5AEW | pdb_00005aew

Crystal structure of II9 variant of Biphenyl dioxygenase from Burkholderia xenovorans LB400 in complex with biphenyl


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

ChainsDomain InfoClassFoldSuperfamilyFamilyDomainSpeciesProvenance Source (Version)
Xd5aewx_ Alpha and beta proteins (a+b) Cystatin-like NTF2-like Ring hydroxylating beta subunit automated matches (Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ], SCOPe (2.08)
Vd5aewv_ Alpha and beta proteins (a+b) Cystatin-like NTF2-like Ring hydroxylating beta subunit automated matches (Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ], SCOPe (2.08)
Td5aewt_ Alpha and beta proteins (a+b) Cystatin-like NTF2-like Ring hydroxylating beta subunit automated matches (Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ], SCOPe (2.08)
Rd5aewr_ Alpha and beta proteins (a+b) Cystatin-like NTF2-like Ring hydroxylating beta subunit automated matches (Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ], SCOPe (2.08)
Pd5aewp_ Alpha and beta proteins (a+b) Cystatin-like NTF2-like Ring hydroxylating beta subunit automated matches (Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ], SCOPe (2.08)
Nd5aewn_ Alpha and beta proteins (a+b) Cystatin-like NTF2-like Ring hydroxylating beta subunit automated matches (Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ], SCOPe (2.08)
Ld5aewl_ Alpha and beta proteins (a+b) Cystatin-like NTF2-like Ring hydroxylating beta subunit automated matches (Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ], SCOPe (2.08)
Jd5aewj_ Alpha and beta proteins (a+b) Cystatin-like NTF2-like Ring hydroxylating beta subunit automated matches (Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ], SCOPe (2.08)
Hd5aewh_ Alpha and beta proteins (a+b) Cystatin-like NTF2-like Ring hydroxylating beta subunit automated matches (Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ], SCOPe (2.08)
Fd5aewf_ Alpha and beta proteins (a+b) Cystatin-like NTF2-like Ring hydroxylating beta subunit automated matches (Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ], SCOPe (2.08)
Dd5aewd_ Alpha and beta proteins (a+b) Cystatin-like NTF2-like Ring hydroxylating beta subunit automated matches (Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ], SCOPe (2.08)
Bd5aewb_ Alpha and beta proteins (a+b) Cystatin-like NTF2-like Ring hydroxylating beta subunit automated matches (Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ], SCOPe (2.08)
Wd5aeww1 All beta proteins ISP domain ISP domain automated matches automated matches (Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ], SCOPe (2.08)
Wd5aeww2 Alpha and beta proteins (a+b) TBP-like Bet v1-like automated matches automated matches (Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ], SCOPe (2.08)
Ud5aewu1 All beta proteins ISP domain ISP domain automated matches automated matches (Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ], SCOPe (2.08)
Ud5aewu2 Alpha and beta proteins (a+b) TBP-like Bet v1-like automated matches automated matches (Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ], SCOPe (2.08)
Sd5aews1 All beta proteins ISP domain ISP domain automated matches automated matches (Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ], SCOPe (2.08)
Sd5aews2 Alpha and beta proteins (a+b) TBP-like Bet v1-like automated matches automated matches (Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ], SCOPe (2.08)
Qd5aewq1 All beta proteins ISP domain ISP domain automated matches automated matches (Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ], SCOPe (2.08)
Qd5aewq2 Alpha and beta proteins (a+b) TBP-like Bet v1-like automated matches automated matches (Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ], SCOPe (2.08)
