spacer
spacer
Go to PDB code: 
protein links
Electron transport PDB id
1bjx
Jmol
Contents
Protein chain
110 a.a. *
* Residue conservation analysis
PDB id:
1bjx
Name: Electron transport
Title: Human protein disulfide isomerase, nmr, 24 structures
Structure: Protein disulfide isomerase. Chain: a. Fragment: b domain. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Cell_line: bl21. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
NMR struc: 24 models
Authors: J.Kemmink,K.Dijkstra,M.Mariani,R.M.Scheek,E.Penka,M.Nilges, N.J.Darby
Key ref: J.Kemmink et al. (1999). The structure in solution of the b domain of protein disulfide isomerase. J Biomol Nmr, 13, 357-368. PubMed id: 10383197 DOI: 10.1023/A:1008341820489
Date:
29-Jun-98     Release date:   13-Jan-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P07237  (PDIA1_HUMAN) -  Protein disulfide-isomerase
Seq:
Struc: 		508 a.a.
110 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.5.3.4.1  - Protein disulfide-isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Rearrangement of both intrachain and interchain disulfide bonds in proteins to form the native structures.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     calcium ion binding     1 term  

 

 
DOI no: 10.1023/A:1008341820489 J Biomol Nmr 13:357-368 (1999)
PubMed id: 10383197  
 
 
The structure in solution of the b domain of protein disulfide isomerase.
J.Kemmink, K.Dijkstra, M.Mariani, R.M.Scheek, E.Penka, M.Nilges, N.J.Darby.
 
