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[ccp4bb] SUMMARY: References for 3D structures of covalent complexes
 

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CCP4bb <-- 2007 <-- April 2007 <-- 05 April 2007
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Subject: Application Scientist for Rigaku Europe
From: Conn Mallett conn {- dot -} mallett {- at -} RIGAKU {- dot -} COM
Date: 2007-04-05 		Next message:
Subject: 3 RA posts in sunny newcastle
From: "R {- dot -} J {- dot -} Lewis" r {- dot -} lewis {- at -} NCL {- dot -} AC {- dot -} UK
Date: 2007-04-05


Subject: SUMMARY: References for 3D structures of covalent complexes
From: Lionel Mourey Lionel {- dot -} Mourey {- at -} IPBS {- dot -} FR
Date: 2007-04-05






Dear colleagues,



Thanks to all who replied to my question. Among the most helpful
answers was the one from Ralf W. Grosse-Kunstleve who carried out
Protein Data Bank searches (see below).



Best regards,



Lionel



Original posting

I would be very interested and much grateful having references
(bibliographic data, PDB entry code, web link...) on 3D structures of
covalently linked (engineered or not) protein-protein complexes (e.g.
heterodimers). Our own survey of the literature was not very
"successful".



Here is a summary of the responses:



Marko Hyvönen href="mailto:marko@cryst.bioc.cam.ac.uk">marko@cryst.bioc.cam.ac.uk

not sure what you mean exactly with your question, but I have few
suggestions which could be of use. All members of the TGFbeta
superfamily are covalent dimers (see 2arp, 2tgi, 2bmp etc) with a
disulfide in

between. Rad51-BRC4 repeat structure by Luca Pellegrini has a BRC4
peptide bound to Rad51, and construct crystallised had the peptide
covalently fused to the N-terminus rad51. PDB: 1n0w.



Roberto Steiner href="mailto:roberto.steiner@kcl.ac.uk">roberto.steiner@kcl.ac.uk

One example: In the Neuron (2004) 41:573-86 Zhou et al. describe the
structure of a KChIP1/Kv4.2 chimeric complex (PDB code 1S6C).

Recently, Pioletti etl al (2006) Nat. Struct. Mol. Biol., 13:987-995
have solved the structure of the "natural" complex showing (PDB code
2I2R) that the structure of the chimera is non-physiological.



Boaz Shaanan href="mailto:bshaanan@bgu.ac.il">bshaanan@bgu.ac.il

Does an Fv fragment fall into your definition of covalently linked
complex (between Vl and Vh domains) ? If so, you'll probably find a few
in the pdb.



Brad C Bennett href="mailto:bennet02@utk.edu">bennet02@utk.edu

Definitely an engineered example for you: This is a paper describing
(among other things) the 3D structure of a ligand-induced homodimer of
E. coli DHFR (a functional monomer), via covalent linkage of the
ligands themselves.



Designing Protein Dimerizers: The Importance of Ligand Conformational
Equilibria

Jonathan C. T. Carlson, Aaron Kanter,Guruvasuthevan R.
Thuduppathy,Vivian Cody, Pamela E. Pineda,R. Scott McIvor,and Carston
R. Wagner J. Am. Chem. Soc., 125 (6), 1501 -1507, 2003



Menachem Shoham href="mailto:mxs10@case.edu">mxs10@case.edu

Here is one reference from the lab of Cynthia Wolberger at Johns
Hopkins.



Eddins, MJ. A1 - Carlile, CM. A1 - Gomez, KM. A1 - Pickart, CM. A1 -
Wolberger, C. JF - Nature Structural & Molecular Biology VL - 13 IS
- 10 SP - 915 Y1 - 2006 T1 - Mms2-Ubc13 covalently bound to ubiquitin
reveals the structural basis of linkage-specific polyubiquitin chain
formation.



A number of years she had also solved a structure of the
maltose-binding-protein fused to a DNA-binding protein.



