spacer
spacer

PDBsum entry 2q7d

Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Transferase PDB id
2q7d
Jmol
Contents
Protein chain
337 a.a. *
Ligands
SO4 ×12
ANP ×2
Metals
_MN ×4
Waters ×709
* Residue conservation analysis
PDB id:
2q7d
Name: Transferase
Title: Crystal structure of human inositol 1,3,4-trisphosphate 5/6- (itpk1) in complex with amppnp and mn2+
Structure: Inositol-tetrakisphosphate 1-kinase. Chain: a, b. Fragment: catalytic domain. Synonym: inositol- triphosphate 5/6-kinase, inositol 1,3,4- trisphosphate 5/6-kinase, ins1,3,4, p3, 5/6-kinase. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: itpk1. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.60Å     R-factor:   0.196     R-free:   0.236
Authors: P.P.Chamberlain,S.A.Lesley,G.Spraggon
Key ref:
P.P.Chamberlain et al. (2007). Integration of inositol phosphate signaling pathways via human ITPK1. J Biol Chem, 282, 28117-28125. PubMed id: 17616525 DOI: 10.1074/jbc.M703121200
Date:
06-Jun-07     Release date:   03-Jul-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q13572  (ITPK1_HUMAN) -  Inositol-tetrakisphosphate 1-kinase
Seq:
Struc:
414 a.a.
337 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 1: E.C.2.7.1.134  - Inositol-tetrakisphosphate 1-kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
myo-Inositol Phosphate Metabolism
      Reaction: ATP + 1D-myo-inositol 3,4,5,6-tetrakisphosphate = ADP + 1D-myo-inositol 1,3,4,5,6-pentakisphosphate
ATP
+ 1D-myo-inositol 3,4,5,6-tetrakisphosphate
=
ADP
Bound ligand (Het Group name = ANP)
matches with 81.25% similarity
+ 1D-myo-inositol 1,3,4,5,6-pentakisphosphate
   Enzyme class 2: E.C.2.7.1.159  - Inositol-1,3,4-trisphosphate 5/6-kinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction:
1. ATP + 1D-myo-inositol 1,3,4-trisphosphate = ADP + 1D-myo-inositol 1,3,4,5-tetrakisphosphate
2. ATP + 1D-myo-inositol 1,3,4-trisphosphate = ADP + 1D-myo-inositol 1,3,4,6-tetrakisphosphate
ATP
+ 1D-myo-inositol 1,3,4-trisphosphate
=
ADP
Bound ligand (Het Group name = ANP)
matches with 81.25% similarity
+ 1D-myo-inositol 1,3,4,5-tetrakisphosphate
ATP
+ 1D-myo-inositol 1,3,4-trisphosphate
=
ADP
Bound ligand (Het Group name = ANP)
matches with 81.25% similarity
+ 1D-myo-inositol 1,3,4,6-tetrakisphosphate
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   1 term 
  Biological process     inositol trisphosphate metabolic process   1 term 
  Biochemical function     inositol-1,3,4-trisphosphate 6-kinase activity     6 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M703121200 J Biol Chem 282:28117-28125 (2007)
PubMed id: 17616525  
 
 
Integration of inositol phosphate signaling pathways via human ITPK1.
P.P.Chamberlain, X.Qian, A.R.Stiles, J.Cho, D.H.Jones, S.A.Lesley, E.A.Grabau, S.B.Shears, G.Spraggon.
 
