2XAL - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   LEAD DERIVATIVE OF INOSITOL 1,3,4,5,6-PENTAKISPHOSPHATE 2-KINASE FROM A. THALIANA IN COMPLEX WITH ADP AND IP6.

Authors :   B. Gonzalez, J. I. Banos-Sanz, M. Villate, C. A. Brearley, J. Sanz-Apa

Date :   31 Mar 10 (Deposition) - 19 May 10 (Release) - 29 Feb 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.20

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

Keywords :   Transferase, Inositol Polyphosphate Kinase, Phytic Acid Synthase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Gonzalez, J. I. Banos-Sanz, M. Villate, C. A. Brearley, J. Sanz-Aparicio
Inositol 1, 3, 4, 5, 6-Pentakisphosphate 2-Kinase Is A Distant Ipk Member With A Singular Inositide Binding Site For Axial 2-Oh Recognition.
Proc. Natl. Acad. Sci. Usa V. 107 9608 2010
PubMed-ID: 20453199 | Reference-DOI: 10.1073/PNAS.0912979107

Molecule 1 - INOSITOL-PENTAKISPHOSPHATE 2-KINASE
	Chains	:	A, B
	EC Number	:	2.7.1.158
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PKLSLT
	Expression System Strain	:	ROSETTA(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	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, INSP5 2-KINASE, ATIPK1

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 10)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	I6P	2	Ligand/Ion	INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE
3	PB	4	Ligand/Ion	LEAD (II) ION
4	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	I6P	1	Ligand/Ion	INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE
3	PB	-1	Ligand/Ion	LEAD (II) ION
4	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	I6P	1	Ligand/Ion	INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE
3	PB	-1	Ligand/Ion	LEAD (II) ION
4	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLY A:19 , 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 , ASP A:407 , LYS A:411 , ARG A:415 , TYR A:419 , PB A:501 , PB A:502 , ADP A:600	BINDING SITE FOR RESIDUE I6P A 500
02	AC2	SOFTWARE	ASP A:407 , I6P A:500 , ADP A:600	BINDING SITE FOR RESIDUE PB A 501
03	AC3	SOFTWARE	ASP A:407 , SER A:409 , I6P A:500 , ADP A:600	BINDING SITE FOR RESIDUE PB A 502
04	AC4	SOFTWARE	GLY A:19 , GLY A:20 , ALA A:21 , ASN A:22 , VAL A:24 , ARG A:40 , ASN A:147 , ASP A:148 , HIS A:149 , GLU A:166 , ARG A:241 , PHE A:243 , MET A:372 , ASP A:407 , I6P A:500 , PB A:501 , PB A:502	BINDING SITE FOR RESIDUE ADP A 600
05	AC5	SOFTWARE	HIS A:320 , CYS A:330 , CYS A:333 , HIS A:346	BINDING SITE FOR RESIDUE ZN A 700
06	AC6	SOFTWARE	GLY B:19 , GLY B:20 , ARG B:45 , ARG B:130 , LYS B:168 , LYS B:170 , HIS B:196 , LYS B:200 , ASN B:238 , ASP B:368 , ASP B:407 , LYS B:411 , ARG B:415 , TYR B:419 , PB B:503 , PB B:504 , ADP B:600	BINDING SITE FOR RESIDUE I6P B 500
07	AC7	SOFTWARE	ASP B:407 , I6P B:500 , ADP B:600	BINDING SITE FOR RESIDUE PB B 503
08	AC8	SOFTWARE	ASP B:407 , SER B:409 , I6P B:500 , ADP B:600	BINDING SITE FOR RESIDUE PB B 504
09	AC9	SOFTWARE	GLY B:19 , GLY B:20 , ALA B:21 , ASN B:22 , VAL B:24 , VAL B:38 , ARG B:40 , ASN B:147 , ASP B:148 , HIS B:149 , GLU B:166 , MET B:372 , ILE B:406 , ASP B:407 , I6P B:500 , PB B:503 , PB B:504	BINDING SITE FOR RESIDUE ADP B 600
10	BC1	SOFTWARE	HIS B:320 , CYS B:330 , CYS B:333 , HIS B:346	BINDING SITE FOR RESIDUE ZN B 700

Asymmetric Unit

No.	Residues
1	B:330	-	B:333

(no "Cis Peptide Bond" information available for 2XAL)

(no "SAP(SNP)/Variant" information available for 2XAL)

(no "PROSITE Motif" information available for 2XAL)

(no "Exon" information available for 2XAL)

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:420
 aligned with IPPK_ARATH | Q93YN9 from UniProtKB/Swiss-Prot  Length:451

