29)
V [auth T]SCOP2B SuperfamilyMetallo-dependent hydrolases 8035584 3000428 SCOP2B (2022-06-29)
V [auth T]SCOP2B SuperfamilyComposite domain of metallo-dependent hydrolases 8035580 3000176 SCOP2B (2022-06-29)
V [auth T]SCOP2B SuperfamilyComposite domain of metallo-dependent hydrolases 8035580 3000176 SCOP2B (2022-06-29)
V [auth T]SCOP2B SuperfamilyMetallo-dependent hydrolases 8035584 3000428 SCOP2B (2022-06-29)
U [auth R]SCOP2B SuperfamilyMetallo-dependent hydrolases 8035584 3000428 SCOP2B (2022-06-29)
U [auth R]SCOP2B SuperfamilyMetallo-dependent hydrolases 8035584 3000428 SCOP2B (2022-06-29)
U [auth R]SCOP2B SuperfamilyComposite domain of metallo-dependent hydrolases 8035580 3000176 SCOP2B (2022-06-29)
U [auth R]SCOP2B SuperfamilyComposite domain of metallo-dependent hydrolases 8035580 3000176 SCOP2B (2022-06-29)
T [auth P]SCOP2B SuperfamilyMetallo-dependent hydrolases 8035584 3000428 SCOP2B (2022-06-29)
T [auth P]SCOP2B SuperfamilyMetallo-dependent hydrolases 8035584 3000428 SCOP2B (2022-06-29)
T [auth P]SCOP2B SuperfamilyComposite domain of metallo-dependent hydrolases 8035580 3000176 SCOP2B (2022-06-29)
T [auth P]SCOP2B SuperfamilyComposite domain of metallo-dependent hydrolases 8035580 3000176 SCOP2B (2022-06-29)
S [auth N]SCOP2B SuperfamilyComposite domain of metallo-dependent hydrolases 8035580 3000176 SCOP2B (2022-06-29)
S [auth N]SCOP2B SuperfamilyMetallo-dependent hydrolases 8035584 3000428 SCOP2B (2022-06-29)
S [auth N]SCOP2B SuperfamilyComposite domain of metallo-dependent hydrolases 8035580 3000176 SCOP2B (2022-06-29)
S [auth N]SCOP2B SuperfamilyMetallo-dependent hydrolases 8035584 3000428 SCOP2B (2022-06-29)
R [auth L]SCOP2B SuperfamilyMetallo-dependent hydrolases 8035584 3000428 SCOP2B (2022-06-29)
R [auth L]SCOP2B SuperfamilyMetallo-dependent hydrolases 8035584 3000428 SCOP2B (2022-06-29)
R [auth L]SCOP2B SuperfamilyComposite domain of metallo-dependent hydrolases 8035580 3000176 SCOP2B (2022-06-29)
R [auth L]SCOP2B SuperfamilyComposite domain of metallo-dependent hydrolases 8035580 3000176 SCOP2B (2022-06-29)
Q [auth H]SCOP2B SuperfamilyMetallo-dependent hydrolases 8035584 3000428 SCOP2B (2022-06-29)
Q [auth H]SCOP2B SuperfamilyComposite domain of metallo-dependent hydrolases 8035580 3000176 SCOP2B (2022-06-29)
Q [auth H]SCOP2B SuperfamilyComposite domain of metallo-dependent hydrolases 8035580 3000176 SCOP2B (2022-06-29)
Q [auth H]SCOP2B SuperfamilyMetallo-dependent hydrolases 8035584 3000428 SCOP2B (2022-06-29)
P [auth F]SCOP2B SuperfamilyComposite domain of metallo-dependent hydrolases 8035580 3000176 SCOP2B (2022-06-29)
P [auth F]SCOP2B SuperfamilyComposite domain of metallo-dependent hydrolases 8035580 3000176 SCOP2B (2022-06-29)
P [auth F]SCOP2B SuperfamilyMetallo-dependent hydrolases 8035584 3000428 SCOP2B (2022-06-29)
P [auth F]SCOP2B SuperfamilyMetallo-dependent hydrolases 8035584 3000428 SCOP2B (2022-06-29)
O [auth D]SCOP2B SuperfamilyMetallo-dependent hydrolases 8035584 3000428 SCOP2B (2022-06-29)
O [auth D]SCOP2B SuperfamilyComposite domain of metallo-dependent hydrolases 8035580 3000176 SCOP2B (2022-06-29)
O [auth D]SCOP2B SuperfamilyComposite domain of metallo-dependent hydrolases 8035580 3000176 SCOP2B (2022-06-29)
O [auth D]SCOP2B SuperfamilyMetallo-dependent hydrolases 8035584 3000428 SCOP2B (2022-06-29)
N [auth J]SCOP2B SuperfamilyMetallo-dependent hydrolases 8035584 3000428 SCOP2B (2022-06-29)
N [auth J]SCOP2B SuperfamilyComposite domain of metallo-dependent hydrolases 8035580 3000176 SCOP2B (2022-06-29)
N [auth J]SCOP2B SuperfamilyMetallo-dependent hydrolases 8035584 3000428 SCOP2B (2022-06-29)
