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PDBsum entry 1cbs
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Retinoic-acid transport PDB id
1cbs

 

 

 

 

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Contents
Protein chain
137 a.a. *
Ligands
REA
Waters ×100
* Residue conservation analysis
PDB id:
1cbs
Name: Retinoic-acid transport
Title: Crystal structure of cellular retinoic-acid-binding proteins i and ii in complex with all-trans-retinoic acid and a synthetic retinoid
Structure: Cellular retinoic acid binding protein type ii. Chain: a. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Cell_line: bl21. Gene: human crabp-ii. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
1.80Å     R-factor:   0.200     R-free:   0.237
Authors: G.J.Kleywegt,T.Bergfors,T.A.Jones
Key ref:
G.J.Kleywegt et al. (1994). Crystal structures of cellular retinoic acid binding proteins I and II in complex with all-trans-retinoic acid and a synthetic retinoid. Structure, 2, 1241-1258. PubMed id: 7704533 DOI: 10.1016/S0969-2126(94)00125-1
Date:
28-Sep-94     Release date:   26-Jan-95    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P29373  (RABP2_HUMAN) -  Cellular retinoic acid-binding protein 2 from Homo sapiens
Seq:
Struc: 		138 a.a.
137 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1016/S0969-2126(94)00125-1 Structure 2:1241-1258 (1994)
PubMed id: 7704533  
 
 
Crystal structures of cellular retinoic acid binding proteins I and II in complex with all-trans-retinoic acid and a synthetic retinoid.
G.J.Kleywegt, T.Bergfors, H.Senn, P.Le Motte, B.Gsell, K.Shudo, T.A.Jones.
 
  ABSTRACT  
 
BACKGROUND: Retinoic acid (RA) plays a fundamental role in diverse cellular activities. Cellular RA binding proteins (CRABPs) are thought to act by modulating the amount of RA available to nuclear RA receptors. CRABPs and cellular retinol-binding proteins (CRBPs) share a unique fold of two orthogonal beta-sheets that encapsulate their ligands. It has been suggested that a trio of residues are the prime determinants defining the high specificity of CRBPs and CRABPs for their physiological ligands. RESULTS: Bovine/murine CRABP I and human CRABP II have been crystallized in complex with their natural ligand, all-trans-RA. Human CRABP II has also been crystallized in complex with a synthetic retinoid, 'compound 19'. Their structures have been determined and refined at resolutions of 2.9 A, 1.8 A and 2.2 A, respectively. CONCLUSIONS: The retinoid-binding site in CRABPs differs significantly from that observed in CRBP. Structural changes in three juxtaposed areas of the protein create a new, displaced binding site for RA. The carboxylate of the ligand interacts with the expected trio of residues (Arg132, Tyr134 and Arg111; CRABP II numbering). The RA ligand is almost flat with the beta-ionone ring showing a significant deviation (-33 degrees) from a cis conformation relative to the isoprene tail. The edge atoms of the beta-ionone ring are accessible to solvent in a suitable orientation for presentation to metabolizing enzymes. The bulkier synthetic retinoid causes small conformational changes in the protein structure.
 
  Selected figure(s)  
 
Figure 8.
Figure 8. Comparison of retinoid binding in CRABP II and CRBP I. The Ca trace, RA and side-chain atoms of Arg111, Arg132 and Tyr134 of CRABP II have been coloured as in Figure 7, and the solvent-accessible surface of CRABP II has been drawn in purple. For CRBP I, the retinol has been coloured green, its solvent-accessible surface red, and the side-chain atoms of Gln108, Gln128 and Phe130 have been coloured green (carbon), cyan (nitrogen) and pink (oxygen).
 