    Alignment length:435
                                    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 MILEEKDASDWIYRGEGGANLVLAYAGSSPLFVGKVIRIQKARRNDKAIKNANGVVSVLTSDEQHLWRENNELISSPNKEVLEQRYVKNVIIPLLGPKHVDAGVRVSVSKEFLECVDKKVTKQRPLWRVNAANVDTSHDSALILNDHSLFSQGISSGGDCISVEIKPKCGFLPTSRFIGKENMLKTSVSRFKMHQLLKLEYNEISEESEYDPLDLFSGSKESVLEAIKALYSTPQNNFRVFLNGSLILGGSGESTGRTSPEIGYAFEDALKGFIQSEDGHRTECFLQLVSDAVYGSGVLDRLLEIQKLDKLDIEGAIHSYYDLINQPCPICKEGKPLEAELSLHALPLDESLKIVKEYLIAATAKDCSIMISFQSRNAWDSEPSGDYVSLKPTNQTFDYKVHFIDLSLKPLKRMESYYKLDKKIISFYNRKQKAE 437
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhh.eeeeee...eeeeee.........eeeeeeeee....---------...hhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhh.......eeeeehhhhhhhhhhhhhh..hhhhhhheee.....eeeeee...............eeeee................hhhhhh.hhhhhhhhhhhhh.........hhhhhhh.hhhhhhhhhhhhhhh....eeeee..eeee..........hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh.........------..hhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeee...........eeee....eeeeeeeeee.......hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xal A   3 MILEEKDASDWIYRGEGGANLVLAYAGSSPLFVGKVIRIQKARRNDK---------SVLTSDEQHLWRENNELISSPNKEVLEQRYVQNVIIPLLGPKHVDAGVRVSVSKEFLECVDKKVTKQRPLWRVNAANVDTSHDSALILNDHSLFSQGITSGGDCISVEIKPKCGFLPTSRFIGKENMLKTSVSRFKMHQLLKLEYIEISEESEYDPLDLFSGSKERVLEAIKALYSTPQNNFRVFLNGSLILGGSGESTGRTSPEIGYAFEDALKGFIQSEDGHRTECFLQLVSDAVYGSGVLDRLLEIQKLDKLDIEGAIHCYYDIINQPCPICKE------ELSLHALPLDESLKIVKEYLIAATAKDCSIMISFQSRNAWDSEPSGDYVSLKPTNQTFDYKVHFIDLSLKPLKRMESYYKLDKKIISFYNRKQKAE 437
                                    12        22        32        42      |  -      | 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     
                                                                         49        59                                                                                                                                                                                                                                                                                 335    342

Chain B from PDB  Type:PROTEIN  Length:425
 aligned with IPPK_ARATH | Q93YN9 from UniProtKB/Swiss-Prot  Length:451

    Alignment length:438
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430        
           IPPK_ARATH     1 MEMILEEKDASDWIYRGEGGANLVLAYAGSSPLFVGKVIRIQKARRNDKAIKNANGVVSVLTSDEQHLWRENNELISSPNKEVLEQRYVKNVIIPLLGPKHVDAGVRVSVSKEFLECVDKKVTKQRPLWRVNAANVDTSHDSALILNDHSLFSQGISSGGDCISVEIKPKCGFLPTSRFIGKENMLKTSVSRFKMHQLLKLEYNEISEESEYDPLDLFSGSKESVLEAIKALYSTPQNNFRVFLNGSLILGGSGESTGRTSPEIGYAFEDALKGFIQSEDGHRTECFLQLVSDAVYGSGVLDRLLEIQKLDKLDIEGAIHSYYDLINQPCPICKEGKPLEAELSLHALPLDESLKIVKEYLIAATAKDCSIMISFQSRNAWDSEPSGDYVSLKPTNQTFDYKVHFIDLSLKPLKRMESYYKLDKKIISFYNRKQKAEN 438
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) --------------Ins_P5_2-kin-2xalB01 B:15-426                                                                                                                                                                                                                                                                                                                                                                                               ------------ Pfam domains (1)
           Pfam domains (2) --------------Ins_P5_2-kin-2xalB02 B:15-426                                                                                                                                                                                                                                                                                                                                                                                               ------------ Pfam domains (2)
         Sec.struct. author ...eehhhhhh.eeeeee...eeeeee.........eeeeeeeee.hhh....---.....hhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhh.......eeeeehhhhhhhhhhhhhh..hhhhhhheee.....eeeeee.....--------.eeeeee..............hhhhhhhh.hhhhhhhhhhhhh.........hhhhhhh.hhhhhhhhhhhhhhh....eeeee..eeee..........hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhheeeeeeee...--......eeee....eeeeeeeeee.......hhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2xal B   1 MEMILEEKDASDWIYRGEGGANLVLAYAGSSPLFVGKVIRIQKARRNDKAIKN---VVSVLTSDEQHLWRENNELISSPNKEVLEQRYVQNVIIPLLGPKHVDAGVRVSVSKEFLECVDKKVTKQRPLWRVNAANVDTSHDSALILNDHSLF--------DCISVEIKPKCGFLPTSRFIGKENMLKTSVSRFKMHQLLKLEYIEISEESEYDPLDLFSGSKERVLEAIKALYSTPQNNFRVFLNGSLILGGSGESTGRTSPEIGYAFEDALKGFIQSEDGHRTECFLQLVSDAVYGSGVLDRLLEIQKLDKLDIEGAIHCYYDIINQPCPICKEGRPLEAELSLHALPLDESLKIVKEYLIAATAKDCSIMISFQSRNA--SEPSGDYVSLKPTNQTFDYKVHFIDLSLKPLKRMESYYKLDKKIISFYNRKQKAEN 438
                                    10        20        30        40        50  |   | 60        70        80        90       100       110       120       130       140       150 |       -|      170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380  |    390       400       410       420       430        
                                                                               53  57                                                                                            152      161                                                                                                                                                                                                                        380  |                                                       
                                                                                                                                                                                                                                                                                                                                                                                                                        383

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 2XAL)

(no "CATH Domain" information available for 2XAL)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Ins_P5_2-kin] (4)

Family: Ins_P5_2-kin (4)

Arabidopsis thaliana (Mouse-ear cress) (4)

1a	Ins_P5_2-kin-2xalB01	B:15-426
1b	Ins_P5_2-kin-2xalB02	B:15-426

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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	Ligands, Modified Residues, Ions
		ADP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2xal)

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

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.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 10)

Sites (10, 10)

SS Bonds (1, 1)

Cis Peptide Bonds (0, 0)

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