  ABSTRACT  
 
Protein disulfide isomerase (PDI) is a multifunctional protein of the endoplasmic reticulum, which catalyzes the formation, breakage and rearrangement of disulfide bonds during protein folding. It consists of four domains designated a, b, b and a. Both a and a domains contains an active site with the sequence motif -Cys-Gly-His-Cys-involved directly in thiol-disulfide exchange reactions. As expected these domains have structures very similar to the ubiquitous redox protein thioredoxin. A low-resolution NMR structure of the b domain revealed that this domain adopts a fold similar to the PDI a domain and thioredoxin [Kemmink, J., Darby, N.J., Dijkstra, K., Nilges, M. and Creighton, T.E. (1997) Curr. Biol. 7, 239-245]. A refined ensemble of solution structures based on the input of 1865 structural restraints shows that the structure of PDI b is well defined throughout the complete protein except for about 10 residues at the C-terminus of the sequence. 15N relaxation data show that these residues are disordered and not part of this structural domain. Therefore the domain boundaries of PDI can now be fixed with reasonable precision. Structural comparison of the PDI b domain with thioredoxin and PDI a reveals several features important for thiol-disulfide exchange activity.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20625793 E.Pedone, D.Limauro, K.D'Ambrosio, G.De Simone, and S.Bartolucci (2010).
Multiple catalytically active thioredoxin folds: a winning strategy for many functions.
  Cell Mol Life Sci, 67, 3797-3814.  
19187238 A.Y.Denisov, P.Määttänen, C.Dabrowski, G.Kozlov, D.Y.Thomas, and K.Gehring (2009).
Solution structure of the bb' domains of human protein disulfide isomerase.
  FEBS J, 276, 1440-1449.
PDB code: 2k18
17956189 E.Pedone, D.Limauro, and S.Bartolucci (2008).
The machinery for oxidative protein folding in thermophiles.
  Antioxid Redox Signal, 10, 157-170.  
19091013 U.Gowthaman, M.Jayakanthan, and D.Sundar (2008).
Molecular docking studies of dithionitrobenzoic acid and its related compounds to protein disulfide isomerase: computational screening of inhibitors to HIV-1 entry.
  BMC Bioinformatics, 9, S14.  
17892489 F.Hatahet, and L.W.Ruddock (2007).
Substrate recognition by the protein disulfide isomerases.
  FEBS J, 274, 5223-5234.  
18086916 I.Raykhel, H.Alanen, K.Salo, J.Jurvansuu, V.D.Nguyen, M.Latva-Ranta, and L.Ruddock (2007).
A molecular specificity code for the three mammalian KDEL receptors.
  J Cell Biol, 179, 1193-1204.  
16771671 C.S.Sevier, and C.A.Kaiser (2006).
Conservation and diversity of the cellular disulfide bond formation pathways.
  Antioxid Redox Signal, 8, 797-811.  
16815710 C.W.Gruber, M.Cemazar, B.Heras, J.L.Martin, and D.J.Craik (2006).
Protein disulfide isomerase: the structure of oxidative folding.
  Trends Biochem Sci, 31, 455-464.  
16407203 S.J.Li, X.G.Hong, Y.Y.Shi, H.Li, and C.C.Wang (2006).
Annular arrangement and collaborative actions of four domains of protein-disulfide isomerase: a small angle X-ray scattering study in solution.
  J Biol Chem, 281, 6581-6588.  
16677078 S.Mkrtchian, and T.Sandalova (2006).
ERp29, an unusual redox-inactive member of the thioredoxin family.
  Antioxid Redox Signal, 8, 325-337.  
16126486 E.van Anken, and I.Braakman (2005).
Versatility of the endoplasmic reticulum protein folding factory.
  Crit Rev Biochem Mol Biol, 40, 191-228.  
15475357 M.van Lith, N.Hartigan, J.Hatch, and A.M.Benham (2005).
PDILT, a divergent testis-specific protein disulfide isomerase with a non-classical SXXC motif that engages in disulfide-dependent interactions in the endoplasmic reticulum.
  J Biol Chem, 280, 1376-1383.  
14684740 A.Pirneskoski, P.Klappa, M.Lobell, R.A.Williamson, L.Byrne, H.I.Alanen, K.E.Salo, K.I.Kivirikko, R.B.Freedman, and L.W.Ruddock (2004).
Molecular characterization of the principal substrate binding site of the ubiquitous folding catalyst protein disulfide isomerase.
  J Biol Chem, 279, 10374-10381.  
15169950 A.Solovyov, and H.F.Gilbert (2004).
Zinc-dependent dimerization of the folding catalyst, protein disulfide isomerase.
  Protein Sci, 13, 1902-1907.  
14871896 E.M.Frickel, P.Frei, M.Bouvier, W.F.Stafford, A.Helenius, R.Glockshuber, and L.Ellgaard (2004).
ERp57 is a multifunctional thiol-disulfide oxidoreductase.
  J Biol Chem, 279, 18277-18287.  
15252019 K.Barnewitz, C.Guo, M.Sevvana, Q.Ma, G.M.Sheldrick, H.D.Söling, and D.M.Ferrari (2004).
Mapping of a substrate binding site in the protein disulfide isomerase-related chaperone wind based on protein function and crystal structure.
  J Biol Chem, 279, 39829-39837.  
14732712 L.Silvennoinen, J.Myllyharju, M.Ruoppolo, S.Orrù, M.Caterino, K.I.Kivirikko, and P.Koivunen (2004).
Identification and characterization of structural domains of human ERp57: association with calreticulin requires several domains.
  J Biol Chem, 279, 13607-13615.  
13678523 H.I.Alanen, K.E.Salo, M.Pekkala, H.M.Siekkinen, A.Pirneskoski, and L.W.Ruddock (2003).
Defining the domain boundaries of the human protein disulfide isomerases.
  Antioxid Redox Signal, 5, 367-374.  
12717017 M.Ruoppolo, S.Orrù, F.Talamo, J.Ljung, A.Pirneskoski, K.I.Kivirikko, G.Marino, and P.Koivunen (2003).
Mutations in domain a' of protein disulfide isomerase affect the folding pathway of bovine pancreatic ribonuclease A.
  Protein Sci, 12, 939-952.  
12766950 P.M.Clissold, and R.Bicknell (2003).
The thioredoxin-like fold: hidden domains in protein disulfide isomerases and other chaperone proteins.
  Bioessays, 25, 603-611.  
12941941 Q.Ma, C.Guo, K.Barnewitz, G.M.Sheldrick, H.D.Soling, I.Uson, and D.M.Ferrari (2003).
Crystal structure and functional analysis of Drosophila Wind, a protein-disulfide isomerase-related protein.
  J Biol Chem, 278, 44600-44607.
PDB code: 1ovn
12933788 Z.Zhao, Y.Peng, S.F.Hao, Z.H.Zeng, and C.C.Wang (2003).
Dimerization by domain hybridization bestows chaperone and isomerase activities.
  J Biol Chem, 278, 43292-43298.  
12384992 C.Turano, S.Coppari, F.Altieri, and A.Ferraro (2002).
Proteins of the PDI family: unpredicted non-ER locations and functions.
  J Cell Physiol, 193, 154-163.  
11740506 E.Gross, C.S.Sevier, A.Vala, C.A.Kaiser, and D.Fass (2002).
A new FAD-binding fold and intersubunit disulfide shuttle in the thiol oxidase Erv2p.
  Nat Struct Biol, 9, 61-67.
PDB codes: 1jr8 1jra
12070313 F.Vinci, J.Couprie, P.Pucci, E.Quéméneur, and M.Moutiez (2002).
Description of the topographical changes associated to the different stages of the DsbA catalytic cycle.
  Protein Sci, 11, 1600-1612.  
  11435111 E.Liepinsh, M.Baryshev, A.Sharipo, M.Ingelman-Sundberg, G.Otting, and S.Mkrtchian (2001).
Thioredoxin fold as homodimerization module in the putative chaperone ERp29: NMR structures of the domains and experimental model of the 51 kDa dimer.
  Structure, 9, 457-471.
PDB codes: 1g7d 1g7e
10679456 C.Schiene, and G.Fischer (2000).
Enzymes that catalyse the restructuring of proteins.
  Curr Opin Struct Biol, 10, 40-45.  
10788425 P.Klappa, P.Koivunen, A.Pirneskoski, P.Karvonen, L.W.Ruddock, K.I.Kivirikko, and R.B.Freedman (2000).
Mutations that destabilize the a' domain of human protein-disulfide isomerase indirectly affect peptide binding.
  J Biol Chem, 275, 13213-13218.  
11004577 X.X.Sun, Y.Dai, H.P.Liu, S.M.Chen, and C.C.Wang (2000).
Contributions of protein disulfide isomerase domains to its chaperone activity.
  Biochim Biophys Acta, 1481, 45-54.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.