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PDBsum entry 1n0q

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protein ligands Protein-protein interface(s) links
Structural protein PDB id
1n0q
Jmol
Contents
Protein chains
92 a.a. *
Ligands
TFA
Waters ×183
* Residue conservation analysis
PDB id:
1n0q
Name: Structural protein
Title: 3ank: a designed ankyrin repeat protein with three identical repeats
Structure: 3 ankyrin repeats. Chain: a, b. Synonym: 3ank. Engineered: yes
Source: Gene: designed consensus ankyrin repeat. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.26Å     R-factor:   0.172     R-free:   0.187
Authors: L.K.Mosavi,D.L.Minor Jr.,Z-Y.Peng
Key ref:
L.K.Mosavi et al. (2002). Consensus-derived structural determinants of the ankyrin repeat motif. Proc Natl Acad Sci U S A, 99, 16029-16034. PubMed id: 12461176 DOI: 10.1073/pnas.252537899
Date:
14-Oct-02     Release date:   28-Jan-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
No UniProt id for this chain
Struc: 92 a.a.
Key:    Secondary structure  CATH domain

 

 
DOI no: 10.1073/pnas.252537899 Proc Natl Acad Sci U S A 99:16029-16034 (2002)
PubMed id: 12461176  
 
 
Consensus-derived structural determinants of the ankyrin repeat motif.
L.K.Mosavi, D.L.Minor, Z.Y.Peng.
 
  ABSTRACT  
 
The ankyrin repeat is one of the most common, modular, protein-protein interaction motifs in nature. To understand the structural determinants of this family of proteins and extract the consensus information that defines the architecture of this motif, we have designed a series of idealized ankyrin repeat proteins containing one, two, three, or four repeats by using statistical analysis of approximately 4,000 ankyrin repeat sequences from the PFAM database. Biophysical and x-ray crystallographic studies of the three and four repeat constructs (3ANK and 4ANK) to 1.26 and 1.5 A resolution, respectively, demonstrate that these proteins are well-folded, monomeric, display high thermostability, and adopt a very regular, tightly packed ankyrin repeat fold. Mapping the degree of amino acid conservation at each position on the 4ANK structure shows that most nonconserved residues are clustered on the surface of the molecule that has been designated as the binding site in naturally occurring ankyrin repeat proteins. Thus, the consensus amino acid sequence contains all information required to define the ankyrin repeat fold. Our results suggest that statistical analysis and the consensus sequence approach can be used as an effective method to design proteins with complex topologies. These generic ankyrin repeat proteins can serve as prototypes for dissecting the rules of molecular recognition mediated by ankyrin repeats and for engineering proteins with novel biological functions.
 
  Selected figure(s)  
 
Figure 3.
Fig 3. X-ray crystal structures of 3ANK and 4ANK. (a) Stereo representation showing the initial electron density map of residues 37-40 of 4ANK, including the TPLH motif, contoured at 1.5 . The figure was made with O and rendered by using MOLRAY (43). (b) Overlay of 3ANK (cyan) and 4ANK (orange) backbone structures. This figure and all following structural representations were made with MOLMOL (44). (c) Hydrogen bonding network in -hairpin/loop region of 4ANK. Each repeat is colored differently and hydrogen bonds are represented by letters: a, D32(OD1) and N34(HN); b, D32(O) and G35(HN); c, D32(OD1) and R36(HN); d, D32(HN) and R36(O); e, R36(O) and H7(HNE2); f, A30(O) and H7(HNE2); g, A30(HN) and D27(O); h, D27(OD1) and N29(HN); i, N29(OD1) and D60(HN); j, N29(ND2) and G58(O); k, N34(O) and K66(HN); and l, R36(HNE) and D65(OD2). Equivalent hydrogen bonds in adjacent repeats are represented by the letter followed by ' or " and for all residue numbers i > 33, the canonical ankyrin repeat position = i - 33. (d) Comparison of intramolecular packing of ankyrin repeat proteins based on the occluded surface area analysis. For each protein, the average ray length of all residues was plotted against the average occluded surface packing (OSP) value of all buried residues with exposed surface area of <5%. The average values of 152 high-resolution structures in PDB are shown by the dashed lines on the graph (31).
