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(-) Description

Title :  CRYSTAL STRUCTURE OF E.COLI GUANYLATE KINASE IN COMPLEX WITH GANCICLOVIR MONOPHOSPHATE
 
Authors :  G. Hible, J. Cherfils
Date :  22 Nov 05  (Deposition) - 30 May 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.16
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Transferase, Gmp Kinase, Guanylate Kinase, Nucleotide Analogue (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Hible, P. Daalova, A. M. Gilles, J. Cherfils
Crystal Structures Of Gmp Kinase In Complex With Ganciclovi Monophosphate And Ap5G.
Biochimie V. 88 1157 2006
PubMed-ID: 16690197  |  Reference-DOI: 10.1016/J.BIOCHI.2006.04.002

(-) Compounds

Molecule 1 - GUANYLATE KINASE
    Chains: A, B, C, D, E, F
    EC Number: 2.7.4.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24A
    Expression System Strain: BLI5
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: GMK, SPOR
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: GMP KINASE

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1LGP4Ligand/IonN9-1-HYDROXY-PROP-2-OXYMETHYL-GUANINE-3'-MONOPHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:38 , ARG A:42 , ARG A:45 , TYR A:54 , GLU A:73 , TYR A:82 , THR A:84BINDING SITE FOR RESIDUE LGP A 300
2AC2SOFTWARESER B:38 , ARG B:42 , ARG B:45 , TYR B:54 , GLU B:73 , ALA B:75 , VAL B:77 , TYR B:82 , THR B:84BINDING SITE FOR RESIDUE LGP A 301
3AC3SOFTWARESER E:38 , ARG E:42 , ARG E:45 , TYR E:54 , GLU E:73 , TYR E:82BINDING SITE FOR RESIDUE LGP A 302
4AC4SOFTWARESER F:38 , ARG F:45 , TYR F:54 , GLU F:73 , TYR F:82 , HOH F:210 , HOH F:211BINDING SITE FOR RESIDUE LGP A 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2F3T)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2F3T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2F3T)

(-) PROSITE Motifs  (2, 12)

Asymmetric/Biological Unit (2, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GUANYLATE_KINASE_2PS50052 Guanylate kinase-like domain profile.KGUA_ECOLI4-184
 
 
 
 
 		  6A:4-184
B:4-184
C:4-184
D:4-184
E:4-184
F:4-184
2GUANYLATE_KINASE_1PS00856 Guanylate kinase-like signature.KGUA_ECOLI40-57
 
 
 
 
 		  6A:40-57
B:40-57
C:40-57
D:40-57
E:40-57
F:40-57

(-) Exons   (0, 0)

(no "Exon" information available for 2F3T)

(-) 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:205
 aligned with KGUA_ECOLI | P60546 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:205
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201     
           KGUA_ECOLI     2 AQGTLYIVSAPSGAGKSSLIQALLKTQPLYDTQVSVSHTTRQPRPGEVHGEHYFFVNHDEFKEMISRDAFLEHAEVFGNYYGTSREAIEQVLATGVDVFLDIDWQGAQQIRQKMPHARSIFILPPSKIELDRRLRGRGQDSEEVIAKRMAQAVAEMSHYAEYDYLIVNDDFDTALTDLKTIIRAERLRMSRQKQRHDALISKLLA 206
               SCOP domains d2f3ta_ A: Guanylate kinase                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.....hhhhhhhhhhh......eee..eee.............eee.hhhhhhhhhhh..eeeeeee..eeeeeehhhhhhhhhh..eeeee.hhhhhhhhhhhh...eeeeee..hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.eeee..hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --GUANYLATE_KINASE_2  PDB: A:4-184 UniProt: 4-184                                                                                                                                      ---------------------- PROSITE (1)
                PROSITE (2) --------------------------------------GUANYLATE_KINASE_1----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f3t A   2 AQGTLYIVSAPSGAGKSSLIQALLKTQPLYDTQVSVSHTTRQPRPGEVHGEHYFFVNHDEFKEMISRDAFLEHAEVFGNYYGTSREAIEQVLATGVDVFLDIDWQGAQQIRQKMPHARSIFILPPSKIELDRRLRGRGQDSEEVIAKRMAQAVAEMSHYAEYDYLIVNDDFDTALTDLKTIIRAERLRMSRQKQRHDALISKLLA 206
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201     


