spacer
spacer

PDBsum entry 1eq3

Go to PDB code: 
protein links
Isomerase PDB id
1eq3
Jmol
Contents
Protein chain
96 a.a. *
* Residue conservation analysis
PDB id:
1eq3
Name: Isomerase
Title: Nmr structure of human parvulin hpar14
Structure: Peptidyl-prolyl cis/trans isomerase (ppiase). Chain: a. Fragment: ppiase domain (residues 36-131). Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Organ: lung. Cell: endothelial cells. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: homo sapiens
NMR struc: 25 models
Authors: E.Sekerina,U.J.Rahfeld,J.Muller,G.Fischer,P.Bayer
Key ref:
E.Sekerina et al. (2000). NMR solution structure of hPar14 reveals similarity to the peptidyl prolyl cis/trans isomerase domain of the mitotic regulator hPin1 but indicates a different functionality of the protein. J Mol Biol, 301, 1003-1017. PubMed id: 10966801 DOI: 10.1006/jmbi.2000.4013
Date:
02-Apr-00     Release date:   04-Apr-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9Y237  (PIN4_HUMAN) -  Peptidyl-prolyl cis-trans isomerase NIMA-interacting 4
Seq:
Struc:
131 a.a.
96 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.5.2.1.8  - Peptidylprolyl isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Peptidylproline (omega=180) = peptidylproline (omega=0)
Peptidylproline (omega=180)
= peptidylproline (omega=0)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     isomerase activity     1 term  

 

 
    Added reference    
 
 
DOI no: 10.1006/jmbi.2000.4013 J Mol Biol 301:1003-1017 (2000)
PubMed id: 10966801  
 
 
NMR solution structure of hPar14 reveals similarity to the peptidyl prolyl cis/trans isomerase domain of the mitotic regulator hPin1 but indicates a different functionality of the protein.
E.Sekerina, J.U.Rahfeld, J.Müller, J.Fanghänel, C.Rascher, G.Fischer, P.Bayer.
 
  ABSTRACT  
 
The 131-amino acid residue parvulin-like human peptidyl-prolyl cis/trans isomerase (PPIase) hPar14 was shown to exhibit sequence similarity to the regulator enzyme for cell cycle transitions human hPin1, but specificity for catalyzing pSer(Thr)-Pro cis/trans isomerizations was lacking. To determine the solution structure of hPar14 the (1)H, (13)C, and (15)N chemical shifts of this protein have been assigned using heteronuclear two and three-dimensional NMR experiments on unlabeled and uniformly (15)N/(13)C-labeled recombinant protein isolated from Escherichia coli cells that overexpress the protein. The chemical shift assignments were used to interpret the NOE data, which resulted in a total of 1042 NOE restraints. The NOE restraints were used along with 71 dihedral angle restraints and 38 hydrogen bonding restraints to produce 50 low-energy structures. The hPar14 folds into a betaalpha(3)betaalphabeta(2) structure, and contains an unstructured 35-amino acid basic tail N-terminal to the catalytic core that replaces the WW domain of hPin1 homologs. The three-dimensional structures of hPar14 and the PPIase domain of human hPin1 reveal a high degree of conservation. The root-mean-square deviations of the mean atomic coordinates of the heavy atoms of the backbone between residues 38 to 45, 50 to 58, 64 to 70, 81 to 86, 115 to 119 and 122 to 128 of hPar14 were 0.81(+/-0.07) A. The hPar14 model structure provides insight into how this class of PPIases may select preferential secondary catalytic sites, and also allows identification of a putative DNA-binding motif in parvulin-like PPIases.
 
  Selected figure(s)  
 
