8HC1 | pdb_00008hc1

CryoEM structure of Helicobacter pylori UreFD/urease complex


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ASCOP2B SuperfamilyUrease, gamma-subunit 8035578 3001945 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyUrease, beta-subunit 8035575 3001949 SCOP2B (2022-06-29)
CA [auth c]SCOP2B SuperfamilyUrease, beta-subunit 8035575 3001949 SCOP2B (2022-06-29)
CA [auth c]SCOP2B SuperfamilyUrease, gamma-subunit 8035578 3001945 SCOP2B (2022-06-29)
ESCOP2B SuperfamilyUrease, gamma-subunit 8035578 3001945 SCOP2B (2022-06-29)
ESCOP2B SuperfamilyUrease, beta-subunit 8035575 3001949 SCOP2B (2022-06-29)
GA [auth g]SCOP2B SuperfamilyUrease, beta-subunit 8035575 3001949 SCOP2B (2022-06-29)
GA [auth g]SCOP2B SuperfamilyUrease, gamma-subunit 8035578 3001945 SCOP2B (2022-06-29)
ISCOP2B SuperfamilyUrease, gamma-subunit 8035578 3001945 SCOP2B (2022-06-29)
ISCOP2B SuperfamilyUrease, beta-subunit 8035575 3001949 SCOP2B (2022-06-29)
MSCOP2B SuperfamilyUrease, beta-subunit 8035575 3001949 SCOP2B (2022-06-29)
MSCOP2B SuperfamilyUrease, gamma-subunit 8035578 3001945 SCOP2B (2022-06-29)
OA [auth o]SCOP2B SuperfamilyUrease, beta-subunit 8035575 3001949 SCOP2B (2022-06-29)
OA [auth o]SCOP2B SuperfamilyUrease, gamma-subunit 8035578 3001945 SCOP2B (2022-06-29)
QSCOP2B SuperfamilyUrease, beta-subunit 8035575 3001949 SCOP2B (2022-06-29)
QSCOP2B SuperfamilyUrease, gamma-subunit 8035578 3001945 SCOP2B (2022-06-29)
SA [auth s]SCOP2B SuperfamilyUrease, gamma-subunit 8035578 3001945 SCOP2B (2022-06-29)
SA [auth s]SCOP2B SuperfamilyUrease, beta-subunit 8035575 3001949 SCOP2B (2022-06-29)
USCOP2B SuperfamilyUrease, beta-subunit 8035575 3001949 SCOP2B (2022-06-29)
USCOP2B SuperfamilyUrease, gamma-subunit 8035578 3001945 SCOP2B (2022-06-29)
YSCOP2B SuperfamilyUrease, beta-subunit 8035575 3001949 SCOP2B (2022-06-29)
YSCOP2B SuperfamilyUrease, gamma-subunit 8035578 3001945 SCOP2B (2022-06-29)
KA [auth k]SCOP2B SuperfamilyUrease, beta-subunit 8035575 3001949 SCOP2B (2022-06-29)
KA [auth k]SCOP2B SuperfamilyUrease, gamma-subunit 8035578 3001945 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)
BSCOP2B SuperfamilyMetallo-dependent hydrolases 8035584 3000428 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyComposite domain of metallo-dependent hydrolases 8035580 3000176 SCOP2B (2022-06-29)
DA [auth d]SCOP2B SuperfamilyMetallo-dependent hydrolases 8035584 3000428 SCOP2B (2022-06-29)
DA [auth d]SCOP2B SuperfamilyComposite domain of metallo-dependent hydrolases 8035580 3000176 SCOP2B (2022-06-29)
DA [auth d]SCOP2B SuperfamilyMetallo-dependent hydrolases 8035584 3000428 SCOP2B (2022-06-29)
DA [auth d]SCOP2B SuperfamilyComposite domain of metallo-dependent hydrolases 8035580 3000176 SCOP2B (2022-06-29)
FSCOP2B SuperfamilyComposite domain of metallo-dependent hydrolases 8035580 3000176 SCOP2B (2022-06-29)
FSCOP2B SuperfamilyComposite domain of metallo-dependent hydrolases 8035580 3000176 SCOP2B (2022-06-29)
FSCOP2B SuperfamilyMetallo-dependent hydrolases 8035584 3000428 SCOP2B (2022-06-29)
FSCOP2B SuperfamilyMetallo-dependent hydrolases 8035584 3000428 SCOP2B (2022-06-29)
JSCOP2B SuperfamilyComposite domain of metallo-dependent hydrolases 8035580 3000176 SCOP2B (2022-06-29)
JSCOP2B SuperfamilyMetallo-dependent hydrolases 8035584 3000428 SCOP2B (2022-06-29)
JSCOP2B SuperfamilyMetallo-dependent hydrolases 8035584 3000428 SCOP2B (2022-06-29)
JSCOP2B SuperfamilyComposite domain of metallo-dependent hydrolases 8035580 3000176 SCOP2B (2022-06-29)
LA [auth l]SCOP2B SuperfamilyMetallo-dependent hydrolases 8035584 3000428 SCOP2B (2022-06-29)
LA [auth l]SCOP2B SuperfamilyComposite domain of metallo-dependent hydrolases 8035580 3000176 SCOP2B (2022-06-29)
LA [auth l]SCOP2B SuperfamilyMetallo-dependent hydrolases 8035584 3000428 SCOP2B (2022-06-29)
LA [auth l]SCOP2B SuperfamilyComposite domain of metallo-dependent hydrolases 8035580 3000176 SCOP2B (2022-06-29)
NSCOP2B SuperfamilyComposite domain of metallo-dependent hydrolases 8035580 3000176 SCOP2B (2022-06-29)
NSCOP2B SuperfamilyMetallo-dependent hydrolases 8035584 3000428 SCOP2B (2022-06-29)
NSCOP2B SuperfamilyMetallo-dependent hydrolases 8035584 3000428 SCOP2B (2022-06-29)
NSCOP2B SuperfamilyComposite domain of metallo-dependent hydrolases 8035580 3000176 SCOP2B (2022-06-29)
