3UDT - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   INOSITOL 1,3,4,5,6-PENTAKISPHOSPHATE 2-KINASE FROM A. THALIANA IN COMPLEX WITH ADP AND IP5.

Authors :   V. Gosein, T. -F. Leung, O. Krajden, G. J. Miller

Date :   28 Oct 11 (Deposition) - 14 Mar 12 (Release) - 09 May 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.10

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A,B  (1x)

Keywords :   Transferase, Inositol, Ipk, Ins5P 2-K, Atipk1, Ip5 2-K, Polyphosphate Kinase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. Gosein, T. F. Leung, O. Krajden, G. J. Miller
Inositol Phosphate-Induced Stabilization Of Inositol 1, 3, 4, 5, 6-Pentakisphosphate 2-Kinase And Its Role In Substrate Specificity.
Protein Sci. V. 21 737 2012
PubMed-ID: 22362712 | Reference-DOI: 10.1002/PRO.2049

Molecule 1 - INOSITOL-PENTAKISPHOSPHATE 2-KINASE
	Chains	:	A, B
	EC Number	:	2.7.1.158
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21-AI
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	AT5G42810, IPK1, MJB21.19
	Organism Common	:	MOUSE-EAR CRESS,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	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 8)

No.	Name	Count	Type	Full Name
1	5MY	2	Ligand/Ion	MYO-INOSITOL-(1,3,4,5,6)-PENTAKISPHOSPHATE
2	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
3	MG	2	Ligand/Ion	MAGNESIUM ION
4	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	5MY	1	Ligand/Ion	MYO-INOSITOL-(1,3,4,5,6)-PENTAKISPHOSPHATE
2	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	5MY	1	Ligand/Ion	MYO-INOSITOL-(1,3,4,5,6)-PENTAKISPHOSPHATE
2	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (2, 4)

No.	Name	Count	Type	Full Name
1	5MY	2	Ligand/Ion	MYO-INOSITOL-(1,3,4,5,6)-PENTAKISPHOSPHATE
2	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:20 , ALA A:21 , ARG A:45 , ARG A:130 , LYS A:168 , LYS A:170 , HIS A:196 , LYS A:200 , ASN A:238 , ASP A:368 , LYS A:411 , ARG A:415 , TYR A:419	BINDING SITE FOR RESIDUE 5MY A 911
2	AC2	SOFTWARE	ARG A:16 , GLU A:18 , GLY A:19 , GLY A:20 , ALA A:21 , ASN A:22 , VAL A:24 , ARG A:40 , ASN A:147 , HIS A:149 , GLU A:166 , MET A:372 , ASP A:407 , MG A:913	BINDING SITE FOR RESIDUE ADP A 912
3	AC3	SOFTWARE	ASP A:368 , SER A:370 , ASP A:407 , ADP A:912	BINDING SITE FOR RESIDUE MG A 913
4	AC4	SOFTWARE	HIS A:320 , CYS A:330 , CYS A:333 , HIS A:346	BINDING SITE FOR RESIDUE ZN A 914
5	AC5	SOFTWARE	GLY B:20 , ALA B:21 , ARG B:45 , ARG B:130 , LYS B:168 , LYS B:170 , HIS B:196 , LYS B:200 , ASN B:238 , ASP B:368 , LYS B:411 , ARG B:415 , TYR B:419	BINDING SITE FOR RESIDUE 5MY B 911
6	AC6	SOFTWARE	ARG B:16 , GLU B:18 , GLY B:19 , GLY B:20 , ALA B:21 , ASN B:22 , VAL B:24 , VAL B:38 , ARG B:40 , LEU B:146 , ASN B:147 , HIS B:149 , GLU B:166 , ARG B:241 , MET B:372 , ASP B:407 , MG B:913	BINDING SITE FOR RESIDUE ADP B 912
7	AC7	SOFTWARE	SER B:370 , ASP B:407 , ADP B:912	BINDING SITE FOR RESIDUE MG B 913
8	AC8	SOFTWARE	HIS B:320 , CYS B:330 , CYS B:333 , HIS B:346	BINDING SITE FOR RESIDUE ZN B 914

(no "SS Bond" information available for 3UDT)

(no "Cis Peptide Bond" information available for 3UDT)

(no "SAP(SNP)/Variant" information available for 3UDT)

(no "PROSITE Motif" information available for 3UDT)

(no "Exon" information available for 3UDT)

Asymmetric 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
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:385
 aligned with IPPK_ARATH | Q93YN9 from UniProtKB/Swiss-Prot  Length:451

