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(-) Description

Title :  CRYSTAL STRUCTURE OF UNLIGANDED FORM OF MYCOBACTERIUM TUBERCULOSIS GUANYLATE KINASE
 
Authors :  G. Hible, P. Christova, L. Renault, E. Seclaman, A. Thompson, E. Girard H. Munier-Lehmann, J. Cherfils
Date :  12 May 05  (Deposition) - 29 Nov 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Guanylate Kinase, Gmp Kinase, Atp:Gmp-Phosphotransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Hible, P. Christova, L. Renault, E. Seclaman, A. Thompson, E. Girard, H. Munier-Lehmann, J. Cherfils
Unique Gmp-Binding Site In Mycobacterium Tuberculosis Guanosine Monophosphate Kinase
Proteins V. 62 489 2006
PubMed-ID: 16288457  |  Reference-DOI: 10.1002/PROT.20662

(-) Compounds

Molecule 1 - GUANYLATE KINASE
    Chains: A
    EC Number: 2.7.4.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: GMK (RV1389)
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Synonym: GMP KINASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1ZNW)

(-) Sites  (0, 0)

(no "Site" information available for 1ZNW)

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:40 -A:193

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GUANYLATE_KINASE_2PS50052 Guanylate kinase-like domain profile.KGUA_MYCTO21-201  1A:21-201
KGUA_MYCTU21-201  1A:21-201
2GUANYLATE_KINASE_1PS00856 Guanylate kinase-like signature.KGUA_MYCTO55-72  1A:55-72
KGUA_MYCTU55-72  1A:55-72

(-) Exons   (0, 0)

(no "Exon" information available for 1ZNW)

(-) 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:182
 aligned with KGUA_MYCTO | P9WKE8 from UniProtKB/Swiss-Prot  Length:208

    Alignment length:182
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199  
           KGUA_MYCTO    20 VGRVVVLSGPSAVGKSTVVRCLRERIPNLHFSVSATTRAPRPGEVDGVDYHFIDPTRFQQLIDQGELLEWAEIHGGLHRSGTLAQPVRAAAATGVPVLIEVDLAGARAIKKTMPEAVTVFLAPPSWQDLQARLIGRGTETADVIQRRLDTARIELAAQGDFDKVVVNRRLESACAELVSLLV 201
               SCOP domains d1znwa_ A: automated matches                                                                                                                                                           SCOP domains
               CATH domains 1znwA01 A:20-51,A:115-201       1znwA02 A:52-114 Guanylate Kinase phosphate binding domain     1znwA01 A:20-51,A:115-201 P-loop containing nucleotide triphosphate hydrolases          CATH domains
               Pfam domains Guanylate_kin-1znwA01 A:20-201                                                                                                                                                         Pfam domains
         Sec.struct. author ...eeeee.....hhhhhhhhhhhhh...ee...ee..............ee.hhhhhhhhhhh..eeeeeee....eeeeeehhhhhhhhhh...eeee.hhhhhhhhhhhh...eeeeee..hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.eeee..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -GUANYLATE_KINASE_2  PDB: A:21-201 UniProt: 21-201                                                                                                                                     PROSITE (2)
                PROSITE (3) -----------------------------------GUANYLATE_KINASE_1--------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1znw A  20 VGRVVVLSGPSAVGKSTVVRCLRERIPNLHFSVSATTRAPRPGEVDGVDYHFIDPTRFQQLIDQGELLEWAEIHGGLHRSGTLAQPVRAAAATGVPVLIEVDLAGARAIKKTMPEAVTVFLAPPSWQDLQARLIGRGTETADVIQRRLDTARIELAAQGDFDKVVVNRRLESACAELVSLLV 201
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199  


Chain A from PDB  Type:PROTEIN  Length:182
 aligned with KGUA_MYCTU | P9WKE9 from UniProtKB/Swiss-Prot  Length:208

    Alignment length:182
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199  
           KGUA_MYCTU    20 VGRVVVLSGPSAVGKSTVVRCLRERIPNLHFSVSATTRAPRPGEVDGVDYHFIDPTRFQQLIDQGELLEWAEIHGGLHRSGTLAQPVRAAAATGVPVLIEVDLAGARAIKKTMPEAVTVFLAPPSWQDLQARLIGRGTETADVIQRRLDTARIELAAQGDFDKVVVNRRLESACAELVSLLV 201
               SCOP domains d1znwa_ A: automated matches                                                                                                                                                           SCOP domains
               CATH domains 1znwA01 A:20-51,A:115-201       1znwA02 A:52-114 Guanylate Kinase phosphate binding domain     1znwA01 A:20-51,A:115-201 P-loop containing nucleotide triphosphate hydrolases          CATH domains
               Pfam domains Guanylate_kin-1znwA01 A:20-201                                                                                                                                                         Pfam domains
         Sec.struct. author ...eeeee.....hhhhhhhhhhhhh...ee...ee..............ee.hhhhhhhhhhh..eeeeeee....eeeeeehhhhhhhhhh...eeee.hhhhhhhhhhhh...eeeeee..hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.eeee..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -GUANYLATE_KINASE_2  PDB: A:21-201 UniProt: 21-201                                                                                                                                     PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) -----------------------------------GUANYLATE_KINASE_1--------------------------------------------------------------------------------------------------------------------------------- PROSITE (4)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1znw A  20 VGRVVVLSGPSAVGKSTVVRCLRERIPNLHFSVSATTRAPRPGEVDGVDYHFIDPTRFQQLIDQGELLEWAEIHGGLHRSGTLAQPVRAAAATGVPVLIEVDLAGARAIKKTMPEAVTVFLAPPSWQDLQARLIGRGTETADVIQRRLDTARIELAAQGDFDKVVVNRRLESACAELVSLLV 201
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199
   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  (16, 26)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (KGUA_MYCTO | P9WKE8)
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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain A   (KGUA_MYCTU | P9WKE9)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0019003    GDP binding    Interacting selectively and non-covalently with GDP, guanosine 5'-diphosphate.
    GO:0019002    GMP binding    Interacting selectively and non-covalently with GMP, guanosine monophosphate.
    GO:0004017    adenylate kinase activity    Catalysis of the reaction: ATP + AMP = 2 ADP.
    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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    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:0040007    growth    The increase in size or mass of an entire organism, a part of an organism or a cell.
    GO:0046939    nucleotide phosphorylation    The process of introducing one or more phosphate groups into a nucleotide to produce a phosphorylated nucleoside.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        KGUA_MYCTO | P9WKE8: 1s4q 1z8f 1znx 1zny 1znz
        KGUA_MYCTU | P9WKE9: 1s4q 1z8f 1znx 1zny 1znz

(-) Related Entries Specified in the PDB File

1znx CRYSTAL STRUCTURE OF THE M.TUBERCULOSIS PROTEIN LIGANDED WITH GMP
1zny CRYSTAL STRUCTURE OF THE M.TUBERCULOSIS PROTEIN LIGANDED WITH GDP
1znz CRYSTAL STRUCTURE OF THE REDUCED FORM OF THE M.TUBERCULOSIS PROTEIN LIGANDED WITH GDP