  ABSTRACT  
 
Inositol 1,3,4-trisphosphate 5/6-kinase (ITPK1) is a reversible, poly-specific inositol phosphate kinase that has been implicated as a modifier gene in cystic fibrosis. Upon activation of phospholipase C at the plasma membrane, inositol 1,4,5-trisphosphate enters the cytosol and is inter-converted by an array of kinases and phosphatases into other inositol phosphates with diverse and critical cellular activities. In mammals it has been established that inositol 1,3,4-trisphosphate, produced from inositol 1,4,5-trisphosphate, lies in a branch of the metabolic pathway that is separate from inositol 3,4,5,6-tetrakisphosphate, which inhibits plasma membrane chloride channels. We have determined the molecular mechanism for communication between these two pathways, showing that phosphate is transferred between inositol phosphates via ITPK1-bound nucleotide. Intersubstrate phosphate transfer explains how competing substrates are able to stimulate each others' catalysis by ITPK1. We further show that these features occur in the human protein, but not in plant or protozoan homologues. The high resolution structure of human ITPK1 identifies novel secondary structural features able to impart substrate selectivity and enhance nucleotide binding, thereby promoting intersubstrate phosphate transfer. Our work describes a novel mode of substrate regulation and provides insight into the enzyme evolution of a signaling mechanism from a metabolic role.
 
  Selected figure(s)  
 
Figure 2.
FIGURE 2. Sequential intersubstrate phosphate transfer hypotheses for hITPK1. This graphic shows hypothetical intersubstrate phosphate transfer mechanisms by which levels of Ins(1,3,4)P[3] could regulate the synthesis of Ins(3,4,5,6)P[4]. Panel A shows the two candidate phosphate carriers with enzyme represented as "E" with the transferred phosphate highlighted in red. Panel B expands the nucleotide-mediated phosphate transfer hypothesis in which enzyme-bound nucleotide acts as the phosphate carrier. Unliganded ITPK1 is represented by E; phosphotransferase reactions are indicated by red graphics. The position of the [^32P] group that is transferred between inositol phosphates is shown in red.An asterisk indicates a reaction for which Ins(1,3,4,5)P[4] is also produced at a reduced rate. We do not rule out the possibility that a phosphoenzyme intermediate might also participate in these reactions.
Figure 5.
FIGURE 5. Detail of the hITPK1 inositol phosphate binding pocket. Identical projections for eITPK1 (A) and hITPK1 (B), showing the reduction in inositol phosphate binding site volume and ATP solvent accessibility for hITPK1. Ins(1,3,4)P[3] is shown modeled into the hITPK1 based on structural alignment with eITPK1 and exhibits a steric clash with His-162. A solvent-accessible surface is shown for each molecule. The position of the ATP -phosphate is indicated by " ". Metal ions are shown as green spheres. Panel C is a stereodiagram showing structural superposition of hITPK1 with eITPK1. hITPK1 is shown with blue carbons atoms, with a bound sulfate shown in gold and red. Residues capable of carrying a phosphate that are proximal to the ATP -phosphate are shown in yellow. eITPK1 in complex with Ins(1,3,4)P[3] is shown with orange carbon atoms for protein, magenta carbons for the inositol.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 28117-28125) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19914276 P.W.Majerus, D.B.Wilson, C.Zhang, P.J.Nicholas, and M.P.Wilson (2010).
Expression of inositol 1,3,4-trisphosphate 5/6-kinase (ITPK1) and its role in neural tube defects.
  Adv Enzyme Regul, 50, 365-372.  
19439500 S.B.Shears (2009).
Diphosphoinositol polyphosphates: metabolic messengers?
  Mol Pharmacol, 76, 236-252.  
17943301 A.R.Alcázar-Román, and S.R.Wente (2008).
Inositol polyphosphates: a new frontier for regulating gene expression.
  Chromosoma, 117, 1.  
18474240 A.R.Stiles, X.Qian, S.B.Shears, and E.A.Grabau (2008).
Metabolic and signaling properties of an Itpk gene family in Glycine max.
  FEBS Lett, 582, 1853-1858.  
18951024 J.Mitchell, X.Wang, G.Zhang, M.Gentzsch, D.J.Nelson, and S.B.Shears (2008).
An expanded biological repertoire for Ins(3,4,5,6)P4 through its modulation of ClC-3 function.
  Curr Biol, 18, 1600-1605.  
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.