N [auth J]SCOP2B SuperfamilyComposite domain of metallo-dependent hydrolases 8035580 3000176 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyMetallo-dependent hydrolases 8035584 3000428 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyComposite domain of metallo-dependent hydrolases 8035580 3000176 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyComposite domain of metallo-dependent hydrolases 8035580 3000176 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyMetallo-dependent hydrolases 8035584 3000428 SCOP2B (2022-06-29)
M [auth W]SCOP2B SuperfamilyUrease, beta-subunit 8035575 3001949 SCOP2B (2022-06-29)
M [auth W]SCOP2B SuperfamilyUrease, gamma-subunit 8035578 3001945 SCOP2B (2022-06-29)
L [auth U]SCOP2B SuperfamilyUrease, beta-subunit 8035575 3001949 SCOP2B (2022-06-29)
L [auth U]SCOP2B SuperfamilyUrease, gamma-subunit 8035578 3001945 SCOP2B (2022-06-29)
K [auth S]SCOP2B SuperfamilyUrease, beta-subunit 8035575 3001949 SCOP2B (2022-06-29)
K [auth S]SCOP2B SuperfamilyUrease, gamma-subunit 8035578 3001945 SCOP2B (2022-06-29)
J [auth Q]SCOP2B SuperfamilyUrease, beta-subunit 8035575 3001949 SCOP2B (2022-06-29)
J [auth Q]SCOP2B SuperfamilyUrease, gamma-subunit 8035578 3001945 SCOP2B (2022-06-29)
I [auth O]SCOP2B SuperfamilyUrease, gamma-subunit 8035578 3001945 SCOP2B (2022-06-29)
I [auth O]SCOP2B SuperfamilyUrease, beta-subunit 8035575 3001949 SCOP2B (2022-06-29)
H [auth M]SCOP2B SuperfamilyUrease, beta-subunit 8035575 3001949 SCOP2B (2022-06-29)
H [auth M]SCOP2B SuperfamilyUrease, gamma-subunit 8035578 3001945 SCOP2B (2022-06-29)
G [auth K]SCOP2B SuperfamilyUrease, beta-subunit 8035575 3001949 SCOP2B (2022-06-29)
G [auth K]SCOP2B SuperfamilyUrease, gamma-subunit 8035578 3001945 SCOP2B (2022-06-29)
F [auth I]SCOP2B SuperfamilyUrease, beta-subunit 8035575 3001949 SCOP2B (2022-06-29)
F [auth I]SCOP2B SuperfamilyUrease, gamma-subunit 8035578 3001945 SCOP2B (2022-06-29)
E [auth G]SCOP2B SuperfamilyUrease, beta-subunit 8035575 3001949 SCOP2B (2022-06-29)
E [auth G]SCOP2B SuperfamilyUrease, gamma-subunit 8035578 3001945 SCOP2B (2022-06-29)
D [auth E]SCOP2B SuperfamilyUrease, beta-subunit 8035575 3001949 SCOP2B (2022-06-29)
D [auth E]SCOP2B SuperfamilyUrease, gamma-subunit 8035578 3001945 SCOP2B (2022-06-29)
CSCOP2B SuperfamilyUrease, gamma-subunit 8035578 3001945 SCOP2B (2022-06-29)
CSCOP2B SuperfamilyUrease, beta-subunit 8035575 3001949 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyUrease, gamma-subunit 8035578 3001945 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyUrease, beta-subunit 8035575 3001949 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
XPG_binding_1e6qsuX1 A: a/b three-layered sandwichesX: cradle loop barrelH: N-terminal domain of poxinT: N-terminal domain of poxinF: PG_binding_1ECOD (v294.1)
W [auth V]PG_binding_1e6qsuV1 A: a/b three-layered sandwichesX: cradle loop barrelH: N-terminal domain of poxinT: N-terminal domain of poxinF: PG_binding_1ECOD (v294.1)
V [auth T]PG_binding_1e6qsuT1 A: a/b three-layered sandwichesX: cradle loop barrelH: N-terminal domain of poxinT: N-terminal domain of poxinF: PG_binding_1ECOD (v294.1)
U [auth R]PG_binding_1e6qsuR1 A: a/b three-layered sandwichesX: cradle loop barrelH: N-terminal domain of poxinT: N-terminal domain of poxinF: PG_binding_1ECOD (v294.1)
T [auth P]PG_binding_1e6qsuP1 A: a/b three-layered sandwichesX: cradle loop barrelH: N-terminal domain of poxinT: N-terminal domain of poxinF: PG_binding_1ECOD (v294.1)
S [auth N]PG_binding_1e6qsuN1 A: a/b three-layered sandwichesX: cradle loop barrelH: N-terminal domain of poxinT: N-terminal domain of poxinF: PG_binding_1ECOD (v294.1)
R [auth L]PG_binding_1e6qsuL1 A: a/b three-layered sandwichesX: cradle loop barrelH: N-terminal domain of poxinT: N-terminal domain of poxinF: PG_binding_1ECOD (v294.1)