Figure 4.
Fig 4. Conservation level of residues mapped onto the structure of 4ANK. Colors represent the conservation level: blue, well-conserved; pink, semiconserved of the same type; green, semiconserved of different type; and yellow, nonconserved. The C-terminal tyrosine is colored in gray. (a) Front (concave) surface of 4ANK. (b) Back surface of 4ANK. The ribbon diagrams on the left show orientations. (c) Longitudinal cross-section of the protein displaying the interior residues. Protein is in the same orientation as in b.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21329696 I.DeVries, D.U.Ferreiro, I.E.Sánchez, and E.A.Komives (2011).
Folding kinetics of the cooperatively folded subdomain of the IκBα ankyrin repeat domain.
  J Mol Biol, 408, 163-176.  
21397186 T.Aksel, A.Majumdar, and D.Barrick (2011).
The contribution of entropy, enthalpy, and hydrophobic desolvation to cooperativity in repeat-protein folding.
  Structure, 19, 349-360.
PDB code: 2l6b
21082325 Z.G.Zhao, S.S.Zhu, Y.H.Zhang, X.F.Bian, Y.Wang, L.Jiang, X.Liu, L.M.Chen, S.J.Liu, W.W.Zhang, H.Ikehashi, and J.M.Wan (2011).
Molecular analysis of an additional case of hybrid sterility in rice (Oryza sativa L.).
  Planta, 233, 485-494.  
20955552 B.Schmierer, B.Novák, and C.J.Schofield (2010).
Hypoxia-dependent sequestration of an oxygen sensor by a widespread structural motif can shape the hypoxic response--a predictive kinetic model.
  BMC Syst Biol, 4, 139.  
20055496 D.U.Ferreiro, and E.A.Komives (2010).
Molecular mechanisms of system control of NF-kappaB signaling by IkappaBalpha.
  Biochemistry, 49, 1560-1567.  
19945965 E.Brient-Litzler, A.Plückthun, and H.Bedouelle (2010).
Knowledge-based design of reagentless fluorescent biosensors from a designed ankyrin repeat protein.
  Protein Eng Des Sel, 23, 229-241.  
19962898 S.Al-Khodor, C.T.Price, A.Kalia, and Y.Abu Kwaik (2010).
Functional diversity of ankyrin repeats in microbial proteins.
  Trends Microbiol, 18, 132-139.  
20862721 S.Eisenbeis, and B.Höcker (2010).
Evolutionary mechanism as a template for protein engineering.
  J Pept Sci, 16, 538-544.  
19836330 E.H.Lee, J.Hsin, M.Sotomayor, G.Comellas, and K.Schulten (2009).
Discovery through the computational microscope.
  Structure, 17, 1295-1306.  
19439446 E.Ho, T.Irvine, G.J.Vilk, G.Lajoie, K.S.Ravichandran, S.J.D'Souza, and L.Dagnino (2009).
Integrin-linked kinase interactions with ELMO2 modulate cell polarity.
  Mol Biol Cell, 20, 3033-3043.  
19081931 L.Kelly, M.A.McDonough, M.L.Coleman, P.J.Ratcliffe, and C.J.Schofield (2009).
Asparagine beta-hydroxylation stabilizes the ankyrin repeat domain fold.
  Mol Biosyst, 5, 52-58.
PDB codes: 2zgd 2zgg
18936059 M.E.Cockman, J.D.Webb, H.B.Kramer, B.M.Kessler, and P.J.Ratcliffe (2009).
Proteomics-based identification of novel factor inhibiting hypoxia-inducible factor (FIH) substrates indicates widespread asparaginyl hydroxylation of ankyrin repeat domain-containing proteins.