Chain B from PDB  Type:PROTEIN  Length:203
 aligned with KGUA_ECOLI | P60546 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:206
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201      
           KGUA_ECOLI     2 AQGTLYIVSAPSGAGKSSLIQALLKTQPLYDTQVSVSHTTRQPRPGEVHGEHYFFVNHDEFKEMISRDAFLEHAEVFGNYYGTSREAIEQVLATGVDVFLDIDWQGAQQIRQKMPHARSIFILPPSKIELDRRLRGRGQDSEEVIAKRMAQAVAEMSHYAEYDYLIVNDDFDTALTDLKTIIRAERLRMSRQKQRHDALISKLLAD 207
               SCOP domains d2f3tb_ B: Guanylate kinase                                                                                                                                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.....hhhhhhhhhhh......eee..eee.............eee.hhhhhhhhhhh..eeeeeee..eeeeeehhhhhhhhh...eeeee.hhhhhhhhhhhh...eeeeee..hhhhhhhhhh..---hhhhhhhhhhhhhhhhhhhhhh.eeee..hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --GUANYLATE_KINASE_2  PDB: B:4-184 UniProt: 4-184                                                                                                                                      ----------------------- PROSITE (1)
                PROSITE (2) --------------------------------------GUANYLATE_KINASE_1------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f3t B   2 AQGTLYIVSAPSGAGKSSLIQALLKTQPLYDTQVSVSHTTRQPRPGEVHGEHYFFVNHDEFKEMISRDAFLEHAEVFGNYYGTSREAIEQVLATGVDVFLDIDWQGAQQIRQKMPHARSIFILPPSKIELDRRLRGR---SEEVIAKRMAQAVAEMSHYAEYDYLIVNDDFDTALTDLKTIIRAERLRMSRQKQRHDALISKLLAD 207
                                    11        21        31        41        51        61        71        81        91       101       111       121       131      |  -|      151       161       171       181       191       201      
                                                                                                                                                                  138 142                                                                 


Chain C from PDB  Type:PROTEIN  Length:201
 aligned with KGUA_ECOLI | P60546 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:205
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201     
           KGUA_ECOLI     2 AQGTLYIVSAPSGAGKSSLIQALLKTQPLYDTQVSVSHTTRQPRPGEVHGEHYFFVNHDEFKEMISRDAFLEHAEVFGNYYGTSREAIEQVLATGVDVFLDIDWQGAQQIRQKMPHARSIFILPPSKIELDRRLRGRGQDSEEVIAKRMAQAVAEMSHYAEYDYLIVNDDFDTALTDLKTIIRAERLRMSRQKQRHDALISKLLA 206
               SCOP domains d2f3tc_ C: Guanylate kinase                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.....hhhhhhhhhhh......eee..eee.............eee.hhhhhhhhhhh..eeeeeee..eeeeeehhhhhhhhh...eeeee.hhhhhhhhhhhh..eeeeeee..hhhhhhhhhh----.hhhhhhhhhhhhhhhhhhhhhh.eeee..hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --GUANYLATE_KINASE_2  PDB: C:4-184 UniProt: 4-184                                                                                                                                      ---------------------- PROSITE (1)
                PROSITE (2) --------------------------------------GUANYLATE_KINASE_1----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f3t C   2 AQGTLYIVSAPSGAGKSSLIQALLKTQPLYDTQVSVSHTTRQPRPGEVHGEHYFFVNHDEFKEMISRDAFLEHAEVFGNYYGTSREAIEQVLATGVDVFLDIDWQGAQQIRQKMPHARSIFILPPSKIELDRRLR----DSEEVIAKRMAQAVAEMSHYAEYDYLIVNDDFDTALTDLKTIIRAERLRMSRQKQRHDALISKLLA 206
                                    11        21        31        41        51        61        71        81        91       101       111       121       131    |  141       151       161       171       181       191       201     
                                                                                                                                                                136  141                                                                 


Chain D from PDB  Type:PROTEIN  Length:205
 aligned with KGUA_ECOLI | P60546 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:205
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201     
           KGUA_ECOLI     2 AQGTLYIVSAPSGAGKSSLIQALLKTQPLYDTQVSVSHTTRQPRPGEVHGEHYFFVNHDEFKEMISRDAFLEHAEVFGNYYGTSREAIEQVLATGVDVFLDIDWQGAQQIRQKMPHARSIFILPPSKIELDRRLRGRGQDSEEVIAKRMAQAVAEMSHYAEYDYLIVNDDFDTALTDLKTIIRAERLRMSRQKQRHDALISKLLA 206
               SCOP domains d2f3td_ D: Guanylate kinase                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.....hhhhhhhhhhh......eee..eee.............eee.hhhhhhhhhhh..eeeeeee..eeeeeehhhhhhhhh...eeeee.hhhhhhhhhhhh...eeeeee..hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.eeee..hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --GUANYLATE_KINASE_2  PDB: D:4-184 UniProt: 4-184                                                                                                                                      ---------------------- PROSITE (1)
                PROSITE (2) --------------------------------------GUANYLATE_KINASE_1----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f3t D   2 AQGTLYIVSAPSGAGKSSLIQALLKTQPLYDTQVSVSHTTRQPRPGEVHGEHYFFVNHDEFKEMISRDAFLEHAEVFGNYYGTSREAIEQVLATGVDVFLDIDWQGAQQIRQKMPHARSIFILPPSKIELDRRLRGRGQDSEEVIAKRMAQAVAEMSHYAEYDYLIVNDDFDTALTDLKTIIRAERLRMSRQKQRHDALISKLLA 206
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201     


