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(-) Description

Title :  CRYSTAL STRUCTURE OF INOSITOL 1,3,4,5,6-PENTAKISPHOSPHATE 2-KINASE E82C/S142C
 
Authors :  V. Gosein, G. J. Miller
Date :  26 Jul 13  (Deposition) - 06 Nov 13  (Release) - 06 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Transferase, Ipk, Ins5P 2-K, Atipk1, Ip5 2-K, Inositol Phosphorylation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Gosein, G. J. Miller
Conformational Stability Of Ipk1 Dictates Its Substrate Selectivity
J. Biol. Chem. 2013
PubMed: search  |  Reference-DOI: 10.1074/JBC.M113.512731

(-) Compounds

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
    Mutation: YES
    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

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric Unit (4, 8)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2IHP2Ligand/IonINOSITOL HEXAKISPHOSPHATE
3MG2Ligand/IonMAGNESIUM ION
4ZN2Ligand/IonZINC ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2IHP1Ligand/IonINOSITOL HEXAKISPHOSPHATE
3MG-1Ligand/IonMAGNESIUM ION
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2IHP1Ligand/IonINOSITOL HEXAKISPHOSPHATE
3MG-1Ligand/IonMAGNESIUM ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY 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 , ADP A:502 , MG A:503BINDING SITE FOR RESIDUE IHP A 501
2AC2SOFTWAREGLY A:17 , GLY A:19 , GLY A:20 , ALA A:21 , ASN A:22 , VAL A:24 , VAL A:38 , ARG A:40 , ASN A:147 , ASP A:148 , HIS A:149 , GLU A:166 , ARG A:241 , PHE A:243 , MET A:372 , ILE A:406 , ASP A:407 , IHP A:501 , MG A:503BINDING SITE FOR RESIDUE ADP A 502
3AC3SOFTWAREARG A:40 , ASP A:407 , SER A:409 , IHP A:501 , ADP A:502BINDING SITE FOR RESIDUE MG A 503
4AC4SOFTWAREHIS A:320 , CYS A:330 , CYS A:333 , HIS A:346BINDING SITE FOR RESIDUE ZN A 504
5AC5SOFTWAREGLY B:19 , GLY B:20 , ALA B:21 , 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 , ADP B:502 , MG B:503BINDING SITE FOR RESIDUE IHP B 501
6AC6SOFTWAREARG B:16 , GLY B:17 , GLU B:18 , GLY B:19 , GLY B:20 , ALA B:21 , ASN B:22 , VAL B:24 , ARG B:40 , ASN B:147 , ASP B:148 , HIS B:149 , GLU B:166 , ARG B:241 , ASP B:407 , IHP B:501 , MG B:503BINDING SITE FOR RESIDUE ADP B 502
7AC7SOFTWAREGLY B:19 , ASP B:407 , IHP B:501 , ADP B:502BINDING SITE FOR RESIDUE MG B 503
8AC8SOFTWAREHIS B:320 , CYS B:330 , CYS B:333 , HIS B:346BINDING SITE FOR RESIDUE ZN B 504

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:82 -A:142
2B:82 -B:142

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4LV7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4LV7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4LV7)

(-) Exons   (0, 0)

(no "Exon" information available for 4LV7)

(-) Sequences/Alignments

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:390
                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eehhhhhh.eeeeee...eeeeee.........eeeeeeeee....hhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhh.......eeeeehhhhhhhhhhhhhhhhhhhhhhheee.....eeeeee.......eeeee.............hhhhhhhhh.hhhhhhhhhhhhh.........hhhhhh..hhhhhhhhhhhhhhh....eeeee..eeee..........hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhh.eeeeeee.e........eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4lv7 A   3 MILEEKDASDWIYRGEGGANLVLAYAGSSPLFVGKVIRIQKARRSVLTSDEQHLWRENNELISSPNKCVLEQRYVQNVIIPLLGPKHVDAGVRVSVSKEFLECVDKKVTKQRPLWRVNAANVDTSHDCALILNDHSLFDCISVEIKPKCGFLPTSRFIGKENILKTSVSRFKMHQLLKLEYIEISEESEYDPLDLFSGSKERVLEAIKALYSTPQNNFRVFLNGSLILGGSGESTGRTSPEIGYAFEDALKGFIQSHRTECFLQLVSDAVYGSGVLDRLLEIQKLDKLDIEGAIHCYYDIINQPCPICSLHALPLDESLKIVKEYLIAATAKDCSIMISFQYVSLKPTNQTFDYKVHFIDLSLKPLKRMESYYKLDKKIISFYNRKQKAE 437
                                    12        22        32        42   ||   64        74        84        94       104       114       124       134       144       162       172       182       192       202       212       222       232       242       252       262       272     ||285       295       305       315       325       345       355       365       375||     397       407       417       427       437
                                                                      46|                                                                                          152|                                                                                                                  278|                                                333|                             376|                                                
                                                                       59                                                                                           161                                                                                                                   282                                                 344                              389                                                


Chain B from PDB  Type:PROTEIN  Length:394
                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhh.eeeeee...eeeeee.........eeeeeeee...hhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhh.......eeeeehhhhhhhhhhhhhhhhhhhhhhhhee.....eeeeee........eeeeee.............hhhhhhhhh.hhhhhhhhhhhhh.........hhhhhh..hhhhhhhhhhhhhhh....eeeee..eeee..........hhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhh..eeeeeeee..ee........eeeeeeee.......hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lv7 B   3 MILEEKDASDWIYRGEGGANLVLAYAGSSPLFVGKVIRIQKASVLTSDEQHLWRENNELISSPNKCVLEQRYVQNVIIPLLGPKHVDAGVRVSVSKEFLECVDKKVTKQRPLWRVNAANVDTSHDCALILNDHSLFSQDCISVEIKPKCGFLPTSRFIGKENILKTSVSRFKMHQLLKLEYIEISEESEYDPLDLFSGSKERVLEAIKALYSTPQNNFRVFLNGSLILGGSGESTGRTSPEIGYAFEDALKGFIQSGHRTECFLQLVSDAVYGSGVLDRLLEIQKLDKLDIEGAIHCYYDIINQPCPICSLHALPLDESLKIVKEYLIAATAKDCSIMISFQSRDYVSLKPTNQTFDYKVHFIDLSLKPLKRMESYYKLDKKIISFYNRKQKAE 437
                                    12        22        32        42 ||     66        76        86        96       106       116       126       136       146       162       172       182       192       202       212       222       232       242       252       262       272     ||284       294       304       314       324       344       354       364       374   ||  393       403       413       423       433    
                                                                    44|                                                                                            154|                                                                                                                  278|                                                 333|                               378|                                                 
                                                                     59                                                                                             161                                                                                                                   281                                                  344                                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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4LV7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4LV7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4LV7)

(-) Gene Ontology  (18, 18)

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

(-) Related Entries Specified in the PDB File

3udz INOSITOL 1,3,4,5,6-PENTAKISPHOSPHATE 2-KINASE FROM A. THALIANA IN COMPLEX WITH ADP AND IP6.