Od5aewo1 All beta proteins ISP domain ISP domain automated matches automated matches (Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ], SCOPe (2.08)
Od5aewo2 Alpha and beta proteins (a+b) TBP-like Bet v1-like automated matches automated matches (Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ], SCOPe (2.08)
Md5aewm1 All beta proteins ISP domain ISP domain automated matches automated matches (Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ], SCOPe (2.08)
Md5aewm2 Alpha and beta proteins (a+b) TBP-like Bet v1-like automated matches automated matches (Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ], SCOPe (2.08)
Kd5aewk1 All beta proteins ISP domain ISP domain automated matches automated matches (Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ], SCOPe (2.08)
Kd5aewk2 Alpha and beta proteins (a+b) TBP-like Bet v1-like automated matches automated matches (Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ], SCOPe (2.08)
Id5aewi1 All beta proteins ISP domain ISP domain automated matches automated matches (Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ], SCOPe (2.08)
Id5aewi2 Alpha and beta proteins (a+b) TBP-like Bet v1-like automated matches automated matches (Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ], SCOPe (2.08)
Gd5aewg1 All beta proteins ISP domain ISP domain automated matches automated matches (Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ], SCOPe (2.08)
Gd5aewg2 Alpha and beta proteins (a+b) TBP-like Bet v1-like automated matches automated matches (Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ], SCOPe (2.08)
Ed5aewe1 All beta proteins ISP domain ISP domain automated matches automated matches (Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ], SCOPe (2.08)
Ed5aewe2 Alpha and beta proteins (a+b) TBP-like Bet v1-like automated matches automated matches (Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ], SCOPe (2.08)
Cd5aewc1 All beta proteins ISP domain ISP domain automated matches automated matches (Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ], SCOPe (2.08)
Cd5aewc2 Alpha and beta proteins (a+b) TBP-like Bet v1-like automated matches automated matches (Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ], SCOPe (2.08)
Ad5aewa1 All beta proteins ISP domain ISP domain automated matches automated matches (Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ], SCOPe (2.08)
Ad5aewa2 Alpha and beta proteins (a+b) TBP-like Bet v1-like automated matches automated matches (Paraburkholderia xenovorans LB400 ) [TaxId: 266265 ], SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
XSCOP2B SuperfamilyNTF2-like 8074179 3000472 SCOP2B (2022-06-29)
VSCOP2B SuperfamilyNTF2-like 8074179 3000472 SCOP2B (2022-06-29)
TSCOP2B SuperfamilyNTF2-like 8074179 3000472 SCOP2B (2022-06-29)
RSCOP2B SuperfamilyNTF2-like 8074179 3000472 SCOP2B (2022-06-29)
PSCOP2B SuperfamilyNTF2-like 8074179 3000472 SCOP2B (2022-06-29)
NSCOP2B SuperfamilyNTF2-like 8074179 3000472 SCOP2B (2022-06-29)
LSCOP2B SuperfamilyNTF2-like 8074179 3000472 SCOP2B (2022-06-29)
JSCOP2 FamilyRing hydroxylating beta subunit-like 8074178 4001024 SCOP2 (2022-06-29)
JSCOP2 SuperfamilyNTF2-like 8074179 3000472 SCOP2 (2022-06-29)
HSCOP2B SuperfamilyNTF2-like 8074179 3000472 SCOP2B (2022-06-29)
FSCOP2B SuperfamilyNTF2-like 8074179 3000472 SCOP2B (2022-06-29)
DSCOP2B SuperfamilyNTF2-like 8074179 3000472 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyNTF2-like 8074179 3000472 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
XBAHe5aewX1 A: a/b three-layered sandwichesX: Alpha-beta plaitsH: SH3T: SH3F: BAHECOD (v294.1)