  The above figure is reprinted by permission from Cell Press: Structure (1994, 2, 1241-1258) copyright 1994.  
  Figure was selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20415582 N.Noy (2010).
Between death and survival: retinoic acid in regulation of apoptosis.
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19603486 C.Vasileiou, W.Wang, X.Jia, K.S.Lee, C.T.Watson, J.H.Geiger, and B.Borhan (2009).
Elucidating the exact role of engineered CRABPII residues for the formation of a retinal protonated Schiff base.
  Proteins, 77, 812-822.
PDB code: 3i17
20004166 D.M.Himmel, K.A.Maegley, T.A.Pauly, J.D.Bauman, K.Das, C.Dharia, A.D.Clark, K.Ryan, M.J.Hickey, R.A.Love, S.H.Hughes, S.Bergqvist, and E.Arnold (2009).
Structure of HIV-1 reverse transcriptase with the inhibitor beta-Thujaplicinol bound at the RNase H active site.
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PDB codes: 3ig1 3k2p
19018099 S.Vaezeslami, X.Jia, C.Vasileiou, B.Borhan, and J.H.Geiger (2008).
Structural analysis of site-directed mutants of cellular retinoic acid-binding protein II addresses the relationship between structural integrity and ligand binding.
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PDB codes: 3cwk 3d95 3d96
17164531 G.J.Kleywegt (2007).
Crystallographic refinement of ligand complexes.
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17407165 K.S.Sandhu, and D.Dash (2007).
Dynamic alpha-helices: conformations that do not conform.
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17512406 T.T.Schug, D.C.Berry, N.S.Shaw, S.N.Travis, and N.Noy (2007).
Opposing effects of retinoic acid on cell growth result from alternate activation of two different nuclear receptors.
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17958379 V.Sjoelund, and I.A.Kaltashov (2007).
Transporter-to-trap conversion: a disulfide bond formation in cellular retinoic acid binding protein I mutant triggered by retinoic acid binding irreversibly locks the ligand inside the protein.
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Structure of conkunitzin-S1, a neurotoxin and Kunitz-fold disulfide variant from cone snail.
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PDB code: 1y62
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Two crystal structures of the isochorismate pyruvate lyase from Pseudomonas aeruginosa.
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PDB codes: 2h9c 2h9d
16524881 Z.Ignatova, and L.M.Gierasch (2006).
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15907702 H.Xiao, and I.A.Kaltashov (2005).
Transient structural disorder as a facilitator of protein-ligand binding: native H/D exchange-mass spectrometry study of cellular retinoic acid binding protein I.
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16204887 J.Aishima, D.S.Russel, L.J.Guibas, P.D.Adams, and A.T.Brunger (2005).
Automated crystallographic ligand building using the medial axis transform of an electron-density isosurface.
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15146492 C.DeWeese-Scott, and J.Moult (2004).
Molecular modeling of protein function regions.
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15572777 G.J.Kleywegt, M.R.Harris, J.Y.Zou, T.C.Taylor, A.Wählby, and T.A.Jones (2004).
The Uppsala Electron-Density Server.
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15299032 J.P.Xiong, T.Stehle, S.L.Goodman, and M.A.Arnaout (2004).
A novel adaptation of the integrin PSI domain revealed from its crystal structure.
  J Biol Chem, 279, 40252-40254.
PDB code: 1u8c
14696180 K.Gunasekaran, A.T.Hagler, and L.M.Gierasch (2004).
Sequence and structural analysis of cellular retinoic acid-binding proteins reveals a network of conserved hydrophobic interactions.
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15152096 L.L.Burns-Hamuro, P.M.Dalessio, and I.J.Ropson (2004).
Replacement of proline with valine does not remove an apparent proline isomerization-dependent folding event in CRABP I.
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15572776 P.H.Zwart, G.G.Langer, and V.S.Lamzin (2004).
Modelling bound ligands in protein crystal structures.
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14579352 A.V.Pastukhov, and I.J.Ropson (2003).
Fluorescent dyes as probes to study lipid-binding proteins.
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12745220 H.Xiao, I.A.Kaltashov, and S.J.Eyles (2003).
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14991674 K.S.Rotondi, and L.M.Gierasch (2003).
Local sequence information in cellular retinoic acid-binding protein I: specific residue roles in beta-turns.
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12486725 M.Kurz, V.Brachvogel, H.Matter, S.Stengelin, H.Thüring, and W.Kramer (2003).
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PDB codes: 1o1u 1o1v
