Primary Citation PubMed: 16413482
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Effects of macromolecular crowding on protein conformational changes.
(2010) PLoS Comput Biol 6
PubMed: 20617196 | PubMedCentral: PMC2895631 | DOI: 10.1371/journal.pcbi.1000833
Protein Organism Subcellular location Biological Function PDB code AdK Escherichia coli cytoplasm ATP-AMP transphosphorylase 4AKE & 1AKE yPDI Saccharomyces cerevisiae lumen of endoplasmic reti... ulum catalyses rearrangement of protein disulfide bonds 3BOA & 2B5E ODCase Saccharomyces cerevisiae cytoplasm converts orotidine mono- phosphate to uridine mono-phosphate, the last step in biosynthesis of pyrimidine nucleotides 1DQW & 1DQX TrpR Escherichia coli cytoplasm regulates transcription in tryptophan biosynthesis 1WRP & 3WRP Hb Homo sapiens cytoplasm oxygen transport 2DN1 & 2DN2 BGT Enterobacteria phage T4 cytoplasm of host cell catalyzes transfer of glucose from uridine diphosphoglucose to hydroxymethylcytosine in DNA 1JEJ & 1JG6 Ap 4 Aase Lupinus angustifolius cytoplasm catalyses cleavage of diadenosine tetraphosphate into ATP and AMP 1F3Y & 1JKN Results/Discussion The X-ray structures of AdK in the open and closed states are shown in Figure 1 ; comparison of open and closed structures for all the seven proteins is found in Figure S1 .
Publication Year: 2010
Structure of the non-catalytic domain of the protein disulfide isomerase-related protein (PDIR) reveals function in protein binding.
(2013) PLoS One 8
PubMed: 23614004 | PubMedCentral: PMC3629029 | DOI: 10.1371/journal.pone.0062021
The highest structural similarity was to the N-terminal, catalytic domain a of human ERp57 (PDB entry 3f8u; Z-score of 14.7)  and the corresponding domain of yeast PDI (PDB entry 2b5e; Z-score of ... 4.2)  .
Publication Year: 2013
Substrate-induced unfolding of protein disulfide isomerase displaces the cholera toxin A1 subunit from its holotoxin.
(2014) PLoS Pathog 10
PubMed: 24516389 | PubMedCentral: PMC3916401 | DOI: 10.1371/journal.ppat.1003925
The percentages of oxidoreductase secondary structure calculated by FTIR spectroscopy were consistent with the secondary structure content predicted from crystal structures for PDI (PDB 2B5E and PDB 4... KZ), ERp57 (PDB 3F8U), and ERp72 (reconstructed from PDBs 2DJ3, 2DJ2, 2DJ1, and 3EC3).
Publication Year: 2014
Compact conformations of human protein disulfide isomerase.
(2014) PLoS One 9
PubMed: 25084354 | PubMedCentral: PMC4118876 | DOI: 10.1371/journal.pone.0103472
The crystal structures of yeast PDI (yPDI) at 4°C (PDB code 2B5E)  and 22°C (PDB code 3BOA)  and hPDI in oxidized (PDB code 4EL1) and reduced (PDB code 4EKZ) states  were s... lved only recently.
High-resolution NMR studies of structure and dynamics of human ERp27 indicate extensive interdomain flexibility.
(2013) Biochem J 450
PubMed: 23234573 | PubMedCentral: PMC4203274 | DOI: 10.1042/BJ20121635
Normal modes of motion were generated for both full-length ERp27 (molecule B) and for the central bb ′ domains of full-length yeast PDI (from PDB code 2B5E).
The N- and C-termini of ERp27 b are labelled N and C. ERp27 b is aligned with ( A ) human Trx (PDB code 1ERT, residues 1–105, RMSD=1.8 Å over 95 residues), ( B ) human PDI b domain (PDB code 2BJX, residues 119–216, RMSD=1.8 Å over 98 residues), ( C ) yeast PDI b domain (PDB code 2B5E, residues 142–237, RMSD=2.3 Å over 90 residues) and ( D ) human ERp57 b ′ domain (PDB code 2H8L, residues 135–240, RMSD=1.9 Å over 97 residues).
The orientation in the PDB code 2B5E crystal structure of PDI is indicated by a grey arrow and that in the ERp27 crystal structure (PDB code 4F9Z [ 43 ]) by a black arrow.
The Eps1p protein disulfide isomerase conserves classic thioredoxin superfamily amino acid motifs but not their functional geometries.
PubMed: 25437863 | PubMedCentral: PMC4249923 | DOI: 10.1371/journal.pone.0113431
First, an edited structure of the first domain of yeast Pdi1p (pdb ID code 2B5E, residues 22–139) was used to search for the first Trx domain, and suitable rotation and translation solutions w... re found.
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