Chain E from PDB  Type:PROTEIN  Length:204
 aligned with KGUA_ECOLI | P60546 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:204
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201    
           KGUA_ECOLI     2 AQGTLYIVSAPSGAGKSSLIQALLKTQPLYDTQVSVSHTTRQPRPGEVHGEHYFFVNHDEFKEMISRDAFLEHAEVFGNYYGTSREAIEQVLATGVDVFLDIDWQGAQQIRQKMPHARSIFILPPSKIELDRRLRGRGQDSEEVIAKRMAQAVAEMSHYAEYDYLIVNDDFDTALTDLKTIIRAERLRMSRQKQRHDALISKLL 205
               SCOP domains d2f3te_ E: Guanylate kinase                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeee.....hhhhhhhhhhh......eee..eee.............eee.hhhhhhhhhhh..eeeeeee..eeeeeehhhhhhhhh...eeeee.hhhhhhhhhhhh...eeeeee..hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) --GUANYLATE_KINASE_2  PDB: E:4-184 UniProt: 4-184                                                                                                                                      --------------------- PROSITE (1)
                PROSITE (2) --------------------------------------GUANYLATE_KINASE_1---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2f3t E   2 AQGTLYIVSAPSGAGKSSLIQALLKTQPLYDTQVSVSHTTRQPRPGEVHGEHYFFVNHDEFKEMISRDAFLEHAEVFGNYYGTSREAIEQVLATGVDVFLDIDWQGAQQIRQKMPHARSIFILPPSKIELDRRLRGRGQDSEEVIAKRMAQAVAEMSHYAEYDYLIVNDDFDTALTDLKTIIRAERLRMSRQKQRHDALISKLL 205
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201    


Chain F from PDB  Type:PROTEIN  Length:205
 aligned with KGUA_ECOLI | P60546 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:205
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201     
           KGUA_ECOLI     2 AQGTLYIVSAPSGAGKSSLIQALLKTQPLYDTQVSVSHTTRQPRPGEVHGEHYFFVNHDEFKEMISRDAFLEHAEVFGNYYGTSREAIEQVLATGVDVFLDIDWQGAQQIRQKMPHARSIFILPPSKIELDRRLRGRGQDSEEVIAKRMAQAVAEMSHYAEYDYLIVNDDFDTALTDLKTIIRAERLRMSRQKQRHDALISKLLA 206
               SCOP domains d2f3tf_ F: Guanylate kinase                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.....hhhhhhhhhhh......eee..eee.............eee.hhhhhhhhhhh..eeeeeee..eeeeeehhhhhhhhh...eeeee.hhhhhhhhhhhh...eeeeee..hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.eeee..hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --GUANYLATE_KINASE_2  PDB: F:4-184 UniProt: 4-184                                                                                                                                      ---------------------- PROSITE (1)
                PROSITE (2) --------------------------------------GUANYLATE_KINASE_1----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f3t F   2 AQGTLYIVSAPSGAGKSSLIQALLKTQPLYDTQVSVSHTTRQPRPGEVHGEHYFFVNHDEFKEMISRDAFLEHAEVFGNYYGTSREAIEQVLATGVDVFLDIDWQGAQQIRQKMPHARSIFILPPSKIELDRRLRGRGQDSEEVIAKRMAQAVAEMSHYAEYDYLIVNDDFDTALTDLKTIIRAERLRMSRQKQRHDALISKLLA 206
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201
   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, 6)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2F3T)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2F3T)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (KGUA_ECOLI | P60546)
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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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  2f3t
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  KGUA_ECOLI | P60546
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  2.7.4.8
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 Related Entries

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

UniProtKB/Swiss-Prot
        KGUA_ECOLI | P60546: 1s96 2an9 2anb 2anc 2f3r

(-) Related Entries Specified in the PDB File

2f3r THE SAME PROTEIN COMPLEXED WITH AP5G