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(-) Description

Title :  STRUCTURE OF T. GONDII ADENOSINE KINASE BOUND TO ADENOSINE
 
Authors :  M. A. Schumacher, D. M. Scott, I. I. Mathews, S. E. Ealick, D. S. Roos, B. Ullman, R. G. Brennan
Date :  17 Apr 02  (Deposition) - 15 May 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha-Beta Structure, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Schumacher, D. M. Scott, I. I. Mathews, S. E. Ealick, D. S. Roos, B. Ullman, R. G. Brennan
Crystal Structures Of Toxoplasma Gondii Adenosine Kinase Reveal A Novel Catalytic Mechanism And Prodrug Binding.
J. Mol. Biol. V. 298 875 2000
PubMed-ID: 10801355  |  Reference-DOI: 10.1006/JMBI.2000.3753
(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
    Expression System Plasmid: PBACE
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: TOXOPLASMA GONDII
    Organism Taxid: 5811

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1ADN2Ligand/IonADENOSINE
2CL1Ligand/IonCHLORIDE ION
3SO41Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:136 , ASN A:223 , GLY A:317 , HOH A:1034 , HOH A:1056 , HOH A:1098BINDING SITE FOR RESIDUE SO4 A 999
2AC2SOFTWAREASP A:35 , LYS A:80BINDING SITE FOR RESIDUE CL A 899
3AC3SOFTWAREASN A:20 , ILE A:22 , ASP A:24 , GLY A:68 , GLY A:69 , SER A:70 , ASN A:73 , THR A:140 , TYR A:169 , ASP A:318 , HOH A:1038 , HOH A:1040 , HOH A:1041 , HOH A:1056BINDING SITE FOR RESIDUE ADN A 699
4AC4SOFTWAREGLY A:280 , HIS A:281 , VAL A:302 , ASN A:342 , ALA A:345 , GLN A:346 , HOH A:1032 , HOH A:1076BINDING SITE FOR RESIDUE ADN A 799

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1LIK)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1LIK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1LIK)

(-) 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 1LIK)

(-) 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:330
 aligned with ADK_TOXGO | Q9TVW2 from UniProtKB/Swiss-Prot  Length:363

    Alignment length:348
                                    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        
            ADK_TOXGO    11 GPMRVFAIGNPILDLVAEVPSSFLDEFFLKRGDATLATPEQMRIYSTLDQFNPTSLPGGSALNSVRVVQKLLRKPGSAGYMGAIGDDPRGQVLKELCDKEGLATRFMVAPGQSTGVCAVLINEKERTLCTHLGACGSFRLPEDWTTFASGALIFYATAYTLTATPKNALEVAGYAHGIPNAIFTLNLSAPFCVELYKDAMQSLLLHTNILFGNEEEFAHLAKVHNLVAAEKTALSTANKEHAVEVCTGALRLLTAGQNTGATKLVVMTRGHNPVIAAEQTADGTVVVHEVGVPVVAAEKIVDTNGAGDAFVGGFLYALSQGKTVKQCIMCGNACAQDVIQHVGFSLSF 358
               SCOP domains d1lika_ A: Adenosine kinase                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1likA01    1likA02 A:22-66,A:125-141                    1likA01 A:11-21,A:67-124,A:142-355                        1likA02          1likA01 A:11-21,A:67-124,A:142-355  [code=3.40.1190.20, no name defined]                                                                                                                                              --- CATH domains
               Pfam domains ----------------------------------PfkB-1likA01 A:45-358                                                                                                                                                                                                                                                                                                      Pfam domains
         Sec.struct. author ....eeee...eeeeeee.hhhhhhhh......eee.hhhhhhhhhhhhhhh.eeee.hhhhhhhhhhhhhhh....eeeeeeee.hhhhhhhhhhhhhh..eeeeeee.....eeeeeeee..eeeeeeehhhhhhh....hhhhhh....eeeee.hhhhh.hhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhhh...---hhhhhhhhhhhhh---------------.....eeeeee..eeeeeeee.....eeeeee.....hhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PFKB_KINASES_2--------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1lik A  11 GPMRVFAIGNPILDLVAEVPSSFLDEFFLKRGDATLATPEQMRIYSTLDQFNPTSLPGGSALNSVRVVQKLLRKPGSAGYMGAIGDDPRGQVLKELCDKEGLATRFMVAPGQSTGTCAVLINEKERTLCTHLGACGSFRIPENWTTFASGALIFYATAYTLTATPKNALEVAGYAHGIPNAIFTLNLSAPFCVELYKDAMQSLLLHTNILFGNEEEFAHLAKVHNLV---KVALSVANKEHAV---------------TGATKLVVMTRGHNPVIAAEQTADGTVVVHEVGVPVVAAEKIVDTNGAGDAFVGGFLYGLSQGKTVKQCIMCGNACAQDVIQHVGFSLSF 358
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230      |  -|      250  |      -       270       280       290       300       310       320       330       340       350        
                                                                                                                                                                                                                                                            237 241         253             269
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Ribokinase (55)

(-) 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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  2.7.1.20
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 Related Entries

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

UniProtKB/Swiss-Prot
        ADK_TOXGO | Q9TVW2: 1dgm 1lii 1lij 1lio 2a9y 2a9z 2aa0 2ab8 2abs

(-) Related Entries Specified in the PDB File

1lii STRUCTURE OF T. GONDII ADENOSINE KINASE BOUND TO ADENOSINE 2 AND AMP-PCP
1lij STRUCTURE OF T. GONDII ADENOSINE KINASE BOUND TO PRODRUG 2 7-IODOTUBERCIDIN AND AMP-PCP
1lio STRUCTURE OF APO T. GONDII ADENOSINE KINASE