VBAHe5aewV1 A: a/b three-layered sandwichesX: Alpha-beta plaitsH: SH3T: SH3F: BAHECOD (v294.1)
TBAHe5aewT1 A: a/b three-layered sandwichesX: Alpha-beta plaitsH: SH3T: SH3F: BAHECOD (v294.1)
RBAHe5aewR1 A: a/b three-layered sandwichesX: Alpha-beta plaitsH: SH3T: SH3F: BAHECOD (v294.1)
PBAHe5aewP1 A: a/b three-layered sandwichesX: Alpha-beta plaitsH: SH3T: SH3F: BAHECOD (v294.1)
NBAHe5aewN1 A: a/b three-layered sandwichesX: Alpha-beta plaitsH: SH3T: SH3F: BAHECOD (v294.1)
LBAHe5aewL1 A: a/b three-layered sandwichesX: Alpha-beta plaitsH: SH3T: SH3F: BAHECOD (v294.1)
JBAHe5aewJ1 A: a/b three-layered sandwichesX: Alpha-beta plaitsH: SH3T: SH3F: BAHECOD (v294.1)
HBAHe5aewH1 A: a/b three-layered sandwichesX: Alpha-beta plaitsH: SH3T: SH3F: BAHECOD (v294.1)
FBAHe5aewF1 A: a/b three-layered sandwichesX: Alpha-beta plaitsH: SH3T: SH3F: BAHECOD (v294.1)
DBAHe5aewD1 A: a/b three-layered sandwichesX: Alpha-beta plaitsH: SH3T: SH3F: BAHECOD (v294.1)
BBAHe5aewB1 A: a/b three-layered sandwichesX: Alpha-beta plaitsH: SH3T: SH3F: BAHECOD (v294.1)
WBAHe5aewW1 A: a/b three-layered sandwichesX: Alpha-beta plaitsH: SH3T: SH3F: BAHECOD (v294.1)
UBAHe5aewU2 A: a/b three-layered sandwichesX: Alpha-beta plaitsH: SH3T: SH3F: BAHECOD (v294.1)
SBAHe5aewS1 A: a/b three-layered sandwichesX: Alpha-beta plaitsH: SH3T: SH3F: BAHECOD (v294.1)
QBAHe5aewQ1 A: a/b three-layered sandwichesX: Alpha-beta plaitsH: SH3T: SH3F: BAHECOD (v294.1)
OBAHe5aewO1 A: a/b three-layered sandwichesX: Alpha-beta plaitsH: SH3T: SH3F: BAHECOD (v294.1)
MBAHe5aewM1 A: a/b three-layered sandwichesX: Alpha-beta plaitsH: SH3T: SH3F: BAHECOD (v294.1)
KBAHe5aewK2 A: a/b three-layered sandwichesX: Alpha-beta plaitsH: SH3T: SH3F: BAHECOD (v294.1)
IBAHe5aewI1 A: a/b three-layered sandwichesX: Alpha-beta plaitsH: SH3T: SH3F: BAHECOD (v294.1)
GBAHe5aewG2 A: a/b three-layered sandwichesX: Alpha-beta plaitsH: SH3T: SH3F: BAHECOD (v294.1)
EBAHe5aewE1 A: a/b three-layered sandwichesX: Alpha-beta plaitsH: SH3T: SH3F: BAHECOD (v294.1)
CBAHe5aewC1 A: a/b three-layered sandwichesX: Alpha-beta plaitsH: SH3T: SH3F: BAHECOD (v294.1)
ABAHe5aewA1 A: a/b three-layered sandwichesX: Alpha-beta plaitsH: SH3T: SH3F: BAHECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
X3.10.450.50 Alpha Beta Roll Nuclear Transport Factor 2 Chain: A,CATH (4.3.0)
V3.10.450.50 Alpha Beta Roll Nuclear Transport Factor 2 Chain: A,CATH (4.3.0)
T3.10.450.50 Alpha Beta Roll Nuclear Transport Factor 2 Chain: A,CATH (4.3.0)
R3.10.450.50 Alpha Beta Roll Nuclear Transport Factor 2 Chain: A,CATH (4.3.0)
P3.10.450.50 Alpha Beta Roll Nuclear Transport Factor 2 Chain: A,CATH (4.3.0)
N3.10.450.50 Alpha Beta Roll Nuclear Transport Factor 2 Chain: A,CATH (4.3.0)
L3.10.450.50 Alpha Beta Roll Nuclear Transport Factor 2 Chain: A,CATH (4.3.0)
J3.10.450.50 Alpha Beta Roll Nuclear Transport Factor 2 Chain: A,CATH (4.3.0)
H3.10.450.50 Alpha Beta Roll Nuclear Transport Factor 2 Chain: A,CATH (4.3.0)
F3.10.450.50 Alpha Beta Roll Nuclear Transport Factor 2 Chain: A,CATH (4.3.0)
D3.10.450.50 Alpha Beta Roll Nuclear Transport Factor 2 Chain: A,CATH (4.3.0)
B3.10.450.50 Alpha Beta Roll Nuclear Transport Factor 2 Chain: A,CATH (4.3.0)
W3.90.380.10 Alpha Beta Alpha-Beta Complex Naphthalene 1,2-dioxygenase Alpha Subunit Chain A, domain 1CATH (4.3.0)
W2.102.10.10 Mainly Beta 3-layer Sandwich Rieske Iron-sulfur Protein Rieske [2Fe-2S] iron-sulphur domainCATH (4.3.0)
U3.90.380.10 Alpha Beta Alpha-Beta Complex Naphthalene 1,2-dioxygenase Alpha Subunit Chain A, domain 1CATH (4.3.0)
U2.102.10.10 Mainly Beta 3-layer Sandwich Rieske Iron-sulfur Protein Rieske [2Fe-2S] iron-sulphur domainCATH (4.3.0)