  Mol Cell Proteomics, 8, 535-546.  
19845602 M.E.Cockman, J.D.Webb, and P.J.Ratcliffe (2009).
FIH-dependent asparaginyl hydroxylation of ankyrin repeat domain-containing proteins.
  Ann N Y Acad Sci, 1177, 9.  
19137598 S.Tong, H.Zhou, Y.Gao, Z.Zhu, X.Zhang, M.Teng, and L.Niu (2009).
Crystal structure of human osteoclast stimulating factor.
  Proteins, 75, 245-251.
PDB codes: 3ehq 3ehr
19289204 T.Aksel, and D.Barrick (2009).
Analysis of repeat-protein folding using nearest-neighbor statistical mechanical models.
  Methods Enzymol, 455, 95.  
  19177351 T.O.Street, and D.Barrick (2009).
Predicting repeat protein folding kinetics from an experimentally determined folding energy landscape.
  Protein Sci, 18, 58-68.  
19202291 T.Yamanaka, M.Miyama, and Y.Tada (2009).
Transcriptome profiling of the mangrove plant Bruguiera gymnorhiza and identification of salt tolerance genes by Agrobacterium functional screening.
  Biosci Biotechnol Biochem, 73, 304-310.  
19805120 Y.Javadi, and E.R.Main (2009).
Exploring the folding energy landscape of a series of designed consensus tetratricopeptide repeat proteins.
  Proc Natl Acad Sci U S A, 106, 17383-17388.  
18232717 C.B.Phelps, R.J.Huang, P.V.Lishko, R.R.Wang, and R.Gaudet (2008).
Structural analyses of the ankyrin repeat domain of TRPV6 and related TRPV ion channels.
  Biochemistry, 47, 2476-2484.
PDB code: 2rfa
18305166 C.Löw, U.Weininger, P.Neumann, M.Klepsch, H.Lilie, M.T.Stubbs, and J.Balbach (2008).
Structural insights into an equilibrium folding intermediate of an archaeal ankyrin repeat protein.
  Proc Natl Acad Sci U S A, 105, 3779-3784.
PDB code: 2rfm
18243686 D.Barrick, D.U.Ferreiro, and E.A.Komives (2008).
Folding landscapes of ankyrin repeat proteins: experiments meet theory.
  Curr Opin Struct Biol, 18, 27-34.  
18221561 D.Wang, Y.Guo, C.Wu, G.Yang, Y.Li, and C.Zheng (2008).
Genome-wide analysis of CCCH zinc finger family in Arabidopsis and rice.
  BMC Genomics, 9, 44.  
17963718 E.Kloss, N.Courtemanche, and D.Barrick (2008).
Repeat-protein folding: new insights into origins of cooperativity, stability, and topology.
  Arch Biochem Biophys, 469, 83-99.  
18279343 F.Habyarimana, S.Al-Khodor, A.Kalia, J.E.Graham, C.T.Price, M.T.Garcia, and Y.A.Kwaik (2008).
Role for the Ankyrin eukaryotic-like genes of Legionella pneumophila in parasitism of protozoan hosts and human macrophages.
  Environ Microbiol, 10, 1460-1474.  
18241884 M.E.Yanez, K.V.Korotkov, J.Abendroth, and W.G.Hol (2008).
Structure of the minor pseudopilin EpsH from the Type 2 secretion system of Vibrio cholerae.
  J Mol Biol, 377, 91.
PDB code: 2qv8
18481120 P.Sklenovský, P.Banás, and M.Otyepka (2008).
Two C-terminal ankyrin repeats form the minimal stable unit of the ankyrin repeat protein p18INK4c.
  J Mol Model, 14, 747-759.  
