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Catalytic Site Atlas Version 2.2.12
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CSA entry for 1l6p
Original Entry
Title:
Electron transport
Compound:
Thiol:disulfide interchange protein dsbd
Mutant:
No
UniProt/Swiss-Prot:
P36655-DSBD_ECOLI
EC Class:
1.8.1.8
Other CSA Entries:
Overview of all sites for 1l6p
Homologues of 1l6p
Entries for UniProt/Swiss-Prot: P36655
Entries for EC: 1.8.1.8
Other Databases:
PDB entry: 1l6p
PDBsum entry: 1l6p
UniProt/Swiss-Prot: P36655
IntEnz entry: 1.8.1.8
Literature Report:
Introduction:
The N terminal region of the thioloxidoreductase enzyme DsbD from E.coli is able to reduce the disulphide bond in DsbC thus participates in the pathway whereby electrons from NADPH are used to break incorrectly formed disulphides in proteins in the periplasm. It displays a unique Ig fold, but still shows homology with the thioloxidoreductase family.
Mechanism:
Cys 109 is the primary nucleophile that attacks the intramolecular disulphide to form a disulphide between DsbD and DsbC. Cys 103 then acts as a secondary nucleophile to reduce this disulphide, activated by a Asp 68-Tyr 42 diad which acts as a proton relay system. This results in the reduced form intermediate, stabilised by contacts with Tyr 71 and Phe 70
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Found by:
Literature reference 

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
TYRA 42 61Sidechain
Acid/baseSubstrate
Acts to deprotonate Cys 103 thus allowing it to form the intramolecular disulphide with Cys 109 that characterises the reduced form of the enzyme.
Evidence from paper Evidence concerns Evidence type
PubMed ID 12033924 Current protein Residue is positioned appropriately
PubMed ID 12033924 Current protein Conservation of residue

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
ASPA 68 87Sidechain
ElectrostaticResidue
Activates Tyr 42 to allow it to act as a general acid-base, thus is part of an Asp-Tyr diad which functions as a proton relay system to activate Cys 103.
Evidence from paper Evidence concerns Evidence type
PubMed ID 12033924 Current protein Residue is positioned appropriately
PubMed ID 12033924 Current protein Conservation of residue

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
PHEA 70 89Sidechain
ElectrostaticTransition state
Makes hydrophobic contact with intramolecular disulphide of reduced form to stabilise it by preventing nucleophilic attack by a water molecule.
Evidence from paper Evidence concerns Evidence type
PubMed ID 12234918 Current protein Residue is positioned appropriately
PubMed ID 12234918 Current protein Conservation of residue

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
TYRA 71 90Sidechain
ElectrostaticTransition state
Acts to shield the reduced form from nucleophilic attack, thus stabilising it.
Evidence from paper Evidence concerns Evidence type
PubMed ID 12033924 Current protein Conservation of residue
PubMed ID 12033924 Current protein Residue is positioned appropriately

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
CYSA 103 122Sidechain
NucleophileSubstrate
Acts as nucleophile to reduce disulphide bond between DsbC and DsbD, forming the reduced intermediate.
Evidence from paper Evidence concerns Evidence type
PubMed ID 1203394 Current protein Conservation of residue
PubMed ID 1203394 Current protein Residue is covalently bound to intermediate, based on structural data

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
CYSA 109 128Sidechain
NucleophileSubstrate
Acts as primary nucleophile to break the intramolecular disulphide bond in DsbC which leads to the reduced form tof the enzyme with an intramolecular disulphide bond between Cys 109 and 103.
Evidence from paper Evidence concerns Evidence type
PubMed ID 12033924 Current protein Conservation of residue
PubMed ID 12033924 Current protein Mutagenesis of residue
PubMed ID 12033924 Current protein Residue is covalently bound to intermediate, based on structural data
Notes:
The pdb file refers only to the N terminal domain of the protein.
References:
1
Thiol-disulfide exchange in an immunoglobulin-like fold: structure of the N-terminal domain of DsbD.
C. W. Goulding and M. R. Sawaya and A. Parseghian and V. Lim and D. Eisenberg and D. Missiakas
Biochemistry 41, (22) 6920-7, (2002).
12033924
2
The disulfide bond isomerase DsbC is activated by an immunoglobulin-fold thiol oxidoreductase: crystal structure of the DsbC-DsbDalpha complex.
P. W. Haebel and D. Goldstone and F. Katzen and J. Beckwith and P. Metcalf
EMBO J 21, (18) 4774-84, (2002).
12234918
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