S3.90.380.10 Alpha Beta Alpha-Beta Complex Naphthalene 1,2-dioxygenase Alpha Subunit Chain A, domain 1CATH (4.3.0)
S2.102.10.10 Mainly Beta 3-layer Sandwich Rieske Iron-sulfur Protein Rieske [2Fe-2S] iron-sulphur domainCATH (4.3.0)
Q3.90.380.10 Alpha Beta Alpha-Beta Complex Naphthalene 1,2-dioxygenase Alpha Subunit Chain A, domain 1CATH (4.3.0)
Q2.102.10.10 Mainly Beta 3-layer Sandwich Rieske Iron-sulfur Protein Rieske [2Fe-2S] iron-sulphur domainCATH (4.3.0)
O3.90.380.10 Alpha Beta Alpha-Beta Complex Naphthalene 1,2-dioxygenase Alpha Subunit Chain A, domain 1CATH (4.3.0)
O2.102.10.10 Mainly Beta 3-layer Sandwich Rieske Iron-sulfur Protein Rieske [2Fe-2S] iron-sulphur domainCATH (4.3.0)
M3.90.380.10 Alpha Beta Alpha-Beta Complex Naphthalene 1,2-dioxygenase Alpha Subunit Chain A, domain 1CATH (4.3.0)
M2.102.10.10 Mainly Beta 3-layer Sandwich Rieske Iron-sulfur Protein Rieske [2Fe-2S] iron-sulphur domainCATH (4.3.0)
K3.90.380.10 Alpha Beta Alpha-Beta Complex Naphthalene 1,2-dioxygenase Alpha Subunit Chain A, domain 1CATH (4.3.0)
K2.102.10.10 Mainly Beta 3-layer Sandwich Rieske Iron-sulfur Protein Rieske [2Fe-2S] iron-sulphur domainCATH (4.3.0)
I3.90.380.10 Alpha Beta Alpha-Beta Complex Naphthalene 1,2-dioxygenase Alpha Subunit Chain A, domain 1CATH (4.3.0)
I2.102.10.10 Mainly Beta 3-layer Sandwich Rieske Iron-sulfur Protein Rieske [2Fe-2S] iron-sulphur domainCATH (4.3.0)
G3.90.380.10 Alpha Beta Alpha-Beta Complex Naphthalene 1,2-dioxygenase Alpha Subunit Chain A, domain 1CATH (4.3.0)
G2.102.10.10 Mainly Beta 3-layer Sandwich Rieske Iron-sulfur Protein Rieske [2Fe-2S] iron-sulphur domainCATH (4.3.0)
E3.90.380.10 Alpha Beta Alpha-Beta Complex Naphthalene 1,2-dioxygenase Alpha Subunit Chain A, domain 1CATH (4.3.0)
E2.102.10.10 Mainly Beta 3-layer Sandwich Rieske Iron-sulfur Protein Rieske [2Fe-2S] iron-sulphur domainCATH (4.3.0)
C3.90.380.10 Alpha Beta Alpha-Beta Complex Naphthalene 1,2-dioxygenase Alpha Subunit Chain A, domain 1CATH (4.3.0)
C2.102.10.10 Mainly Beta 3-layer Sandwich Rieske Iron-sulfur Protein Rieske [2Fe-2S] iron-sulphur domainCATH (4.3.0)
A3.90.380.10 Alpha Beta Alpha-Beta Complex Naphthalene 1,2-dioxygenase Alpha Subunit Chain A, domain 1CATH (4.3.0)
A2.102.10.10 Mainly Beta 3-layer Sandwich Rieske Iron-sulfur Protein Rieske [2Fe-2S] iron-sulphur domainCATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
B, D, F, H, J
PF00866Ring hydroxylating beta subunit (Ring_hydroxyl_B)Ring hydroxylating beta subunitThis subunit has a similar structure to NTF-2 and scytalone dehydratase. Domain
A, C, E, G, I
PF00848Ring hydroxylating alpha subunit (catalytic domain) (Ring_hydroxyl_A)Ring hydroxylating alpha subunit (catalytic domain)This family is the catalytic domain of aromatic-ring- hydroxylating dioxygenase systems. The active site contains a non-heme ferrous ion coordinated by three ligands. Domain
A, C, E, G, I
PF00355Rieske [2Fe-2S] domain (Rieske)Rieske [2Fe-2S] domainThe rieske domain has a [2Fe-2S] centre. Two conserved cysteines coordinate one Fe ion, while the other Fe ion is coordinated by two conserved histidines. In hyperthermophilic archaea there is a SKTPCX(2-3)C motif at the C-terminus. The cysteines in ...The rieske domain has a [2Fe-2S] centre. Two conserved cysteines coordinate one Fe ion, while the other Fe ion is coordinated by two conserved histidines. In hyperthermophilic archaea there is a SKTPCX(2-3)C motif at the C-terminus. The cysteines in this motif form a disulphide bridge, which stabilises the protein [4].
Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
B, D, F, H, J
BIPHENYL DIOXYGENASE SUBUNIT BETA -
A, C, E, G, I
BIPHENYL DIOXYGENASE SUBUNIT ALPHA - -

InterPro: Protein Family Classification InterPro Database Homepage