Philippe Dumas href="mailto:Philippe.Dumas@ibmc.u-strasbg.fr">Philippe.Dumas@ibmc.u-strasbg.fr

To my knowledge the most amazing example of such covalently linked
proteins is from a virus structure solved in Jack Johnson's group. This
virus has a protein shell with a (shell thickness)-to-(virion radius)
ratio close to that of a football and everything holds together because
the protomers are litterally sewed by covalent links.



Valerie Hindie href="mailto:vhindie@pasteur.fr">vhindie@pasteur.fr

from this database you can find all complexes pdb-id:

href="http://www.mrc-lmb.cam.ac.uk/genomes/elevy/3dcomplex/Home.cgi">http://www.mrc-lmb.cam.ac.uk/genomes/elevy/3dcomplex/Home.cgi



Janet Deane href="mailto:janet.deane@path.ox.ac.uk">janet.deane@path.ox.ac.uk

We successfully solved the structure of a protein with it's binding
partner (although this was a fraction of the full protein that turned
out to be peptide-like).



PDB code: 1RUT

Tandem LIM domains provide synergistic binding in the LMO4:Ldb1
complex. Deane JE, Ryan DP, Sunde M, Maher MJ, Guss JM, Visvader JE,
Matthews JM. EMBO J. 2004 Sep 15; 23(18): 3589-3598.



Paper describing the engineering was:

Design, production and characterization of FLIN2 and FLIN4: the
engineering of intramolecular ldb1:LMO complexes. Protein Eng. 2001
Jul;14(7):493-9.



Ralf W. Grosse-Kunstleve href="mailto:rwgk@yahoo.com">rwgk@yahoo.com

I found this question interesting, therefore I quickly searched the
entire PDB V3 ( href="http://wwpdb-remediation.rutgers.edu/">http://wwpdb-remediation.rutgers.edu/)
for LINK records
linking two standard amino acid residues, excluding chain links and
same-chain disulfides. Here are the results:



href="http://cci.lbl.gov/%7Erwgk/tmp/protein_protein_links/2007_02_26_1220/file_names_protein_protein_links">http://cci.lbl.gov/~rwgk/tmp/protein_protein_links/2007_02_26_1220/file_names_protein_protein_links

href="http://cci.lbl.gov/%7Erwgk/tmp/protein_protein_links/2007_02_26_1220/protein_protein_links">http://cci.lbl.gov/~rwgk/tmp/protein_protein_links/2007_02_26_1220/protein_protein_links



In the second file, look for "protein_protein_links" to find the LINK
records. At first sight there are only a few false positives (residue
linked to itself), which I didn't filter out because I want to tell the
wwPDB about it. Let me know if you find more false positives.



See also



href="http://cci.lbl.gov/%7Erwgk/tmp/protein_protein_links/2007_03_05_1256/file_names_intra_chain_ssbonds">http://cci.lbl.gov/~rwgk/tmp/protein_protein_links/2007_03_05_1256/file_names_intra_chain_ssbonds

href="http://cci.lbl.gov/%7Erwgk/tmp/protein_protein_links/2007_03_05_1256/intra_chain_ssbonds">http://cci.lbl.gov/~rwgk/tmp/protein_protein_links/2007_03_05_1256/intra_chain_ssbonds



for SSBOND records excluding intrachain disulfides.




Lionel Mourey e-mail: lionel dot mourey at ipbs dot fr

Groupe de Biophysique Structurale

Département "Mécanismes Moléculaires des Infections
Mycobactériennes"

IPBS-CNRS UMR 5089 / 205 route de Narbonne 31077 / TOULOUSE
Cedex FRANCE

Tel : +33 (0)561 175 436 Fax : +33 (0)561 175 994




CCP4bb navigation

CCP4bb <-- 2007 <-- April 2007 <-- 05 April 2007
Previous message:
Subject: Application Scientist for Rigaku Europe
From: Conn Mallett conn {- dot -} mallett {- at -} RIGAKU {- dot -} COM
Date: 2007-04-05 		Next message:
Subject: 3 RA posts in sunny newcastle
From: "R {- dot -} J {- dot -} Lewis" r {- dot -} lewis {- at -} NCL {- dot -} AC {- dot -} UK
Date: 2007-04-05


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