4AXC - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   INOSITOL 1,3,4,5,6-PENTAKISPHOSPHATE 2-KINASE APO FORM

Authors :   J. I Banos-Sanz, J. Sanz-Aparicio, B. Gonzalez

Date :   12 Jun 12 (Deposition) - 04 Jul 12 (Release) - 05 Sep 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.25

Chains :   Asym./Biol. Unit : A

Keywords :   Transferase, Phytic Acid, Protein Kinase, Inositide Signalling (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. I. Banos-Sanz, J. Sanz-Aparicio, H. Whitfield, C. Hamilton, C. A. Brearley, B. Gonzalez
Conformational Changes Undergone By Inositol 1, 3, 4, 5, 6-Pentakisphosphate 2-Kinase Upon Substrate Binding: The Role Of N-Lobe And Enantiomeric Substrate Preference
J. Biol. Chem. V. 287 29237 2012
PubMed-ID: 22745128 | Reference-DOI: 10.1074/JBC.M112.363671

Molecule 1 - INOSITOL-PENTAKISPHOSPHATE 2-KINASE
	Chains	:	A
	EC Number	:	2.7.1.158
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	ROSETTA PLYSS
	Expression System Vector	:	PKLSLT
	Organism Common	:	THALE CRESS
	Organism Scientific	:	ARABIDOPSIS THALIANA
	Organism Taxid	:	3702
	Synonym	:	INOSITOL-1,3,4,5,6-PENTAKISPHOSPHATE 2-KINASE, INS(1,3,4,5,6)P5 2-KINASE, ATIPK1, INSP5 2-KINASE

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 6)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	SO4	4	Ligand/Ion	SULFATE ION
3	ZN	1	Ligand/Ion	ZINC ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:320 , CYS A:330 , CYS A:333 , HIS A:346	BINDING SITE FOR RESIDUE ZN A1435
2	AC2	SOFTWARE	GLY A:20 , LYS A:43 , ALA A:133 , ALA A:134 , LYS A:309	BINDING SITE FOR RESIDUE SO4 A1436
3	AC3	SOFTWARE	LYS A:168 , LYS A:200 , ASN A:238 , GLU A:255 , HOH A:2047	BINDING SITE FOR RESIDUE SO4 A1437
4	AC4	SOFTWARE	GLY A:19 , GLY A:20 , ALA A:21 , ASN A:22	BINDING SITE FOR RESIDUE SO4 A1438
5	AC5	SOFTWARE	SER A:374 , PHE A:375 , GLN A:376 , ASP A:400 , LYS A:402	BINDING SITE FOR RESIDUE SO4 A1439

(no "SS Bond" information available for 4AXC)

(no "Cis Peptide Bond" information available for 4AXC)

(no "SAP(SNP)/Variant" information available for 4AXC)

(no "PROSITE Motif" information available for 4AXC)

(no "Exon" information available for 4AXC)

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:394
 aligned with IPPK_ARATH | Q93YN9 from UniProtKB/Swiss-Prot  Length:451

    Alignment length:432
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432  
           IPPK_ARATH     3 MILEEKDASDWIYRGEGGANLVLAYAGSSPLFVGKVIRIQKARRNDKAIKNANGVVSVLTSDEQHLWRENNELISSPNKEVLEQRYVKNVIIPLLGPKHVDAGVRVSVSKEFLECVDKKVTKQRPLWRVNAANVDTSHDSALILNDHSLFSQGISSGGDCISVEIKPKCGFLPTSRFIGKENMLKTSVSRFKMHQLLKLEYNEISEESEYDPLDLFSGSKESVLEAIKALYSTPQNNFRVFLNGSLILGGSGESTGRTSPEIGYAFEDALKGFIQSEDGHRTECFLQLVSDAVYGSGVLDRLLEIQKLDKLDIEGAIHSYYDLINQPCPICKEGKPLEAELSLHALPLDESLKIVKEYLIAATAKDCSIMISFQSRNAWDSEPSGDYVSLKPTNQTFDYKVHFIDLSLKPLKRMESYYKLDKKIISFYNRKQ 434
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhh.eeeeee...eeeeee.........eeeeee....--------------.hhhhhhhhh.hhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhh..........eeeeee....----------.eeeee.............hhhhhhhhh.hhhhhhhhhhhhh.........hhhhhh..hhhhhhhhhhhhhhh....eeeee..eeee..........hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh.......--------.......hhhhhhhhhhhhhhhhhhhhheeeeeeeee...------.eeee....eeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4axc A   3 MILEEKDASDWIYRGEGGANLVLAYAGSSPLFVGKVIRIQKARR--------------LTSDEQHLWRENNELISSPNKEVLEQRYVQNVIIPLLGPKHVDAGVRVSVSKEFLECVDKKVTKQRPLARVNAANVDTSHDSALILNDHSL----------CISVEIKPKCGFLPTSRFIGKENMLKTSVSRFKMHQLLKLEYIEISEESEYDPLDLFSGSKERVLEAIKALYSTPQNNFRVFLNGSLILGGSGESTGRTSPEIGYAFEDALKGFIQSEDGHRTECFLQLVSDAVYGSGVLDRLLEIQKLDKLDIEGAIHCYYDIINQPCPIC--------ELSLHALPLDESLKIVKEYLIAATAKDCSIMISFQSRNAW------DYVSLKPTNQTFDYKVHFIDLSLKPLKRMESYYKLDKKIISFYNRKQ 434
                                    12        22        32        42   |     -        62        72        82        92       102       112       122       132       142        |-       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332|      342       352       362       372        |-     | 392       402       412       422       432  
                                                                      46             61                                                                                       151        162                                                                                                                                                                        333      342                                    381    388