18842000 R.A.Edwards, M.S.Lee, S.E.Tsutakawa, R.S.Williams, J.A.Tainer, and J.N.Glover (2008).
The BARD1 C-terminal domain structure and interactions with polyadenylation factor CstF-50.
  Biochemistry, 47, 11446-11456.  
18414734 R.Gaudet (2008).
A primer on ankyrin repeat function in TRP channels and beyond.
  Mol Biosyst, 4, 372-379.  
  18811729 S.Al-Khodor, C.T.Price, F.Habyarimana, A.Kalia, and Y.Abu Kwaik (2008).
A Dot/Icm-translocated ankyrin protein of Legionella pneumophila is required for intracellular proliferation within human macrophages and protozoa.
  Mol Microbiol, 70, 908-923.  
18824506 S.Bergqvist, G.Ghosh, and E.A.Komives (2008).
The IkappaBalpha/NF-kappaB complex has two hot spots, one at either end of the interface.
  Protein Sci, 17, 2051-2058.  
18511071 S.M.Truhlar, E.Mathes, C.F.Cervantes, G.Ghosh, and E.A.Komives (2008).
Pre-folding IkappaBalpha alters control of NF-kappaB signaling.
  J Mol Biol, 380, 67-82.  
17483477 D.U.Ferreiro, and E.A.Komives (2007).
The plastic landscape of repeat proteins.
  Proc Natl Acad Sci U S A, 104, 7735-7736.  
17342200 J.J.Gillespie, M.S.Beier, M.S.Rahman, N.C.Ammerman, J.M.Shallom, A.Purkayastha, B.S.Sobral, and A.F.Azad (2007).
Plasmids and rickettsial evolution: insight from Rickettsia felis.
  PLoS ONE, 2, e266.  
17067634 K.W.Tripp, and D.Barrick (2007).
Enhancing the stability and folding rate of a repeat protein through the addition of consensus repeats.
  J Mol Biol, 365, 1187-1200.  
17988990 M.Ishikawa, F.Yagasaki, D.Okamura, T.Maeda, Y.Sugahara, I.Jinnai, and M.Bessho (2007).
A novel gene, ANKRD28 on 3p25, is fused with NUP98 on 11p15 in a cryptic 3-way translocation of t(3;5;11)(p25;q35;p15) in an adult patient with myelodysplastic syndrome/acute myelogenous leukemia.
  Int J Hematol, 86, 238-245.  
17360387 T.O.Street, C.M.Bradley, and D.Barrick (2007).
Predicting coupling limits from an experimentally determined energy landscape.
  Proc Natl Acad Sci U S A, 104, 4907-4912.  
16522802 A.C.Hausrath, and A.Goriely (2006).
Repeat protein architectures predicted by a continuum representation of fold space.
  Protein Sci, 15, 753-760.  
16493627 H.K.Binz, A.Kohl, A.Plückthun, and M.G.Grütter (2006).
Crystal structure of a consensus-designed ankyrin repeat protein: implications for stability.
  Proteins, 65, 280-284.
PDB code: 2bkg
16948156 H.Yu, A.Kohl, H.K.Binz, A.Plückthun, M.G.Grütter, and W.F.van Gunsteren (2006).
Molecular dynamics study of the stabilities of consensus designed ankyrin repeat proteins.
  Proteins, 65, 285-295.  
16892288 K.M.Polizzi, J.F.Chaparro-Riggers, E.Vazquez-Figueroa, and A.S.Bommarius (2006).
Structure-guided consensus approach to create a more thermostable penicillin G acylase.
  Biotechnol J, 1, 531-536.  
17003112 M.E.Cockman, D.E.Lancaster, I.P.Stolze, K.S.Hewitson, M.A.McDonough, M.L.Coleman, C.H.Coles, X.Yu, R.T.Hay, S.C.Ley, C.W.Pugh, N.J.Oldham, N.Masson, C.J.Schofield, and P.J.Ratcliffe (2006).
