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(-) Description

Title :  MYO-INOSITOL KINASE FROM THERMOCOCCUS KODAKARENSIS
 
Authors :  M. Fujihashi, Y. Miyamoto, K. Miki
Date :  10 Jan 13  (Deposition) - 12 Jun 13  (Release) - 22 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.78
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Sato, M. Fujihashi, Y. Miyamoto, K. Kuwata, E. Kusaka, H. Fujita, K. Miki, H. Atomi
An Uncharacterized Member Of The Ribokinase Family In Thermococcus Kodakarensis Exhibits Myo-Inositol Kinase Activity.
J. Biol. Chem. V. 288 20856 2013
PubMed-ID: 23737529  |  Reference-DOI: 10.1074/JBC.M113.457259

(-) Compounds

Molecule 1 - CARBOHYDRATE/PYRIMIDINE KINASE, PFKB FAMILY
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TK2285
    Organism Scientific: THERMOCOCCUS KODAKARENSIS
    Organism Taxid: 69014
    Strain: ATCC BAA-918 / JCM 12380 / KOD1

 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  (1, 30)

Asymmetric Unit (1, 30)
No.NameCountTypeFull Name
1IOD30Ligand/IonIODIDE ION
Biological Unit 1 (1, 23)
No.NameCountTypeFull Name
1IOD23Ligand/IonIODIDE ION
Biological Unit 2 (1, 7)
No.NameCountTypeFull Name
1IOD7Ligand/IonIODIDE ION

(-) Sites  (25, 25)

Asymmetric Unit (25, 25)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:11 , ARG B:11BINDING SITE FOR RESIDUE IOD A 401
02AC2SOFTWARESER A:123BINDING SITE FOR RESIDUE IOD A 403
03AC3SOFTWAREIOD A:423BINDING SITE FOR RESIDUE IOD A 404
04AC4SOFTWAREGLN A:174BINDING SITE FOR RESIDUE IOD A 408
05AC5SOFTWAREGLY A:26 , IOD A:416 , IOD A:420 , HOH A:557BINDING SITE FOR RESIDUE IOD A 409
06AC6SOFTWARETHR A:203 , GLU A:269BINDING SITE FOR RESIDUE IOD A 410
07AC7SOFTWAREARG A:23 , ARG A:252BINDING SITE FOR RESIDUE IOD A 412
08AC8SOFTWAREARG A:272BINDING SITE FOR RESIDUE IOD A 413
09AC9SOFTWAREASP A:101 , GLN B:236BINDING SITE FOR RESIDUE IOD A 414
10BC1SOFTWAREGLN A:65 , PRO A:100 , IOD A:421BINDING SITE FOR RESIDUE IOD A 415
11BC2SOFTWAREARG A:85 , IOD A:409BINDING SITE FOR RESIDUE IOD A 416
12BC3SOFTWAREARG A:23BINDING SITE FOR RESIDUE IOD A 417
13BC4SOFTWAREVAL A:112 , ARG A:140 , IOD A:420BINDING SITE FOR RESIDUE IOD A 418
14BC5SOFTWAREGLU A:59BINDING SITE FOR RESIDUE IOD A 419
15BC6SOFTWAREASP A:12 , IOD A:409 , IOD A:418BINDING SITE FOR RESIDUE IOD A 420
16BC7SOFTWAREGLU A:98 , LEU A:99 , PRO A:100 , IOD A:415 , CYS B:232 , GLN B:236 , ARG B:240BINDING SITE FOR RESIDUE IOD A 421
17BC8SOFTWARESER A:141BINDING SITE FOR RESIDUE IOD A 422
18BC9SOFTWAREALA A:217 , IOD A:404BINDING SITE FOR RESIDUE IOD A 423
19CC1SOFTWARELEU B:99BINDING SITE FOR RESIDUE IOD B 301
20CC2SOFTWAREIOD B:303BINDING SITE FOR RESIDUE IOD B 302
21CC3SOFTWAREIOD B:302BINDING SITE FOR RESIDUE IOD B 303
22CC4SOFTWAREGLY B:26 , TYR B:30BINDING SITE FOR RESIDUE IOD B 304
23CC5SOFTWAREVAL A:20 , ARG B:92 , PRO B:144BINDING SITE FOR RESIDUE IOD B 305
24CC6SOFTWARETHR B:203 , GLU B:205 , GLU B:269BINDING SITE FOR RESIDUE IOD B 306
25CC7SOFTWARELEU B:77 , ARG B:85BINDING SITE FOR RESIDUE IOD B 307