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 4AXC)

(no "CATH Domain" information available for 4AXC)

(no "Pfam Domain" information available for 4AXC)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (IPPK_ARATH | Q93YN9)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0035299	inositol pentakisphosphate 2-kinase activity	Catalysis of the reaction: 1D-myo-inositol 1,3,4,5,6-pentakisphosphate + ATP = 1D-myo-inositol hexakisphosphate + ADP + 2 H(+).
	GO:0032942	inositol tetrakisphosphate 2-kinase activity	Catalysis of the reaction: 1D-myo-inositol tetrakisphosphate + ATP = 1D-myo-inositol pentakisphosphate (containing 2-phosphate) + ADP.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0030643	cellular phosphate ion homeostasis	Any process involved in the maintenance of an internal steady state of phosphate ions at the level of a cell.
	GO:0042742	defense response to bacterium	Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
	GO:0050832	defense response to fungus	Reactions triggered in response to the presence of a fungus that act to protect the cell or organism.
	GO:0051607	defense response to virus	Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
	GO:0040007	growth	The increase in size or mass of an entire organism, a part of an organism or a cell.
	GO:0048527	lateral root development	The process whose specific outcome is the progression of the lateral root over time, from its formation to the mature structure. A lateral root is one formed from pericycle cells located on the xylem radius of the root, as opposed to the initiation of the main root from the embryo proper.
	GO:0010264	myo-inositol hexakisphosphate biosynthetic process	The chemical reactions and pathways resulting in the formation of phytic acid, myo-inositol hexakisphosphate, a regulator of intracellular signaling, a highly abundant animal anti-nutrient and a phosphate and mineral storage compound in plant seeds.
	GO:0055062	phosphate ion homeostasis	Any process involved in the maintenance of an internal steady state of phosphate ions within an organism or cell.
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4axc)

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	4axc
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	2.7.1.158
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UniProtKB/Swiss-Prot
	IPPK_ARATH \| Q93YN9	:	2xal 2xam 2xan 2xao 2xar 3uds 3udt 3udz 4aqk 4axd 4axe 4axf 4lv7

2xal	LEAD DERIVATIVE OF INOSITOL 1,3,4,5,6- PENTAKISPHOSPHATE 2-KINASE FROM A. THALIANA IN COMPLEX WITH ADP AND IP6.
2xam	INOSITOL 1,3,4,5,6-PENTAKISPHOSPHATE 2-KINASE FROM A. THALIANA IN COMPLEX WITH ADP AND IP6.
2xan	INOSITOL 1,3,4,5,6-PENTAKISPHOSPHATE 2-KINASE FROM A. THALIANA IN COMPLEX WITH AMP PNP AND IP5
2xao	INOSITOL 1,3,4,5,6-PENTAKISPHOSPHATE 2-KINASE FROM A. THALIANA IN COMPLEX WITH IP5
2xar	INOSITOL 1,3,4,5,6-PENTAKISPHOSPHATE 2-KINASE FROM A. THALIANA IN COMPLEX WITH IP6.
4aqk	INOSITOL 1,3,4,5,6-PENTAKISPHOSPHATE 2-KINASE IN COMPLEX WITH ADP AND IP6
4axd	INOSITOL 1,3,4,5,6-PENTAKISPHOSPHATE 2-KINASE IN COMPLEX WITH AMPPNP
4axe	INOSITOL 1,3,4,5,6-PENTAKISPHOSPHATE 2-KINASE IN COMPLEX WITH ADP
4axf	INSP5 2-K IN COMPLEX WITH INS(3,4,5,6)P4 PLUS AMPPNP

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (18, 18)

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