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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HIS-TAGGED H232R MUTANT OF GLYCEROL KINASE FROM ENTEROCOCCUS CASSELIFLAVUS WITH GLYCEROL
 
Authors :  P. Briozzo
Date :  18 Dec 08  (Deposition) - 20 Jan 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  O,X
Keywords :  Transferase, Atp-Binding, Glycerol Metabolism, Kinase, Nucleotide- Binding, Phosphoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. I. Yeh, R. Kettering, R. Saxl, A. Bourand, E. Darbon, N. Joly, P. Briozzo, J. Deutscher
Structural Characterizations Of Glycerol Kinase: Unraveling Phosphorylation-Induced Long-Range Activation
Biochemistry 2008
PubMed-ID: 19102629  |  Reference-DOI: 10.1021/BI8009407

(-) Compounds

Molecule 1 - GLYCEROL KINASE
    Chains: O, X
    EC Number: 2.7.1.30
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: POXO4
    Expression System Strain: JM109(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: GLPK
    Mutation: YES
    Organism Scientific: ENTEROCOCCUS CASSELIFLAVUS
    Organism Taxid: 37734

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : OX

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG O:84 , GLU O:85 , TRP O:104 , TYR O:136 , ASP O:246 , GLN O:247 , PHE O:271 , SO4 O:508 , HOH O:622BINDING SITE FOR RESIDUE GOL O 507
2AC2SOFTWAREGLY O:13 , THR O:14 , THR O:15 , GLY O:267 , THR O:268 , GOL O:507 , HOH O:558 , HOH O:622 , HOH O:771BINDING SITE FOR RESIDUE SO4 O 508
3AC3SOFTWAREARG X:84 , GLU X:85 , TRP X:104 , TYR X:136 , ASP X:246 , GLN X:247 , PHE X:271 , SO4 X:508 , HOH X:688BINDING SITE FOR RESIDUE GOL X 507
4AC4SOFTWARETHR X:14 , GLY X:267 , THR X:268 , GOL X:507 , HOH X:562 , HOH X:688 , HOH X:816 , HOH X:845BINDING SITE FOR RESIDUE SO4 X 508

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3FLC)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala X:354 -Pro X:355

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3FLC)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FGGY_KINASES_1PS00933 FGGY family of carbohydrate kinases signature 1.GLPK_ENTCA136-148
 		  2O:136-148
X:136-148
2FGGY_KINASES_2PS00445 FGGY family of carbohydrate kinases signature 2.GLPK_ENTCA363-383
 		  2O:363-383
X:363-383

(-) Exons   (0, 0)

(no "Exon" information available for 3FLC)

(-) 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 O from PDB  Type:PROTEIN  Length:495
 aligned with GLPK_ENTCA | O34153 from UniProtKB/Swiss-Prot  Length:506

    Alignment length:497
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       
           GLPK_ENTCA     3 EKNYVMAIDQGTTSSRAIIFDRNGKKIGSSQKEFPQYFPKSGWVEHNANEIWNSVQSVIAGAFIESGIRPEAIAGIGITNQRETTVVWDKTTGQPIANAIVWQSRQSSPIADQLKVDGHTEMIHEKTGLVIDAYFSATKVRWLLDNIEGAQEKADNGELLFGTIDSWLVWKLTDGQVHVTDYSNASRTMLYNIHKLEWDQEILDLLNIPSSMLPEVKSNSEVYGHTRSYHFYGSEVPIAGMAGDQQAALFGQMAFEKGMIKNTYGTGAFIVMNTGEEPQLSDNDLLTTIGYGINGKVYYALEGSIFVAGSAIQWLRDGLRMIETSPQSEELAAKAKGDNEVYVVPAFTGLGAPYWDSEARGAVFGLTRGTTKEDFVRATLQAVAYQSKDVIDTMKKDSGIDIPLLKVDGGAAKNDLLMQFQADILDIDVQRAANLETTALGAAYLAGLAVGFWKDLDELKSMAEEGQMFTPEMPAEERDNLYEGWKQAVAATQTFKF 499
               SCOP domains d3flco1 O:3-254 Glycerol kinase                                                                                                                                                                                                                             d3flco2 O:255-499 Glycerol k inase                                                                                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee...eeeeeeee....eeeeeeee...........eehhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeeee....eeeee.........ee......hhhhhhhhhhh.hhhhhhhhhh......hhhhhhhhhhhhh.hhhhhhhh..eeeeehhhhhhhhhh.....eeehhhhhh...ee....eehhhhhhhh..hhhhh.eee..eeeeee.hhhhh.....eeeeeeehhhhhhhhh.......eeeee...eeeeeeee.....-....eeeeeeee..eeeeeeeeee..hhhhhhhhhhh.......hhhhhhhhh.......eee........-........eee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhhh....hhhhhhh...eeeee....hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------FGGY_KINASES_----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FGGY_KINASES_2       -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3flc O   3 EKNYVMAIDQGTTSSRAIIFDRNGKKIGSSQKEFPQYFPKSGWVEHNANEIWNSVQSVIAGAFIESGIRPEAIAGIGITNQRETTVVWDKTTGQPIANAIVWQSRQSSPIADQLKVDGHTEMIHEKTGLVIDAYFSATKVRWLLDNIEGAQEKADNGELLFGTIDSWLVWKLTDGQVHVTDYSNASRTMLYNIHKLEWDQEILDLLNIPSSMLPEVKSNSEVYGHTRSYRFYGSEVPIAGMAGDQQAALFGQMAFEKGMIKNTYGTGAFIVMNTGEEPQL-DNDLLTTIGYGINGKVYYALEGSIFVAGSAIQWLRDGLRMIETSPQSEELAAKAKGDNEVYVVPAFTGLGA-YWDSEARGAVFGLTRGTTKEDFVRATLQAVAYQSKDVIDTMKKDSGIDIPLLKVDGGAAKNDLLMQFQADILDIDVQRAANLETTALGAAYLAGLAVGFWKDLDELKSMAEEGQMFTPEMPAEERDNLYEGWKQAVAATQTFKF 499
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282 |     292       302       312       322       332       342       352 | |   362       372       382       392       402       412       422       432       442       452       462       472       482       492       
                                                                                                                                                                                                                                                                                                                 282 |                                                                   354 |                                                                                                                                               
                                                                                                                                                                                                                                                                                                                   284                                                                     356                                                                                                                                               


