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(-) Description

Title :  CRYSTAL STRUCTURE OF T. GONDII ADENOSINE KINASE COMPLEXED WITH N6-DIMETHYLADENOSINE
 
Authors :  Y. Zhang, M. H. El Kouni, S. E. Ealick
Date :  12 Jul 05  (Deposition) - 11 Jul 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym./Biol. Unit :  A
Keywords :  Ribokinase Fold; Alpha/Beta, Signaling Protein, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Zhang, M. H. El Kouni, S. E. Ealick
Substrate Analogs Induce An Intermediate Conformational Change In Toxoplasma Gondii Adenosine Kinase
Acta Crystallogr. , Sect. D V. 63 126 2007
PubMed-ID: 17242506  |  Reference-DOI: 10.1107/S0907444906043654
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ADENOSINE KINASE
    Chains: A
    EC Number: 2.7.1.20
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: AK
    Mutation: YES
    Organism Scientific: TOXOPLASMA GONDII
    Organism Taxid: 5811
    Synonym: AK;
ADENOSINE 5'-PHOSPHOTRANSFERASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric/Biological Unit (4, 6)
No.NameCountTypeFull Name
126A2Ligand/Ion6N-DIMETHYLADENOSINE
2ACT1Ligand/IonACETATE ION
3CL1Ligand/IonCHLORIDE ION
4NA2Ligand/IonSODIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:20 , ALA A:71 , THR A:167 , 26A A:1001 , HOH A:6007BINDING SITE FOR RESIDUE CL A 2001
2AC2SOFTWAREASN A:268 , THR A:269 , GLN A:289 , THR A:290 , ALA A:291 , HOH A:6381BINDING SITE FOR RESIDUE NA A 2002
3AC3SOFTWAREVAL A:348 , HIS A:351 , VAL A:352 , GLY A:353 , HOH A:6105 , HOH A:6144BINDING SITE FOR RESIDUE NA A 2003
4AC4SOFTWARETHR A:278 , GLY A:317 , HOH A:6012 , HOH A:6039 , HOH A:6112 , HOH A:6145BINDING SITE FOR RESIDUE ACT A 3001
5AC5SOFTWAREASN A:20 , ILE A:22 , ASP A:24 , GLY A:68 , GLY A:69 , SER A:70 , ASN A:73 , THR A:140 , LEU A:142 , TYR A:169 , GLY A:315 , ASP A:318 , PHE A:354 , CL A:2001 , HOH A:6045 , HOH A:6051 , HOH A:6054 , HOH A:6071BINDING SITE FOR RESIDUE 26A A 1001
6AC6SOFTWARETHR A:278 , GLY A:280 , HIS A:281 , VAL A:284 , VAL A:302 , ILE A:310 , ASN A:342 , ALA A:345 , GLN A:346 , HOH A:6025 , HOH A:6047 , HOH A:6112 , HOH A:6308BINDING SITE FOR RESIDUE 26A A 1002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2A9Y)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:11 -Pro A:12

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2A9Y)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PFKB_KINASES_2PS00584 pfkB family of carbohydrate kinases signature 2.ADK_TOXGO312-325  1A:312-325

(-) Exons   (0, 0)

(no "Exon" information available for 2A9Y)

(-) Sequences/Alignments

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
(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:351
 aligned with ADK_TOXGO | Q9TVW2 from UniProtKB/Swiss-Prot  Length:363

    Alignment length:351
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359 
            ADK_TOXGO    10 TGPMRVFAIGNPILDLVAEVPSSFLDEFFLKRGDATLATPEQMRIYSTLDQFNPTSLPGGSALNSVRVVQKLLRKPGSAGYMGAIGDDPRGQVLKELCDKEGLATRFMVAPGQSTGVCAVLINEKERTLCTHLGACGSFRLPEDWTTFASGALIFYATAYTLTATPKNALEVAGYAHGIPNAIFTLNLSAPFCVELYKDAMQSLLLHTNILFGNEEEFAHLAKVHNLVAAEKTALSTANKEHAVEVCTGALRLLTAGQNTGATKLVVMTRGHNPVIAAEQTADGTVVVHEVGVPVVAAEKIVDTNGAGDAFVGGFLYALSQGKTVKQCIMCGNACAQDVIQHVGFSLSFTS 360
               SCOP domains d2a9ya_ A: Adenosine kinase                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains -2a9yA01    2a9yA02 A:22-66,A:125-141                    2a9yA01 A:11-21,A:67-124,A:142-356                        2a9yA02          2a9yA01 A:11-21,A:67-124,A:142-356  [code=3.40.1190.20, no name defined]                                                                                                                                               ---- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee...eeeeeee.hhhhhhhh......eee.hhhhhhhhhhhhhhh.eeeeehhhhhhhhhhhhhhh....eeeeeeee.hhhhhhhhhhhhhh..eeeeeee.....eeeeeee....eeeeeehhhhhhh....hhhhhh....eeeee.hhhhh.hhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhh...hhhhh.....hhhhhhhhhhhhhhhhhh.......eeeeeee..eeeeeeee.....eeeeee.....hhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PFKB_KINASES_2----------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a9y A  10 TGPMRVFAIGNPILDLVAEVPSSFLDEFFLKRGDATLATPEQMRIYSTLDQFNPTSLPGGSALNSVRVVQKLLRKPGSAGYMGAIGDDPRGQVLKELCDKEGLATRFMVAPGQSTGVCAVLINEKERTLCTHLGACGSFRLPEDWTTFASGALIFYATAYTLTATPKNALEVAGYAHGIPNAIFTLNLSAPFCVELYKDAMQSLLLHTNILFGNEEEFAHLAKVHNLVAAEKTALSTANKEHAVEVCTGALRLLTAGQNTSATKLVVMTRGHNPVIAAEQTADGTVVVHEVGVPVVAAEKIVDTNGAGDAFVGGFLYALSQGKTVKQCIMCGNACAQDVIQHVGFSLSFTF 360
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2A9Y)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ADK_TOXGO | Q9TVW2)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004001    adenosine kinase activity    Catalysis of the reaction: ATP + adenosine = ADP + AMP.
    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:0016773    phosphotransferase activity, alcohol group as acceptor    Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor).
    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:0044209    AMP salvage    The chemical reactions and pathways resulting in the formation of adenosine monophosphate (AMP) from derivatives of it (either adenine, ADP or adenosine 3',5'-bisphosphate) without de novo synthesis.
    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.
    GO:0006166    purine ribonucleoside salvage    Any process which produces a purine nucleoside from derivatives of it, without de novo synthesis.

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  2a9y
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        ADK_TOXGO | Q9TVW2: 1dgm 1lii 1lij 1lik 1lio 2a9z 2aa0 2ab8 2abs

(-) Related Entries Specified in the PDB File

1dgm THE SAME PROTEIN
1lii THE SAME PROTEIN COMPLEXED WITH ADENOSINE AND AMP-PCP
1lij THE SAME PROTEIN COMPLEXED WITH 7-IODOTUBERCIDIN AND AMP-PCP
1lik THE SAME PROTEIN BOUND TO ADENOSINE
1lio THE SAME PROTEIN
2a9z
2aa0
2ab8
2abs