    Alignment length:431
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434 
           IPPK_ARATH     5 LEEKDASDWIYRGEGGANLVLAYAGSSPLFVGKVIRIQKARRNDKAIKNANGVVSVLTSDEQHLWRENNELISSPNKEVLEQRYVKNVIIPLLGPKHVDAGVRVSVSKEFLECVDKKVTKQRPLWRVNAANVDTSHDSALILNDHSLFSQGISSGGDCISVEIKPKCGFLPTSRFIGKENMLKTSVSRFKMHQLLKLEYNEISEESEYDPLDLFSGSKESVLEAIKALYSTPQNNFRVFLNGSLILGGSGESTGRTSPEIGYAFEDALKGFIQSEDGHRTECFLQLVSDAVYGSGVLDRLLEIQKLDKLDIEGAIHSYYDLINQPCPICKEGKPLEAELSLHALPLDESLKIVKEYLIAATAKDCSIMISFQSRNAWDSEPSGDYVSLKPTNQTFDYKVHFIDLSLKPLKRMESYYKLDKKIISFYNRKQK 435
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh.eeeeee...eeeeee.........eeeeeeeee.-------------..hhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhh.......eeee.hhhhhhhhhhhhh...hhhhhhheee.....eeeeee.....--------..eeeee.......................hhhhhhhhhhhhh.........hhhhhh..hhhhhhhhhhhhhhh....eeeee..eeee..........hhhhhhhhhhhhh.....----.hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh.......----------hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee---------.eee.--.....eeeeeeee.......hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3udt A   5 LEEKDASDWIYRGEGGANLVLAYAGSSPLFVGKVIRIQKARR-------------VLTSDEQHLWRENNELISSPNKEVLEQRYVQNVIIPLLGPKHVDAGVRVSVSKEFLECVDKKVTKQRPLWRVNAANVDTSHDSALILNDHSLF--------DCISVEIKPKCGFLPTSRFIGKENILKTSVSRFKMHQLLKLEYIEISEESEYDPLDLFSGSKERVLEAIKALYSTPQNNFRVFLNGSLILGGSGESTGRTSPEIGYAFEDALKGFIQS----RTECFLQLVSDAVYGSGVLDRLLEIQKLDKLDIEGAIHCYYDIINQPCPIC----------SLHALPLDESLKIVKEYLIAATAKDCSIMISFQS---------GDYVS--PTNQTFDYKVHFIDLSLKPLKRMESYYKLDKKIISFYNRKQK 435
                                    14        24        34        44 |       -     |  64        74        84        94       104       114       124       134       144       | -      |164       174       184       194       204       214       224       234       244       254       264       274   |   284       294       304       314       324        |-       344       354       364       374  |      -  |   |394       404       414       424       434 
                                                                    46            60                                                                                         152      161                                                                                                                  278  283                                               333        344                              377       387 391  |                                         
                                                                                                                                                                                                                                                                                                                                                                                                                               394

Chain B from PDB  Type:PROTEIN  Length:385
 aligned with IPPK_ARATH | Q93YN9 from UniProtKB/Swiss-Prot  Length:451

    Alignment length:432
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434  
           IPPK_ARATH     5 LEEKDASDWIYRGEGGANLVLAYAGSSPLFVGKVIRIQKARRNDKAIKNANGVVSVLTSDEQHLWRENNELISSPNKEVLEQRYVKNVIIPLLGPKHVDAGVRVSVSKEFLECVDKKVTKQRPLWRVNAANVDTSHDSALILNDHSLFSQGISSGGDCISVEIKPKCGFLPTSRFIGKENMLKTSVSRFKMHQLLKLEYNEISEESEYDPLDLFSGSKESVLEAIKALYSTPQNNFRVFLNGSLILGGSGESTGRTSPEIGYAFEDALKGFIQSEDGHRTECFLQLVSDAVYGSGVLDRLLEIQKLDKLDIEGAIHSYYDLINQPCPICKEGKPLEAELSLHALPLDESLKIVKEYLIAATAKDCSIMISFQSRNAWDSEPSGDYVSLKPTNQTFDYKVHFIDLSLKPLKRMESYYKLDKKIISFYNRKQKA 436
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhh.eeeeee...eeeeee.........eeeeeeeee.-------------..hhhhhhhh..hhhhhhh.hhhhhhhhhhhhhhhhhhh.......eeee.hhhhhhhhhhhhhhhhhhhhhhheee.....eeeeee.....--------..eeeee.............hhhhh.....hhhhhhhhhhhhh.........hhhhhh..hhhhhhhhhhhhhhh....eeeee..eeee..........hhhhhhhhhhhhh.....----.hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh.......----------hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee----------.ee.--.....eeeeeeee.......hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3udt B   5 LEEKDASDWIYRGEGGANLVLAYAGSSPLFVGKVIRIQKARR-------------VLTSDEQHLWRENNELISSPNKEVLEQRYVQNVIIPLLGPKHVDAGVRVSVSKEFLECVDKKVTKQRPLWRVNAANVDTSHDSALILNDHSLF--------DCISVEIKPKCGFLPTSRFIGKENILKTSVSRFKMHQLLKLEYIEISEESEYDPLDLFSGSKERVLEAIKALYSTPQNNFRVFLNGSLILGGSGESTGRTSPEIGYAFEDALKGFIQS----RTECFLQLVSDAVYGSGVLDRLLEIQKLDKLDIEGAIHCYYDIINQPCPIC----------SLHALPLDESLKIVKEYLIAATAKDCSIMISFQS----------DYVS--PTNQTFDYKVHFIDLSLKPLKRMESYYKLDKKIISFYNRKQKA 436
                                    14        24        34        44 |       -     |  64        74        84        94       104       114       124       134       144       | -      |164       174       184       194       204       214       224       234       244       254       264       274   |   284       294       304       314       324        |-       344       354       364       374  |      -   |  |394       404       414       424       434  
                                                                    46            60                                                                                         152      161                                                                                                                  278  283                                               333        344                              377        388  |  |                                          
                                                                                                                                                                                                                                                                                                                                                                                                                            391  |                                          
                                                                                                                                                                                                                                                                                                                                                                                                                               394

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	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 3UDT)

(no "CATH Domain" information available for 3UDT)

(no "Pfam Domain" information available for 3UDT)

Asymmetric Unit(hide GO term definitions)

Chain A,B (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.

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3uds	INOSITOL 1,3,4,5,6-PENTAKISPHOSPHATE 2-KINASE FROM A. THALIANA IN COMPLEX WITH ADP

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Ligands, Modified Residues, Ions (4, 8)

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