11909957 A.S.Budhu, and N.Noy (2002).
Direct channeling of retinoic acid between cellular retinoic acid-binding protein II and retinoic acid receptor sensitizes mammary carcinoma cells to retinoic acid-induced growth arrest.
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12297624 D.M.Himmel, S.Gourinath, L.Reshetnikova, Y.Shen, A.G.Szent-Györgyi, and C.Cohen (2002).
Crystallographic findings on the internally uncoupled and near-rigor states of myosin: further insights into the mechanics of the motor.
  Proc Natl Acad Sci U S A, 99, 12645-12650.
PDB codes: 1kk7 1kk8 1kqm 1kwo 1l2o
12112737 I.A.Kaltashov, and S.J.Eyles (2002).
Crossing the phase boundary to study protein dynamics and function: combination of amide hydrogen exchange in solution and ion fragmentation in the gas phase.
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11934897 L.Franzoni, C.Lücke, C.Pérez, D.Cavazzini, M.Rademacher, C.Ludwig, A.Spisni, G.L.Rossi, and H.Rüterjans (2002).
Structure and backbone dynamics of Apo- and holo-cellular retinol-binding protein in solution.
  J Biol Chem, 277, 21983-21997.
PDB codes: 1jbh 1kgl
11266607 A.Radominska-Pandya, G.Chen, V.M.Samokyszyn, J.M.Little, W.E.Gall, G.Zawada, N.Terrier, J.Magdalou, and P.Czernik (2001).
Application of photoaffinity labeling with [(3)H] all trans- and 9-cis-retinoic acids for characterization of cellular retinoic acid--binding proteins I and II.
  Protein Sci, 10, 200-211.  
11288179 L.L.Burns, and I.J.Ropson (2001).
Folding of intracellular retinol and retinoic acid binding proteins.
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11406102 S.Goto, K.Kogure, K.Abe, Y.Kimata, K.Kitahama, E.Yamashita, and H.Terada (2001).
Efficient radical trapping at the surface and inside the phospholipid membrane is responsible for highly potent antiperoxidative activity of the carotenoid astaxanthin.
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11567160 Y.W.Chen (2001).
Solution solution: using NMR models for molecular replacement.
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10739930 B.Delagoutte, G.Keith, D.Moras, and J.Cavarelli (2000).
Crystallization and preliminary X-ray crystallographic analysis of yeast arginyl-tRNA synthetase-yeast tRNAArg complexes.
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10806391 C.Lücke, F.Zhang, J.A.Hamilton, J.C.Sacchettini, and H.Rüterjans (2000).
Solution structure of ileal lipid binding protein in complex with glycocholate.
  Eur J Biochem, 267, 2929-2938.
PDB code: 1eio
11058762 D.E.Ong, M.E.Newcomer, J.J.Lareyre, and M.C.Orgebin-Crist (2000).
Epididymal retinoic acid-binding protein.
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11027136 G.Chen, and A.Radominska-Pandya (2000).
Direct photoaffinity labeling of cellular retinoic acid-binding protein I (CRABP-I) with all-trans-retinoic acid: identification of amino acids in the ligand binding site.
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10692339 I.J.Ropson, B.C.Yowler, P.M.Dalessio, L.Banaszak, and J.Thompson (2000).
Properties and crystal structure of a beta-barrel folding mutant.
  Biophys J, 78, 1551-1560.
PDB code: 1dc9
10851191 J.Moult, and E.Melamud (2000).
From fold to function.
  Curr Opin Struct Biol, 10, 384-389.  
  10752611 V.A.Likić, N.Juranić, S.Macura, and F.G.Prendergast (2000).
A "structural" water molecule in the family of fatty acid binding proteins.
  Protein Sci, 9, 497-504.  
10924105 V.V.Krishnan, M.Sukumar, L.M.Gierasch, and M.Cosman (2000).
Dynamics of cellular retinoic acid binding protein I on multiple time scales with implications for ligand binding.
  Biochemistry, 39, 9119-9129.  
11080645 Y.W.Chen, E.J.Dodson, and G.J.Kleywegt (2000).
Does NMR mean "not for molecular replacement"? Using NMR-based search models to solve protein crystal structures.
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11092918 Y.W.Chen, and G.M.Clore (2000).
A systematic case study on using NMR models for molecular replacement: p53 tetramerization domain revisited.
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10625489 Z.Q.Wen, and G.J.Thomas (2000).
Ultraviolet-resonance raman spectroscopy of the filamentous virus Pf3: interactions of Trp 38 specific to the assembled virion subunit.
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10089410 A.A.Vaguine, J.Richelle, and S.J.Wodak (1999).
SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model.
  Acta Crystallogr D Biol Crystallogr, 55, 191-205.  
10531482 B.N.Chaudhuri, G.J.Kleywegt, I.Broutin-L'Hermite, T.Bergfors, H.Senn, P.Le Motte, O.Partouche, and T.A.Jones (1999).
Structures of cellular retinoic acid binding proteins I and II in complex with synthetic retinoids.
  Acta Crystallogr D Biol Crystallogr, 55, 1850-1857.
PDB codes: 2cbr 2cbs 3cbs
  10548048 R.Pattanayek, and M.E.Newcomer (1999).
Protein and ligand adaptation in a retinoic acid binding protein.