Figure 7.
Figure 7. Overlay of the active center of hPin1 (blue) and hPar14 (red). Superposition of the putative active site and the supposed catalytic active amino acid residues in both human parvulins. The gray ribbon represents the backbone fold of hPar14.
Figure 9.
Figure 9. GRASP representation of molecular surfaces of hPin1 and hPar14^36-131. The electrostatic surface potential is indicated by colours (red, acidic; blue, basic). (a) View on the surface along the active center of hPar14. Conserved residues are labeled in red, yellow, green or magenta. Color codes mark residues from which counterparts can be found at simular spatial positions in hPin1 (d). (b) Surface backside of hPar14. The quadruple of residues forming two salt bridges are labeled. (c) Negative spot surrounded by hydrophobic side-chains on the surface of hPar14. The acidic region is formed by amino acid residues of the loop region from Pro102 to Pro109, the following b-strand Val110 to Thr112 and the conserved turn Asp113 to Pro115. (d) View on the surface along the active center of hPin1. Color codes used as in (a).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 301, 1003-1017) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19645725 L.Martino, Y.He, K.L.Hands-Taylor, E.R.Valentine, G.Kelly, C.Giancola, and M.R.Conte (2009).
The interaction of the Escherichia coli protein SlyD with nickel ions illuminates the mechanism of regulation of its peptidyl-prolyl isomerase activity.
  FEBS J, 276, 4529-4544.
PDB code: 2kfw
19309529 O.Heikkinen, R.Seppala, H.Tossavainen, S.Heikkinen, H.Koskela, P.Permi, and I.Kilpeläinen (2009).
Solution structure of the parvulin-type PPIase domain of Staphylococcus aureus PrsA--implications for the catalytic mechanism of parvulins.
  BMC Struct Biol, 9, 17.
PDB code: 2jzv
19369196 S.Fujiyama-Nakamura, H.Yoshikawa, K.Homma, T.Hayano, T.Tsujimura-Takahashi, K.Izumikawa, H.Ishikawa, N.Miyazawa, M.Yanagida, Y.Miura, T.Shinkawa, Y.Yamauchi, T.Isobe, and N.Takahashi (2009).
Parvulin (Par14), a peptidyl-prolyl cis-trans isomerase, is a novel rRNA processing factor that evolved in the metazoan lineage.
  Mol Cell Proteomics, 8, 1552-1565.  
  19787094 J.W.Mueller, and P.Bayer (2008).
Small family with key contacts: par14 and par17 parvulin proteins, relatives of pin1, now emerge in biomedical research.
  Perspect Medicin Chem, 2, 11-20.  
18760284 V.Lamour, S.T.Rutherford, K.Kuznedelov, U.A.Ramagopal, R.L.Gourse, K.Severinov, and S.A.Darst (2008).
Crystal structure of Escherichia coli Rnk, a new RNA polymerase-interacting protein.
  J Mol Biol, 383, 367-379.
PDB code: 3bmb
17875217 D.Kessler, P.Papatheodorou, T.Stratmann, E.A.Dian, C.Hartmann-Fatu, J.Rassow, P.Bayer, and J.W.Mueller (2007).
The DNA binding parvulin Par17 is targeted to the mitochondrial matrix by a recently evolved prepeptide uniquely present in Hominidae.
  BMC Biol, 5, 37.  
16522211 J.W.Mueller, D.Kessler, D.Neumann, T.Stratmann, P.Papatheodorou, C.Hartmann-Fatu, and P.Bayer (2006).
Characterization of novel elongated Parvulin isoforms that are ubiquitously expressed in human tissues and originate from alternative transcription initiation.
  BMC Mol Biol, 7, 9.  
15322281 A.Kühlewein, G.Voll, B.Hernandez Alvarez, H.Kessler, G.Fischer, J.U.Rahfeld, and G.Gemmecker (2004).
Solution structure of Escherichia coli Par10: The prototypic member of the Parvulin family of peptidyl-prolyl cis/trans isomerases.
  Protein Sci, 13, 2378-2387.
PDB codes: 1jns 1jnt
14976191 M.Vitikainen, I.Lappalainen, R.Seppala, H.Antelmann, H.Boer, S.Taira, H.Savilahti, M.Hecker, M.Vihinen, M.Sarvas, and V.P.Kontinen (2004).
Structure-function analysis of PrsA reveals roles for the parvulin-like and flanking N- and C-terminal domains in protein folding and secretion in Bacillus subtilis.
  J Biol Chem, 279, 19302-19314.  
12686540 D.M.Jacobs, K.Saxena, M.Vogtherr, P.Bernado, M.Pons, and K.M.Fiebig (2003).
Peptide binding induces large scale changes in inter-domain mobility in human Pin1.
  J Biol Chem, 278, 26174-26182.  
12573694 T.Uchida, M.Takamiya, M.Takahashi, H.Miyashita, H.Ikeda, T.Terada, Y.Matsuo, M.Shirouzu, S.Yokoyama, F.Fujimori, and T.Hunter (2003).
Pin1 and Par14 peptidyl prolyl isomerase inhibitors block cell proliferation.
  Chem Biol, 10, 15-24.  
12429090 E.Bitto, and D.B.McKay (2002).
Crystallographic structure of SurA, a molecular chaperone that facilitates folding of outer membrane porins.
  Structure, 10, 1489-1498.
PDB code: 1m5y
11960984 S.Fujiyama, M.Yanagida, T.Hayano, Y.Miura, T.Isobe, F.Fujimori, T.Uchida, and N.Takahashi (2002).
Isolation and proteomic characterization of human Parvulin-associating preribosomal ribonucleoprotein complexes.
  J Biol Chem, 277, 23773-23780.  
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.