Chain X from PDB  Type:PROTEIN  Length:496
 aligned with GLPK_ENTCA | O34153 from UniProtKB/Swiss-Prot  Length:506

    Alignment length:497
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       
           GLPK_ENTCA     3 EKNYVMAIDQGTTSSRAIIFDRNGKKIGSSQKEFPQYFPKSGWVEHNANEIWNSVQSVIAGAFIESGIRPEAIAGIGITNQRETTVVWDKTTGQPIANAIVWQSRQSSPIADQLKVDGHTEMIHEKTGLVIDAYFSATKVRWLLDNIEGAQEKADNGELLFGTIDSWLVWKLTDGQVHVTDYSNASRTMLYNIHKLEWDQEILDLLNIPSSMLPEVKSNSEVYGHTRSYHFYGSEVPIAGMAGDQQAALFGQMAFEKGMIKNTYGTGAFIVMNTGEEPQLSDNDLLTTIGYGINGKVYYALEGSIFVAGSAIQWLRDGLRMIETSPQSEELAAKAKGDNEVYVVPAFTGLGAPYWDSEARGAVFGLTRGTTKEDFVRATLQAVAYQSKDVIDTMKKDSGIDIPLLKVDGGAAKNDLLMQFQADILDIDVQRAANLETTALGAAYLAGLAVGFWKDLDELKSMAEEGQMFTPEMPAEERDNLYEGWKQAVAATQTFKF 499
               SCOP domains d3flcx1 X:3-254 Glycerol kinase                                                                                                                                                                                                                             d3flcx2 X:255-499 Glycerol  kinase                                                                                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee...eeeeeeee....eeeeeeee...........eehhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeeee....eeeee.........ee......hhhhhhhhhhh.hhhhhhhhhh......hhhhhhhhhhhhh.hhhhhhhh..eeeeehhhhhhhhhh.....eeehhhhhh...ee....eehhhhhhhh..hhhhh.eee..eeeeee.hhhhhh....eeeeeeehhhhhhhhh.......eeeee...eeeeeeee...-......eeeeeeee..eeeeeeeeee..hhhhhhhhhhh.......hhhhhhhhhh......eee.................eee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhhh....hhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------FGGY_KINASES_----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FGGY_KINASES_2       -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3flc X   3 EKNYVMAIDQGTTSSRAIIFDRNGKKIGSSQKEFPQYFPKSGWVEHNANEIWNSVQSVIAGAFIESGIRPEAIAGIGITNQRETTVVWDKTTGQPIANAIVWQSRQSSPIADQLKVDGHTEMIHEKTGLVIDAYFSATKVRWLLDNIEGAQEKADNGELLFGTIDSWLVWKLTDGQVHVTDYSNASRTMLYNIHKLEWDQEILDLLNIPSSMLPEVKSNSEVYGHTRSYRFYGSEVPIAGMAGDQQAALFGQMAFEKGMIKNTYGTGAFIVMNTGEEP-LSDNDLLTTIGYGINGKVYYALEGSIFVAGSAIQWLRDGLRMIETSPQSEELAAKAKGDNEVYVVPAFTGLGAPYWDSEARGAVFGLTRGTTKEDFVRATLQAVAYQSKDVIDTMKKDSGIDIPLLKVDGGAAKNDLLMQFQADILDIDVQRAANLETTALGAAYLAGLAVGFWKDLDELKSMAEEGQMFTPEMPAEERDNLYEGWKQAVAATQTFKF 499
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       
                                                                                                                                                                                                                                                                                                               280 |                                                                                                                                                                                                                         
                                                                                                                                                                                                                                                                                                                 282
   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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3FLC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3FLC)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain O,X   (GLPK_ENTCA | O34153)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004370    glycerol kinase activity    Catalysis of the reaction: ATP + glycerol = sn-glycerol 3-phosphate + ADP + 2 H(+).
    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: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:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0019563    glycerol catabolic process    The chemical reactions and pathways resulting in the breakdown of glycerol, 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids.
    GO:0006071    glycerol metabolic process    The chemical reactions and pathways involving glycerol, 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids.
    GO:0006072    glycerol-3-phosphate metabolic process    The chemical reactions and pathways involving glycerol-3-phosphate, a phosphoric monoester of glycerol.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GLPK_ENTCA | O34153: 1r59 1xup 3d7e 3h3n 3h3o 3h45 3h46

(-) Related Entries Specified in the PDB File

1r59 APO FORM OF GLYCEROL KINASE
1xup ENTEROCOCCUS CASSELIFLAVUS GLYCEROL KINASE COMPLEXED WITH GLYCEROL