Posttranslational hydroxylation of ankyrin repeats in IkappaB proteins by the hypoxia-inducible factor (HIF) asparaginyl hydroxylase, factor inhibiting HIF (FIH).
  Proc Natl Acad Sci U S A, 103, 14767-14772.  
16895918 N.Bhattacharya, S.Ghosh, D.Sept, and J.A.Cooper (2006).
Binding of myotrophin/V-1 to actin-capping protein: implications for how capping protein binds to the filament barbed end.
  J Biol Chem, 281, 31021-31030.  
16373474 R.J.Hosse, A.Rothe, and B.E.Power (2006).
A new generation of protein display scaffolds for molecular recognition.
  Protein Sci, 15, 14-27.  
16934999 S.M.Truhlar, C.H.Croy, J.W.Torpey, J.R.Koeppe, and E.A.Komives (2006).
Solvent accessibility of protein surfaces by amide H/2H exchange MALDI-TOF mass spectrometry.
  J Am Soc Mass Spectrom, 17, 1490-1497.  
17148610 S.M.Truhlar, J.W.Torpey, and E.A.Komives (2006).
Regions of IkappaBalpha that are critical for its inhibition of NF-kappaB.DNA interaction fold upon binding to NF-kappaB.
  Proc Natl Acad Sci U S A, 103, 18951-18956.  
16407126 S.S.Cho, Y.Levy, and P.G.Wolynes (2006).
P versus Q: structural reaction coordinates capture protein folding on smooth landscapes.
  Proc Natl Acad Sci U S A, 103, 586-591.  
15975904 A.Vespa, S.J.D'Souza, and L.Dagnino (2005).
A novel role for integrin-linked kinase in epithelial sheet morphogenesis.
  Mol Biol Cell, 16, 4084-4095.  
15889240 B.A.Niemeyer (2005).
Structure-function analysis of TRPV channels.
  Naunyn Schmiedebergs Arch Pharmacol, 371, 285-294.  
15824314 E.R.Main, K.Stott, S.E.Jackson, and L.Regan (2005).
Local and long-range stability in tandemly arrayed tetratricopeptide repeats.
  Proc Natl Acad Sci U S A, 102, 5721-5726.  
16211069 H.K.Binz, P.Amstutz, and A.Plückthun (2005).
Engineering novel binding proteins from nonimmunoglobulin domains.
  Nat Biotechnol, 23, 1257-1268.  
15984913 H.Ogata, P.Renesto, S.Audic, C.Robert, G.Blanc, P.E.Fournier, H.Parinello, J.M.Claverie, and D.Raoult (2005).
The genome sequence of Rickettsia felis identifies the first putative conjugative plasmid in an obligate intracellular parasite.
  PLoS Biol, 3, e248.  
16030207 I.Iturbe-Ormaetxe, G.R.Burke, M.Riegler, and S.L.O'Neill (2005).
Distribution, expression, and motif variability of ankyrin domain genes in Wolbachia pipientis.
  J Bacteriol, 187, 5136-5145.  
15929745 J.Y.Li, R.Kuick, R.C.Thompson, D.E.Misek, Y.M.Lai, Y.Q.Liu, B.X.Chai, S.M.Hanash, and I.Gantz (2005).
Arcuate nucleus transcriptome profiling identifies ankyrin repeat and suppressor of cytokine signalling box-containing protein 4 as a gene regulated by fasting in central nervous system feeding circuits.
  J Neuroendocrinol, 17, 394-404.  
16098192 M.C.Miles, M.L.Janket, E.D.Wheeler, A.Chattopadhyay, B.Majumder, J.Dericco, E.A.Schafer, and V.Ayyavoo (2005).
Molecular and functional characterization of a novel splice variant of ANKHD1 that lacks the KH domain and its role in cell survival and apoptosis.
  FEBS J, 272, 4091-4102.  