PA [auth p]SCOP2B SuperfamilyComposite domain of metallo-dependent hydrolases 8035580 3000176 SCOP2B (2022-06-29)
PA [auth p]SCOP2B SuperfamilyMetallo-dependent hydrolases 8035584 3000428 SCOP2B (2022-06-29)
PA [auth p]SCOP2B SuperfamilyComposite domain of metallo-dependent hydrolases 8035580 3000176 SCOP2B (2022-06-29)
PA [auth p]SCOP2B SuperfamilyMetallo-dependent hydrolases 8035584 3000428 SCOP2B (2022-06-29)
RSCOP2B SuperfamilyComposite domain of metallo-dependent hydrolases 8035580 3000176 SCOP2B (2022-06-29)
RSCOP2B SuperfamilyComposite domain of metallo-dependent hydrolases 8035580 3000176 SCOP2B (2022-06-29)
RSCOP2B SuperfamilyMetallo-dependent hydrolases 8035584 3000428 SCOP2B (2022-06-29)
RSCOP2B SuperfamilyMetallo-dependent hydrolases 8035584 3000428 SCOP2B (2022-06-29)
VSCOP2B SuperfamilyComposite domain of metallo-dependent hydrolases 8035580 3000176 SCOP2B (2022-06-29)
VSCOP2B SuperfamilyMetallo-dependent hydrolases 8035584 3000428 SCOP2B (2022-06-29)
VSCOP2B SuperfamilyComposite domain of metallo-dependent hydrolases 8035580 3000176 SCOP2B (2022-06-29)
VSCOP2B SuperfamilyMetallo-dependent hydrolases 8035584 3000428 SCOP2B (2022-06-29)
ZSCOP2B SuperfamilyComposite domain of metallo-dependent hydrolases 8035580 3000176 SCOP2B (2022-06-29)
ZSCOP2B SuperfamilyComposite domain of metallo-dependent hydrolases 8035580 3000176 SCOP2B (2022-06-29)
ZSCOP2B SuperfamilyMetallo-dependent hydrolases 8035584 3000428 SCOP2B (2022-06-29)
ZSCOP2B SuperfamilyMetallo-dependent hydrolases 8035584 3000428 SCOP2B (2022-06-29)
TA [auth t]SCOP2B SuperfamilyMetallo-dependent hydrolases 8035584 3000428 SCOP2B (2022-06-29)
TA [auth t]SCOP2B SuperfamilyMetallo-dependent hydrolases 8035584 3000428 SCOP2B (2022-06-29)
TA [auth t]SCOP2B SuperfamilyComposite domain of metallo-dependent hydrolases 8035580 3000176 SCOP2B (2022-06-29)
TA [auth t]SCOP2B SuperfamilyComposite domain of metallo-dependent hydrolases 8035580 3000176 SCOP2B (2022-06-29)
HA [auth h]SCOP2B SuperfamilyMetallo-dependent hydrolases 8035584 3000428 SCOP2B (2022-06-29)
HA [auth h]SCOP2B SuperfamilyMetallo-dependent hydrolases 8035584 3000428 SCOP2B (2022-06-29)
HA [auth h]SCOP2B SuperfamilyComposite domain of metallo-dependent hydrolases 8035580 3000176 SCOP2B (2022-06-29)
HA [auth h]SCOP2B SuperfamilyComposite domain of metallo-dependent hydrolases 8035580 3000176 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
APkinase, ABC1e8hc1A1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Pkinase, ABC1ECOD (v294.1)
CA [auth c]Pkinase, ABC1e8hc1c1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Pkinase, ABC1ECOD (v294.1)
EPkinase, ABC1e8hc1E1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Pkinase, ABC1ECOD (v294.1)
GA [auth g]Pkinase, ABC1e8hc1g1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Pkinase, ABC1ECOD (v294.1)
IPkinase, ABC1e8hc1I1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Pkinase, ABC1ECOD (v294.1)
MPkinase, ABC1e8hc1M1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Pkinase, ABC1ECOD (v294.1)
OA [auth o]Pkinase, ABC1e8hc1o1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Pkinase, ABC1ECOD (v294.1)
QPkinase, ABC1e8hc1Q1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Pkinase, ABC1ECOD (v294.1)
SA [auth s]Pkinase, ABC1e8hc1s1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Pkinase, ABC1ECOD (v294.1)
UPkinase, ABC1e8hc1U1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Pkinase, ABC1ECOD (v294.1)
YPkinase, ABC1e8hc1Y1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Pkinase, ABC1ECOD (v294.1)
KA [auth k]Pkinase, ABC1e8hc1k1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Pkinase, ABC1ECOD (v294.1)
BPkinase, ABC1e8hc1B1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Pkinase, ABC1ECOD (v294.1)
DA [auth d]Pkinase, ABC1e8hc1d1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Pkinase, ABC1ECOD (v294.1)
FPkinase, ABC1e8hc1F1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Pkinase, ABC1ECOD (v294.1)
JPkinase, ABC1e8hc1J1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Pkinase, ABC1ECOD (v294.1)
LA [auth l]Pkinase, ABC1e8hc1l1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Pkinase, ABC1ECOD (v294.1)
