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PDBsum entry 1e4v
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protein ligands Protein-protein interface(s) links
Transferase(phosphotransferase) PDB id
1e4v

 

 

 

 

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Contents
Protein chains
214 a.a. *
Ligands
AP5 ×2
Waters ×348
* Residue conservation analysis
PDB id:
1e4v
Name: Transferase(phosphotransferase)
Title: Mutant g10v of adenylate kinase from e. Coli, modified in the gly-loop
Structure: Adenylate kinase. Chain: a, b. Synonym: ak,atp-amp transphosphorylase,atp:amp phosphotransferase, adenylate monophosphate kinase. Engineered: yes. Mutation: yes. Other_details: ap5a
Source: Escherichia coli. Organism_taxid: 562. Strain: cv2. Gene: adk, dnaw, plsa, b0474, jw0463. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
1.85Å     R-factor:   0.196    
Authors: C.W.Mueller,G.E.Schulz
Key ref: C.W.Müller and G.E.Schulz (1993). Crystal structures of two mutants of adenylate kinase from Escherichia coli that modify the Gly-loop. Proteins, 15, 42-49. PubMed id: 8451239
Date:
12-Jul-00     Release date:   04-Aug-00    
PROCHECK
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 Headers
 References

Protein chains
P69441  (KAD_ECOLI) -  Adenylate kinase from Escherichia coli (strain K12)
Seq:
Struc: 		214 a.a.
214 a.a.*
Key:    Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.2.7.4.3  - adenylate kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: AMP + ATP = 2 ADP
AMP
 +
ATP
Bound ligand (Het Group name = AP5)
matches with 54.39% similarity 		= 2 × ADP
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
Proteins 15:42-49 (1993)
PubMed id: 8451239  
 
 
Crystal structures of two mutants of adenylate kinase from Escherichia coli that modify the Gly-loop.
C.W.Müller, G.E.Schulz.
 
  ABSTRACT  
 
Two mutants of adenylate kinase from Escherichia coli have been crystallized and analyzed by X-ray diffraction at resolutions of 3.4 and 2.4 A, respectively. These mutants are Pro-9-->Leu and Gly-10-->Val. They were selected for their positions in the highly conserved Gly-loop forming a giant anion hole for the beta-phosphate of ATP (GTP) in adenylate kinases, H-ras-p21, and other nucleotide-binding proteins. Mutants at these positions of H-ras-p21 cause cancer. In adenylate kinase these mutations cause smallish changes at the active site. Relating the structural changes to the known changes in catalysis indicates that these mutants hinder the induced-fit movements. As a side result we find that mutant Pro-9-->Leu and wild-type form one very similar crystal packing contact that is crystallographic in one case and noncrystallographic in the other, while all other packing contacts and the space groups are quite at variance.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19751742 O.Beckstein, E.J.Denning, J.R.Perilla, and T.B.Woolf (2009).
Zipping and unzipping of adenylate kinase: atomistic insights into the ensemble of open<-->closed transitions.
  J Mol Biol, 394, 160-176.  
19130895 R.Liu, A.L.Ström, J.Zhai, J.Gal, S.Bao, W.Gong, and H.Zhu (2009).
Enzymatically inactive adenylate kinase 4 interacts with mitochondrial ADP/ATP translocase.
  Int J Biochem Cell Biol, 41, 1371-1380.  
18676657 N.Kantarci-Carsibasi, T.Haliloglu, and P.Doruker (2008).
Conformational transition pathways explored by Monte Carlo simulation integrated with collective modes.
  Biophys J, 95, 5862-5873.  
18000050 K.Arora, and C.L.Brooks (2007).
Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism.
  Proc Natl Acad Sci U S A, 104, 18496-18501.  
17623846 T.Prakash, K.S.Sandhu, N.K.Singh, Y.Bhasin, C.Ramakrishnan, and S.K.Brahmachari (2007).
Structural assessment of glycyl mutations in invariantly conserved motifs.
  Proteins, 69, 617-632.  
15521058 H.Krishnamurthy, H.Lou, A.Kimple, C.Vieille, and R.I.Cukier (2005).
Associative mechanism for phosphoryl transfer: a molecular dynamics simulation of Escherichia coli adenylate kinase complexed with its substrates.
  Proteins, 58, 88.  
12527760 S.S.Krishna, I.Majumdar, and N.V.Grishin (2003).
Structural classification of zinc fingers: survey and summary.
  Nucleic Acids Res, 31, 532-550.  
11325743 S.Kumar, Y.Y.Sham, C.J.Tsai, and R.Nussinov (2001).
Protein folding and function: the N-terminal fragment in adenylate kinase.
  Biophys J, 80, 2439-2454.  
11369852 T.Krell, J.Maclean, D.J.Boam, A.Cooper, M.Resmini, K.Brocklehurst, S.M.Kelly, N.C.Price, A.J.Lapthorn, and J.R.Coggins (2001).
Biochemical and X-ray crystallographic studies on shikimate kinase: the important structural role of the P-loop lysine.
  Protein Sci, 10, 1137-1149.
PDB code: 1e6c
  7670369 U.Abele, and G.E.Schulz (1995).
High-resolution structures of adenylate kinase from yeast ligated with inhibitor Ap5A, showing the pathway of phosphoryl transfer.
  Protein Sci, 4, 1262-1271.
PDB codes: 1aky 2aky
8026505 E.Schiltz, S.Burger, R.Grafmüller, W.R.Deppert, W.Haehnel, and E.Wagner (1994).
Primary structure of maize chloroplast adenylate kinase.
  Eur J Biochem, 222, 949-954.  
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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