  Protein Sci, 8, 2027-2032.  
9862806 D.M.Lawson, C.E.Williams, L.A.Mitchenall, and R.N.Pau (1998).
Ligand size is a major determinant of specificity in periplasmic oxyanion-binding proteins: the 1.2 A resolution crystal structure of Azotobacter vinelandii ModA.
  Structure, 6, 1529-1539.
PDB code: 1atg
9736621 J.Cavarelli, B.Delagoutte, G.Eriani, J.Gangloff, and D.Moras (1998).
L-arginine recognition by yeast arginyl-tRNA synthetase.
  EMBO J, 17, 5438-5448.
PDB code: 1bs2
9789015 J.L.Schmitke, L.J.Stern, and A.M.Klibanov (1998).
Comparison of x-ray crystal structures of an acyl-enzyme intermediate of subtilisin Carlsberg formed in anhydrous acetonitrile and in water.
  Proc Natl Acad Sci U S A, 95, 12918-12923.
PDB codes: 1be6 1be8
9737883 L.Wang, and H.Yan (1998).
NMR study suggests a major role for Arg111 in maintaining the structure and dynamical properties of type II human cellular retinoic acid binding protein.
  Biochemistry, 37, 13021-13032.
PDB code: 1bm5
9737849 L.Wang, Y.Li, F.Abildgaard, J.L.Markley, and H.Yan (1998).
NMR solution structure of type II human cellular retinoic acid binding protein: implications for ligand binding.
  Biochemistry, 37, 12727-12736.
PDB code: 1blr
9862807 S.A.Moore, H.M.Baker, T.J.Blythe, K.E.Kitson, T.M.Kitson, and E.N.Baker (1998).
Sheep liver cytosolic aldehyde dehydrogenase: the structure reveals the basis for the retinal specificity of class 1 aldehyde dehydrogenases.
  Structure, 6, 1541-1551.
PDB code: 1bxs
9261066 J.Cavarelli, G.Prévost, W.Bourguet, L.Moulinier, B.Chevrier, B.Delagoutte, A.Bilwes, L.Mourey, S.Rifai, Y.Piémont, and D.Moras (1997).
The structure of Staphylococcus aureus epidermolytic toxin A, an atypic serine protease, at 1.7 A resolution.
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PDB code: 1agj
9054409 J.Thompson, N.Winter, D.Terwey, J.Bratt, and L.Banaszak (1997).
The crystal structure of the liver fatty acid-binding protein. A complex with two bound oleates.
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PDB code: 1lfo
8999826 L.Wang, Y.Li, and H.Yan (1997).
Structure-function relationships of cellular retinoic acid-binding proteins. Quantitative analysis of the ligand binding properties of the wild-type proteins and site-directed mutants.
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9360599 P.L.Clark, Z.P.Liu, J.Rizo, and L.M.Gierasch (1997).
Cavity formation before stable hydrogen bonding in the folding of a beta-clam protein.
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Giant protein kinases: domain interactions and structural basis of autoregulation.
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PDB codes: 1koa 1kob
8805582 G.J.Kleywegt, and A.T.Brünger (1996).
Checking your imagination: applications of the free R value.
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8736556 J.Koepke, X.Hu, C.Muenke, K.Schulten, and H.Michel (1996).
The crystal structure of the light-harvesting complex II (B800-850) from Rhodospirillum molischianum.
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PDB code: 1lgh
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Modern developments in molecular replacement.
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8652535 K.Kim, D.P.Cistola, and C.Frieden (1996).
Intestinal fatty acid-binding protein: the structure and stability of a helix-less variant.
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Intrinsic tryptophans of CRABPI as probes of structure and folding.
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7788293 A.E.Sauer-Eriksson, G.J.Kleywegt, M.Uhlén, and T.A.Jones (1995).
Crystal structure of the C2 fragment of streptococcal protein G in complex with the Fc domain of human IgG.
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PDB code: 1fcc
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Interactions with retinol and retinoids of bovine cellular retinol-binding protein.
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Crystal structure of the transthyretin--retinoic-acid complex.
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PDB code: 1tyr
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Crystal structure of the RAR-gamma ligand-binding domain bound to all-trans retinoic acid.
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PDB code: 2lbd
8846220 K.Braig, P.D.Adams, and A.T.Brünger (1995).
Conformational variability in the refined structure of the chaperonin GroEL at 2.8 A resolution.
  Nat Struct Biol, 2, 1083-1094.
PDB code: 1oel
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A critical assessment of comparative molecular modeling of tertiary structures of proteins.
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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.

 

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