NPkinase, ABC1e8hc1N1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Pkinase, ABC1ECOD (v294.1)
PA [auth p]Pkinase, ABC1e8hc1p1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Pkinase, ABC1ECOD (v294.1)
RPkinase, ABC1e8hc1R1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Pkinase, ABC1ECOD (v294.1)
VPkinase, ABC1e8hc1V1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Pkinase, ABC1ECOD (v294.1)
ZPkinase, ABC1e8hc1Z1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Pkinase, ABC1ECOD (v294.1)
TA [auth t]Pkinase, ABC1e8hc1t1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Pkinase, ABC1ECOD (v294.1)
HA [auth h]Pkinase, ABC1e8hc1h1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Pkinase, ABC1ECOD (v294.1)
BA [auth b]Pkinase, ABC1e8hc1b1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Pkinase, ABC1ECOD (v294.1)
DPkinase, ABC1e8hc1D1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Pkinase, ABC1ECOD (v294.1)
FA [auth f]Pkinase, ABC1e8hc1f1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Pkinase, ABC1ECOD (v294.1)
HPkinase, ABC1e8hc1H1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Pkinase, ABC1ECOD (v294.1)
JA [auth j]Pkinase, ABC1e8hc1j1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Pkinase, ABC1ECOD (v294.1)
LPkinase, ABC1e8hc1L1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Pkinase, ABC1ECOD (v294.1)
PPkinase, ABC1e8hc1P1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Pkinase, ABC1ECOD (v294.1)
RA [auth r]Pkinase, ABC1e8hc1r1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Pkinase, ABC1ECOD (v294.1)
TPkinase, ABC1e8hc1T1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Pkinase, ABC1ECOD (v294.1)
VA [auth v]Pkinase, ABC1e8hc1v1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Pkinase, ABC1ECOD (v294.1)
XPkinase, ABC1e8hc1X1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Pkinase, ABC1ECOD (v294.1)
NA [auth n]Pkinase, ABC1e8hc1n1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Pkinase, ABC1ECOD (v294.1)
AA [auth a]Pkinase, ABC1e8hc1a1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Pkinase, ABC1ECOD (v294.1)
CPkinase, ABC1e8hc1C1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Pkinase, ABC1ECOD (v294.1)
EA [auth e]Pkinase, ABC1e8hc1e1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Pkinase, ABC1ECOD (v294.1)
GPkinase, ABC1e8hc1G1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Pkinase, ABC1ECOD (v294.1)
IA [auth i]Pkinase, ABC1e8hc1i1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Pkinase, ABC1ECOD (v294.1)
KPkinase, ABC1e8hc1K1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Pkinase, ABC1ECOD (v294.1)
MA [auth m]Pkinase, ABC1e8hc1m1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Pkinase, ABC1ECOD (v294.1)
OPkinase, ABC1e8hc1O1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Pkinase, ABC1ECOD (v294.1)
QA [auth q]Pkinase, ABC1e8hc1q1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Pkinase, ABC1ECOD (v294.1)
SPkinase, ABC1e8hc1S1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Pkinase, ABC1ECOD (v294.1)
UA [auth u]Pkinase, ABC1e8hc1u1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Pkinase, ABC1ECOD (v294.1)
WPkinase, ABC1e8hc1W1 A: a/b three-layered sandwichesX: RNase A-likeH: RNase A-likeT: RNase A-likeF: Pkinase, ABC1ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
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
PF01774UreD urease accessory protein (UreD)UreD urease accessory protein- Family
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
PF01730UreF (UreF)UreF- Family
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
PF01730UreF (UreF)UreF- Family
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
PF01774UreD urease accessory protein (UreD)UreD urease accessory protein- Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
Urease subunit alpha
Urease subunit beta
Urease accessory protein UreF
Urease accessory protein UreH

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
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
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
IPR002639Urease accessory protein UreFFamily
IPR038277UreF domain superfamilyHomologous Superfamily
IPR002669Urease accessory protein UreDFamily