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:3 -A:39
2B:3 -B:39

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3W4S)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3W4S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3W4S)

(-) Exons   (0, 0)

(no "Exon" information available for 3W4S)

(-) 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:273
 aligned with Q5JDA3_THEKO | Q5JDA3 from UniProtKB/TrEMBL  Length:273

    Alignment length:273
                                    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   
         Q5JDA3_THEKO     1 MKCLVVGHVVRDIVKKGNKVLERLGGGAYYSALALSRFCDVEILTSFSNLPEEWIKELESMAKLQVVPSETTTTYELTYLDGNRRRLKLLERASPIEELPDGEYDVLLMNPVAREVPPALVTSALKKFPFVAVDIQGFIRSSSPGEIQYQPIDGSFLKGVKILHADLGEYQYLQGFSPEFVDVLLLSNGPEPGKAFLHGREYTFEPVHVGVDESTGAGDVFLGAFTGFYSQCPFVQALKRAAAFTALFLKNRSVDFSMDDVNELAMKVEVKRV 273
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...eeeeeee..eeeeeeehhhhhhhhhhh...eeeeeee....hhhhhhhhhhhheeeee......eeeeee.....eeeeeee..............eeee.......hhhhhhhhhhhh..eeeehhhhhh....ee.....ee.hhhh...eeeee.hhhh.ee..hhhhh.eeeeee..eeeeeee..eeeee...........hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh...eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3w4s A   1 MKCLVVGHVVRDIVKKGNKVLERLGGGAYYSALALSRFCDVEILTSFSNLPEEWIKELESMAKLQVVPSETTTTYELTYLDGNRRRLKLLERASPIEELPDGEYDVLLMNPVAREVPPALVTSALKKFPFVAVDIQGFIRSSSPGEIQYQPIDGSFLKGVKILHADLGEYQYLQGFSPEFVDVLLLSNGPEPGKAFLHGREYTFEPVHVGVDESTGAGDVFLGAFTGFYSQCPFVQALKRAAAFTALFLKNRSVDFSMDDVNELAMKVEVKRV 273
                                    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   


Chain B from PDB  Type:PROTEIN  Length:268
 aligned with Q5JDA3_THEKO | Q5JDA3 from UniProtKB/TrEMBL  Length:273

    Alignment length:273
                                    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   
         Q5JDA3_THEKO     1 MKCLVVGHVVRDIVKKGNKVLERLGGGAYYSALALSRFCDVEILTSFSNLPEEWIKELESMAKLQVVPSETTTTYELTYLDGNRRRLKLLERASPIEELPDGEYDVLLMNPVAREVPPALVTSALKKFPFVAVDIQGFIRSSSPGEIQYQPIDGSFLKGVKILHADLGEYQYLQGFSPEFVDVLLLSNGPEPGKAFLHGREYTFEPVHVGVDESTGAGDVFLGAFTGFYSQCPFVQALKRAAAFTALFLKNRSVDFSMDDVNELAMKVEVKRV 273
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...eeeeeee..eeeeeeehhhhhhhhhhh...eeeeeee....hhhhhhhhhhhheeeee......eeeeee.....eeeeeee..............eeee.......hhhhhhhhhhhh..eeeehhhhhh....ee.....ee.hhhh...eeeee.hhhh.ee..hhhhh.eeeeee..eeeeeee..eeeeee...-----..hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh..eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3w4s B   1 MKCLVVGHVVRDIVKKGNKVLERLGGGAYYSALALSRFCDVEILTSFSNLPEEWIKELESMAKLQVVPSETTTTYELTYLDGNRRRLKLLERASPIEELPDGEYDVLLMNPVAREVPPALVTSALKKFPFVAVDIQGFIRSSSPGEIQYQPIDGSFLKGVKILHADLGEYQYLQGFSPEFVDVLLLSNGPEPGKAFLHGREYTFEPVH-----STGAGDVFLGAFTGFYSQCPFVQALKRAAAFTALFLKNRSVDFSMDDVNELAMKVEVKRV 273
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       | -   |   220       230       240       250       260       270   
                                                                                                                                                                                                                                         208   214
   Legend:   → Mismatch (orange background)
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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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3W4S)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3W4S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3W4S)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q5JDA3_THEKO | Q5JDA3)
molecular function
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    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.
biological process
    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.

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        Q5JDA3_THEKO | Q5JDA3: 4xf6 4xf7

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