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PDBsum entry 1zde

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protein metals links
Transferase PDB id
1zde
Jmol
Contents
Protein chain
160 a.a. *
Metals
_CA ×2
_ZN
Waters ×71
* Residue conservation analysis
PDB id:
1zde
Name: Transferase
Title: 1.95 angstrom crystal structure of a dnae intein precursor from synechocystis sp. Pcc 6803
Structure: DNA polymerase iii alpha subunit. Chain: a. Fragment: residues 1-177. Synonym: dnae intein. Engineered: yes
Source: Synechocystis sp. Pcc 6803. Organism_taxid: 1148. Strain: pcc 6803. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.95Å     R-factor:   0.195     R-free:   0.222
Authors: P.Sun,S.Ye,S.Ferrandon,T.C.Evans,M.Q.Xu,Z.Rao
Key ref:
P.Sun et al. (2005). Crystal structures of an intein from the split dnaE gene of Synechocystis sp. PCC6803 reveal the catalytic model without the penultimate histidine and the mechanism of zinc ion inhibition of protein splicing. J Mol Biol, 353, 1093-1105. PubMed id: 16219320 DOI: 10.1016/j.jmb.2005.09.039
Date:
14-Apr-05     Release date:   24-Jan-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam  
P74750  (DPO3A_SYNY3) -  DNA polymerase III subunit alpha (Fragments)
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1355 a.a.
160 a.a.*
Key:    Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     intein-mediated protein splicing   1 term 

 

 
DOI no: 10.1016/j.jmb.2005.09.039 J Mol Biol 353:1093-1105 (2005)
PubMed id: 16219320  
 
 
Crystal structures of an intein from the split dnaE gene of Synechocystis sp. PCC6803 reveal the catalytic model without the penultimate histidine and the mechanism of zinc ion inhibition of protein splicing.
P.Sun, S.Ye, S.Ferrandon, T.C.Evans, M.Q.Xu, Z.Rao.
 
