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(-) Description

Title :  CRYSTAL STRUCTURE OF MOUSE GUANYLATE KINASE IN COMPLEX WITH GMP AND ADP
 
Authors :  N. Sekulic, L. Shuvalova, O. Spangenberg, M. Konrad, A. Lavie
Date :  28 May 02  (Deposition) - 11 Dec 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Transferase, Gmp Kinase, Guanylate Kinase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Sekulic, L. Shuvalova, O. Spangenberg, M. Konrad, A. Lavie
Structural Characterization Of The Closed Conformation Of Mouse Guanylate Kinase.
J. Biol. Chem. V. 277 30236 2002
PubMed-ID: 12036965  |  Reference-DOI: 10.1074/JBC.M204668200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GUANYLATE KINASE
    Chains: A
    EC Number: 2.7.4.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: GMP KINASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
15GP1Ligand/IonGUANOSINE-5'-MONOPHOSPHATE
2ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
3K1Ligand/IonPOTASSIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:37 , ASP A:101 , 5GP A:1202 , HOH A:1207 , HOH A:1214 , HOH A:1248BINDING SITE FOR RESIDUE K A 1203
2AC2SOFTWAREGLY A:14 , ALA A:15 , GLY A:16 , LYS A:17 , SER A:18 , THR A:19 , GLU A:86 , ARG A:89 , ALA A:93 , ARG A:133 , ARG A:137 , ASN A:171 , ASP A:172 , LEU A:174 , HOH A:1204 , HOH A:1211 , HOH A:1212 , HOH A:1213 , HOH A:1221 , HOH A:1226 , HOH A:1237 , HOH A:1259 , HOH A:1303 , HOH A:1319 , HOH A:1372BINDING SITE FOR RESIDUE ADP A 1201
3AC3SOFTWARESER A:37 , ARG A:41 , ARG A:44 , TYR A:53 , GLU A:72 , PHE A:76 , TYR A:81 , GLY A:82 , THR A:83 , ASP A:101 , VAL A:102 , ASP A:103 , GLY A:106 , ARG A:148 , K A:1203 , HOH A:1213 , HOH A:1231 , HOH A:1238 , HOH A:1294BINDING SITE FOR RESIDUE 5GP A 1202

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GUANYLATE_KINASE_1PS00856 Guanylate kinase-like signature.KGUA_MOUSE39-56  1A:39-56

(-) Exons   (0, 0)

(no "Exon" information available for 1LVG)

(-) 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:190
 aligned with KGUA_MOUSE | Q64520 from UniProtKB/Swiss-Prot  Length:198

    Alignment length:190
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194
           KGUA_MOUSE     5 RPVVLSGPSGAGKSTLLKKLFQEHSSIFGFSVSHTTRNPRPGEEDGKDYYFVTREMMQRDIAAGDFIEHAEFSGNLYGTSKEAVRAVQAMNRICVLDVDLQGVRSIKKTDLCPIYIFVQPPSLDVLEQRLRLRNTETEESLAKRLAAARTDMESSKEPGLFDLVIINDDLDKAYATLKQALSEEIKKAQG 194
               SCOP domains d1lvga_ A: Guanylate kinase                                                                                                                                                                    SCOP domains
               CATH domains 1lvgA02 A:5-35,A:96-189        1lvgA01 A:36-95 Guanylate Kinase phosphate binding domain   1lvgA02 A:5-35,A:96-189 P-loop containing nucleotide triphosphate hydrolases                  ----- CATH domains
               Pfam domains Guanylate_kin-1lvgA01 A:5-188                                                                                                                                                           ------ Pfam domains
         Sec.struct. author ..eeee.....hhhhhhhhhhhhhh..eee...ee..............ee.hhhhhhhhhhhh.eeeeeee..eeeeeehhhhhhhhhh..eeeee.hhhhhhhhh......eeeeee..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..........eeee..hhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------GUANYLATE_KINASE_1------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lvg A   5 RPVVLSGPSGAGKSTLLKKLFQEHSSIFGFSVSHTTRNPRPGEEDGKDYYFVTREMMQRDIAAGDFIEHAEFSGNLYGTSKEAVRAVQAMNRICVLDVDLQGVRSIKKTDLCPIYIFVQPPSLDVLEQRLRLRNTETEESLAKRLAAARTDMESSKEPGLFDLVIINDDLDKAYATLKQALSEEIKKAQG 194
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194
   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: P-loop_NTPase (1112)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (KGUA_MOUSE | Q64520)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004385    guanylate kinase activity    Catalysis of the reaction: ATP + GMP = ADP + GDP.
    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.
    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:0046710    GDP metabolic process    The chemical reactions and pathways involving GDP, guanosine 5'-diphosphate.
    GO:0046037    GMP metabolic process    The chemical reactions and pathways involving GMP, guanosine monophosphate.
    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:0006163    purine nucleotide metabolic process    The chemical reactions and pathways involving a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.

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