15837205 M.Sotomayor, D.P.Corey, and K.Schulten (2005).
In search of the hair-cell gating spring elastic properties of ankyrin and cadherin repeats.
  Structure, 13, 669-682.  
16008555 N.Chevalier, L.Bertrand, M.H.Rider, F.R.Opperdoes, D.J.Rigden, and P.A.Michels (2005).
6-Phosphofructo-2-kinase and fructose-2,6-bisphosphatase in Trypanosomatidae. Molecular characterization, database searches, modelling studies and evolutionary analysis.
  FEBS J, 272, 3542-3560.  
16110356 W.Yuan, Y.Zheng, R.Huo, L.Lu, X.Y.Huang, L.L.Yin, J.M.Li, Z.M.Zhou, and J.H.Sha (2005).
Expression of a novel alternative transcript of the novel retinal pigment epithelial cell gene NORPEG in human testes.
  Asian J Androl, 7, 277-288.  
15377792 C.C.Mello, and D.Barrick (2004).
An experimentally determined protein folding energy landscape.
  Proc Natl Acad Sci U S A, 101, 14102-14107.  
14963153 C.Camus-Bouclainville, L.Fiette, S.Bouchiha, B.Pignolet, D.Counor, C.Filipe, J.Gelfi, and F.Messud-Petit (2004).
A virulence factor of myxoma virus colocalizes with NF-kappaB in the nucleus and interferes with inflammation.
  J Virol, 78, 2510-2516.  
15215520 C.H.Croy, S.Bergqvist, T.Huxford, G.Ghosh, and E.A.Komives (2004).
Biophysical characterization of the free IkappaBalpha ankyrin repeat domain in solution.
  Protein Sci, 13, 1767-1777.  
14752198 J.Holton, and T.Alber (2004).
Automated protein crystal structure determination using ELVES.
  Proc Natl Acad Sci U S A, 101, 1537-1542.
PDB codes: 1rb1 1rb4 1rb5 1rb6 3k7z
15520811 J.L.Kadrmas, and M.C.Beckerle (2004).
The LIM domain: from the cytoskeleton to the nucleus.
  Nat Rev Mol Cell Biol, 5, 920-931.  
15152081 L.K.Mosavi, T.J.Cammett, D.C.Desrosiers, and Z.Y.Peng (2004).
The ankyrin repeat as molecular architecture for protein recognition.
  Protein Sci, 13, 1435-1448.  
14760739 P.Forrer, H.K.Binz, M.T.Stumpp, and A.Plückthun (2004).
Consensus design of repeat proteins.
  Chembiochem, 5, 183-189.  
15498935 V.S.Devi, H.K.Binz, M.T.Stumpp, A.Plückthun, H.R.Bosshard, and I.Jelesarov (2004).
Folding of a designed simple ankyrin repeat protein.
  Protein Sci, 13, 2864-2870.  
12885957 A.A.Bondareva, and E.E.Schmidt (2003).
Early vertebrate evolution of the TATA-binding protein, TBP.
  Mol Biol Evol, 20, 1932-1939.  
12566564 A.Kohl, H.K.Binz, P.Forrer, M.T.Stumpp, A.Plückthun, and M.G.Grütter (2003).
Designed to be stable: crystal structure of a consensus ankyrin repeat protein.
  Proc Natl Acad Sci U S A, 100, 1700-1705.
PDB code: 1mj0
12948778 E.R.Main, S.E.Jackson, and L.Regan (2003).
The folding and design of repeat proteins: reaching a consensus.
  Curr Opin Struct Biol, 13, 482-489.  
12737816 E.R.Main, Y.Xiong, M.J.Cocco, L.D'Andrea, and L.Regan (2003).
Design of stable alpha-helical arrays from an idealized TPR motif.
  Structure, 11, 497-508.
PDB codes: 1na0 1na3
12737814 K.W.Tripp, and D.Barrick (2003).
Folding by consensus.
  Structure, 11, 486-487.  
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.