  ABSTRACT  
 
The first naturally occurring split intein was found in the dnaE gene of Synechocystis sp. PCC6803 and belongs to a subclass of inteins without a penultimate histidine residue. We describe two high-resolution crystal structures, one derived from an excised Ssp DnaE intein and the second from a splicing-deficient precursor protein. The X-ray structures indicate that His147 in the conserved block F activates the side-chain N(delta) atom of the intein C-terminal Asn159, leading to a nucleophilic attack on the peptide bond carbonyl carbon atom at the C-terminal splice site. In this process, Arg73 appears to stabilize the transition state by interacting with the carbonyl oxygen atom of the scissile bond. Arg73 also seems to substitute for the conserved penultimate histidine residue in the formation of an oxyanion hole, as previously identified in other inteins. The finding that the precursor structure contains a zinc ion chelating the highly conserved Cys160 and Asp140 reveals the structural basis of Zn2+-mediated inhibition of protein splicing. Furthermore, it is of interest to observe that the carbonyl carbon atom of Asn159 and N(eta) of Arg73 are 2.6 angstroms apart in the free intein structure and 10.6 angstroms apart in the precursor structure. The orientation change of the aromatic ring of Tyr-1 following the initial acyl shift may be a key switching event contributing to the alignment of Arg73 and the C-terminal scissile bond, and may explain the sequential reaction property of the Ssp DnaE intein.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. (a) Diagram of conserved intein motifs of bifunctional inteins, mini inteins and the Ssp DnaE split intein. Blocks A and B (black) in the N-terminal subdomain (magenta) and blocks F and G (black) in the C-terminal subdomain (yellow) are shared by the splicing domains and the endonuclease domain is shown in grey. Residues involved in nucleophilic attack (letters in a box), as well as other highly conserved amino acids are indicated below the block diagram. (b) A representation of the Ssp DnaE intein fusions. The exDnaE fusion protein consists of maltose-binding protein (MBP), the full-length wild-type Ssp DnaE intein (residues 1-159, which include 123 amino acid residues from the N terminus and 36 amino acid residues from the C terminus) with five native extein residues at its N terminus and three native residues at its C terminus, and the CBD. The resulting protein exDnaE is splicing functional. Black arrows indicate the splicing sites of Ssp DnaE intein. preDnaE consists of CBD, Ssp DnaB intein and the full-length Ssp DnaE intein with C1A and N159A mutations (residue 1-159) along with five native extein residues at its N terminus and three native residues at its C terminus. The black arrow shows the cleavage site of the modified Ssp DnaB intein.41 The intein proteins after purification are indicated in red.
Figure 3.
Figure 3. (a) Close-up stereo view of the superposition of the N-terminal subdomain of preDnaE (cyan) and exDnaE (purple). (b) Stereo view of the modeled N-terminal catalytic module of Ssp DnaE intein. (e) Close-up stereo view of the superposition of the C-terminal subdomain of preDnaE (cyan) and exDnaE (purple). (f) Stereo view of the modeled C-terminal catalytic module of Ssp DnaE intein. Residues are shown in ball-and-stick representations. The broken lines indicate hydrogen bonds, and bond distances are labeled. (c), (d), (g), (h) and (i) A chemical mechanism proposed for splicing the Ssp DnaE intein. The red arrows indicate the routes of nucleophilic attacks in the splicing pathway. Broken lines indicate hydrogen bonds. The tetrahedral intermediate formed by an N-S acyl rearrangement at Cys1 is not shown.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 353, 1093-1105) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20820635 G.Volkmann, and H.Iwaï (2010).
Protein trans-splicing and its use in structural biology: opportunities and limitations.
  Mol Biosyst, 6, 2110-2121.  
20512791 L.Berrade, Y.Kwon, and J.A.Camarero (2010).
Photomodulation of protein trans-splicing through backbone photocaging of the DnaE split intein.
  Chembiochem, 11, 1368-1372.  
20209535 L.Zhang, N.Xiao, Y.Pan, Y.Zheng, Z.Pan, Z.Luo, X.Xu, and Y.Liu (2010).
Binding and inhibition of copper ions to RecA inteins from Mycobacterium tuberculosis.
  Chemistry, 16, 4297-4306.  
20449740 S.Elleuche, and S.Pöggeler (2010).
Inteins, valuable genetic elements in molecular biology and biotechnology.
  Appl Microbiol Biotechnol, 87, 479-489.  
20495572 S.Frutos, M.Goger, B.Giovani, D.Cowburn, and T.W.Muir (2010).
Branched intermediate formation stimulates peptide bond cleavage in protein splicing.
  Nat Chem Biol, 6, 527-533.  
19365564 A.S.Aranko, S.Züger, E.Buchinger, and H.Iwaï (2009).
In vivo and in vitro protein ligation by naturally occurring and engineered split DnaE inteins.
  PLoS ONE, 4, e5185.  
19541659 G.Amitai, B.P.Callahan, M.J.Stanger, G.Belfort, and M.Belfort (2009).
Modulation of intein activity by its neighboring extein substrates.
  Proc Natl Acad Sci U S A, 106, 11005-11010.  
19597508 J.A.Kritzer, S.Hamamichi, J.M.McCaffery, S.Santagata, T.A.Naumann, K.A.Caldwell, G.A.Caldwell, and S.Lindquist (2009).
Rapid selection of cyclic peptides that reduce alpha-synuclein toxicity in yeast and animal models.
  Nat Chem Biol, 5, 655-663.  
19462022 L.Zhang, Y.Zheng, Z.Xi, Z.Luo, X.Xu, C.Wang, and Y.Liu (2009).
Metal ions binding to recA inteins from Mycobacterium tuberculosis.
  Mol Biosyst, 5, 644-650.  
19541616 S.W.Lockless, and T.W.Muir (2009).
Traceless protein splicing utilizing evolved split inteins.
  Proc Natl Acad Sci U S A, 106, 10999-11004.  
19462417 T.Kamioka, M.Tawa, S.Sohya, T.Yamazaki, and Y.Kuroda (2009).
Improved protein splicing reaction for low solubility protein fragments without insertion of native extein residues.
  Biopolymers, 92, 465-470.  
19630416 Z.Du, P.T.Shemella, Y.Liu, S.A.McCallum, B.Pereira, S.K.Nayak, G.Belfort, M.Belfort, and C.Wang (2009).
Highly conserved histidine plays a dual catalytic role in protein splicing: a pKa shift mechanism.
  J Am Chem Soc, 131, 11581-11589.  
  18767096 M.Vila-Perelló, Y.Hori, M.Ribó, and T.W.Muir (2008).
Activation of protein splicing by protease- or light-triggered O to N acyl migration.
  Angew Chem Int Ed Engl, 47, 7764-7767.  
17586768 M.A.Johnson, M.W.Southworth, T.Herrmann, L.Brace, F.B.Perler, and K.Wüthrich (2007).
NMR structure of a KlbA intein precursor from Methanococcus jannaschii.
  Protein Sci, 16, 1316-1328.
PDB codes: 2jmz 2jnq
17254599 P.Van Roey, B.Pereira, Z.Li, K.Hiraga, M.Belfort, and V.Derbyshire (2007).
Crystallographic and mutational studies of Mycobacterium tuberculosis recA mini-inteins suggest a pivotal role for a highly conserved aspartate residue.
  J Mol Biol, 367, 162-173.
PDB codes: 2imz 2in0 2in8 2in9
16830226 J.Yang, T.V.Henry-Smith, and M.Qi (2006).
Functional analysis of the split Synechocystis DnaE intein in plant tissues by biolistic particle bombardment.
  Transgenic Res, 15, 583-593.  
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.