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PDBsum entry 1f4m
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protein metals Protein-protein interface(s) links
Transcription PDB id
1f4m

 

 

 

 

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Contents
Protein chains
56 a.a. *
53 a.a. *
Metals
_CA ×6
Waters ×111
* Residue conservation analysis
PDB id:
1f4m
Name: Transcription
Title: P3(2) crystal structure of ala2ile2-6, a version of rop with a repacked hydrophobic core and a new fold.
Structure: Rop ala2ile2-6. Chain: a, b, c, d, e, f. Synonym: regulatory protein rop, rom. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
2.25Å     R-factor:   0.233     R-free:   0.282
Authors: M.A.Willis,B.Bishop,L.Regan,A.T.Brunger
Key ref:
M.A.Willis et al. (2000). Dramatic structural and thermodynamic consequences of repacking a protein's hydrophobic core. Structure, 8, 1319-1328. PubMed id: 11188696 DOI: 10.1016/S0969-2126(00)00544-X
Date:
08-Jun-00     Release date:   10-Jan-01    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P03051  (ROP_ECOLX) -  Regulatory protein rop from Escherichia coli
Seq:
Struc: 		63 a.a.
56 a.a.*
Protein chain
Pfam   ArchSchema ?
P03051  (ROP_ECOLX) -  Regulatory protein rop from Escherichia coli
Seq:
Struc: 		63 a.a.
53 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 19 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D, E, F: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1016/S0969-2126(00)00544-X Structure 8:1319-1328 (2000)
PubMed id: 11188696  
 
 
Dramatic structural and thermodynamic consequences of repacking a protein's hydrophobic core.
M.A.Willis, B.Bishop, L.Regan, A.T.Brunger.
 
  ABSTRACT  
 
BACKGROUND: Rop is an RNA binding, dimeric, four-helix bundle protein with a well-defined, regular hydrophobic core ideally suited for redesign studies. A family of Rop variants in which the hydrophobic core was systematically redesigned has previously been created and characterized. RESULTS: We present a structural and thermodynamic analysis of Ala2Ile2-6, a variant of Rop with an extensively redesigned hydrophobic core. The structure of Ala2Ile2-6 reveals a completely new fold formed by a conformational "flip" of the two protomers around the dimeric interface. The free-energy profile of Ala2Ile2-6 is also very different from that of wild-type Rop. Ala2Ile2-6 has a higher melting temperature than Rop, but undergoes a slightly smaller free-energy change on unfolding. CONCLUSIONS: The structure of Ala2Ile2-6, along with molecular modeling results, demonstrate the importance of tight packing of core residues and the adoption of favorable core side chain rotamer values in determining helix-helix interactions in the four-helix bundle fold. Structural disorder at the N and C termini of Ala2Ile2-6 provides a basis for the large differences in the enthalpy and entropy of Ala2Ile2-6 folding compared with wildtype Rop.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. A Comparison of the Rop and Ala[2]Ile[2]-6 StructuresRop is shown in blue and Ala[2]Ile[2]-6 is shown in yellow. The labels for the polypeptide termini use a subscript to denote either protomer A or B. The key phenylalanine at position 14, at the center of the RNA binding interface, is shown in ball-and-sticks on each protomer to aid viewer orientation.(a) Side-by-side view showing the loops of Ala[2]Ile[2]-6 at the same end of the four-helix bundle and the splitting of the Helix1-Helix1' binding face (pointing out of the page) of wild-type Rop.(b) Overlay view with protomer A (in the back) of Ala[2]Ile[2]-6 best fit to the backbone of protomer A of Rop. Helix 2 of the Ala[2]Ile[2]-6 protomers are shifted by approximately half a turn toward the C terminus with respect to Rop

 
  The above figure is reprinted by permission from Cell Press: Structure (2000, 8, 1319-1328) copyright 2000.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21063741 S.E.Cnudde, M.Prorok, X.Jia, F.J.Castellino, and J.H.Geiger (2011).
The crystal structure of the calcium-bound con-G[Q6A] peptide reveals a novel metal-dependent helical trimer.
  J Biol Inorg Chem, 16, 257-266.  
20223220 C.Beuck, B.R.Szymczyna, D.E.Kerkow, A.B.Carmel, L.Columbus, R.L.Stanfield, and J.R.Williamson (2010).
Structure of the GLD-1 homodimerization domain: insights into STAR protein-mediated translational regulation.
  Structure, 18, 377-389.
PDB codes: 3k6t 3kbl
20401735 J.L.Kitevski-Leblanc, F.Evanics, and R.Scott Prosser (2010).
Approaches to the assignment of (19)F resonances from 3-fluorophenylalanine labeled calmodulin using solution state NMR.
  J Biomol NMR, 47, 113-123.  
20095056 S.B.Hari, C.Byeon, J.J.Lavinder, and T.J.Magliery (2010).
Cysteine-free Rop: a four-helix bundle core mutant has wild-type stability and structure but dramatically different unfolding kinetics.
  Protein Sci, 19, 670-679.
PDB code: 3k79
20179338 T.C.Terwilliger (2010).
Rapid model building of alpha-helices in electron-density maps.
  Acta Crystallogr D Biol Crystallogr, 66, 268-275.  
20179339 T.C.Terwilliger (2010).
Rapid model building of beta-sheets in electron-density maps.
  Acta Crystallogr D Biol Crystallogr, 66, 276-284.  
20179340 T.C.Terwilliger (2010).
Rapid chain tracing of polypeptide backbones in electron-density maps.
  Acta Crystallogr D Biol Crystallogr, 66, 285-294.  
19626713 H.Lammert, A.Schug, and J.N.Onuchic (2009).
Robustness and generalization of structure-based models for protein folding and function.
  Proteins, 77, 881-891.  
19506258 Y.Gambin, A.Schug, E.A.Lemke, J.J.Lavinder, A.C.Ferreon, T.J.Magliery, J.N.Onuchic, and A.A.Deniz (2009).
Direct single-molecule observation of a protein living in two opposed native structures.
  Proc Natl Acad Sci U S A, 106, 10153-10158.  
18436954 A.Go, S.Kim, J.Baum, and M.H.Hecht (2008).
Structure and dynamics of de novo proteins from a designed superfamily of 4-helix bundles.
  Protein Sci, 17, 821-832.
PDB code: 2jua
17608515 L.Hua, X.Huang, P.Liu, R.Zhou, and B.J.Berne (2007).
Nanoscale dewetting transition in protein complex folding.
  J Phys Chem B, 111, 9069-9077.  
15096198 T.J.Magliery, and L.Regan (2004).
Combinatorial approaches to protein stability and structure.
  Eur J Biochem, 271, 1595-1608.  
14501113 J.Koepke, E.I.Scharff, C.Lücke, H.Rüterjans, and G.Fritzsch (2003).
Statistical analysis of crystallographic data obtained from squid ganglion DFPase at 0.85 A resolution.
  Acta Crystallogr D Biol Crystallogr, 59, 1744-1754.
PDB code: 1pjx
12163064 R.L.Dunbrack (2002).
Rotamer libraries in the 21st century.
  Curr Opin Struct Biol, 12, 431-440.  
11420436 V.V.Loladze, D.N.Ermolenko, and G.I.Makhatadze (2001).
Heat capacity changes upon burial of polar and nonpolar groups in proteins.
  Protein Sci, 10, 1343-1352.  
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 codes are shown on the right.

 

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