Q [auth H]PG_binding_1e6qsuH1 A: a/b three-layered sandwichesX: cradle loop barrelH: N-terminal domain of poxinT: N-terminal domain of poxinF: PG_binding_1ECOD (v294.1)
P [auth F]PG_binding_1e6qsuF1 A: a/b three-layered sandwichesX: cradle loop barrelH: N-terminal domain of poxinT: N-terminal domain of poxinF: PG_binding_1ECOD (v294.1)
O [auth D]PG_binding_1e6qsuD1 A: a/b three-layered sandwichesX: cradle loop barrelH: N-terminal domain of poxinT: N-terminal domain of poxinF: PG_binding_1ECOD (v294.1)
N [auth J]PG_binding_1e6qsuJ1 A: a/b three-layered sandwichesX: cradle loop barrelH: N-terminal domain of poxinT: N-terminal domain of poxinF: PG_binding_1ECOD (v294.1)
BPG_binding_1e6qsuB1 A: a/b three-layered sandwichesX: cradle loop barrelH: N-terminal domain of poxinT: N-terminal domain of poxinF: PG_binding_1ECOD (v294.1)
M [auth W]PG_binding_1e6qsuW1 A: a/b three-layered sandwichesX: cradle loop barrelH: N-terminal domain of poxinT: N-terminal domain of poxinF: PG_binding_1ECOD (v294.1)
L [auth U]PG_binding_1e6qsuU1 A: a/b three-layered sandwichesX: cradle loop barrelH: N-terminal domain of poxinT: N-terminal domain of poxinF: PG_binding_1ECOD (v294.1)
K [auth S]PG_binding_1e6qsuS1 A: a/b three-layered sandwichesX: cradle loop barrelH: N-terminal domain of poxinT: N-terminal domain of poxinF: PG_binding_1ECOD (v294.1)
J [auth Q]PG_binding_1e6qsuQ1 A: a/b three-layered sandwichesX: cradle loop barrelH: N-terminal domain of poxinT: N-terminal domain of poxinF: PG_binding_1ECOD (v294.1)
I [auth O]PG_binding_1e6qsuO1 A: a/b three-layered sandwichesX: cradle loop barrelH: N-terminal domain of poxinT: N-terminal domain of poxinF: PG_binding_1ECOD (v294.1)
H [auth M]PG_binding_1e6qsuM1 A: a/b three-layered sandwichesX: cradle loop barrelH: N-terminal domain of poxinT: N-terminal domain of poxinF: PG_binding_1ECOD (v294.1)
G [auth K]PG_binding_1e6qsuK1 A: a/b three-layered sandwichesX: cradle loop barrelH: N-terminal domain of poxinT: N-terminal domain of poxinF: PG_binding_1ECOD (v294.1)
F [auth I]PG_binding_1e6qsuI1 A: a/b three-layered sandwichesX: cradle loop barrelH: N-terminal domain of poxinT: N-terminal domain of poxinF: PG_binding_1ECOD (v294.1)
E [auth G]PG_binding_1e6qsuG1 A: a/b three-layered sandwichesX: cradle loop barrelH: N-terminal domain of poxinT: N-terminal domain of poxinF: PG_binding_1ECOD (v294.1)
D [auth E]PG_binding_1e6qsuE1 A: a/b three-layered sandwichesX: cradle loop barrelH: N-terminal domain of poxinT: N-terminal domain of poxinF: PG_binding_1ECOD (v294.1)
CPG_binding_1e6qsuC1 A: a/b three-layered sandwichesX: cradle loop barrelH: N-terminal domain of poxinT: N-terminal domain of poxinF: PG_binding_1ECOD (v294.1)
APG_binding_1e6qsuA1 A: a/b three-layered sandwichesX: cradle loop barrelH: N-terminal domain of poxinT: N-terminal domain of poxinF: PG_binding_1ECOD (v294.1)

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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
Urease subunit beta
Urease subunit alpha

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
IPR029754Urease nickel binding siteBinding Site
IPR017950Urease active siteActive Site
IPR006680Amidohydrolase-relatedDomain
IPR011059Metal-dependent hydrolase, composite domain superfamilyHomologous Superfamily
IPR032466Metal-dependent hydrolaseHomologous Superfamily
IPR011612Urease alpha-subunit, N-terminal domainDomain
IPR050112Urease Alpha SubunitFamily
IPR005848Urease, alpha subunitFamily
IPR017951Urease alpha subunit, C-terminalDomain
IPR002019Urease, beta subunit-likeFamily
IPR050069Urease subunitFamily
IPR008223Urease, gamma-beta subunitFamily
IPR036461Urease, beta subunit superfamilyHomologous Superfamily
IPR002026Urease, gamma/gamma-beta subunitFamily
IPR036463Urease, gamma subunit superfamilyHomologous Superfamily