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(-) Description

Title :  ESCHERICHIA COLI GLYCEROL KINASE MUTANT WITH BOUND ATP ANALOG SHOWING SUBSTANTIAL DOMAIN MOTION
 
Authors :  C. E. Bystrom, D. W. Pettigrew, B. P. Branchaud, S. J. Remington
Date :  24 Sep 98  (Deposition) - 18 May 99  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  O,Y
Keywords :  Phosphotransferase, Kinase, Domain Motion, Allosteric Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. E. Bystrom, D. W. Pettigrew, B. P. Branchaud, P. O'Brien, S. J. Remington
Crystal Structures Of Escherichia Coli Glycerol Kinase Variant S58-->W In Complex With Nonhydrolyzable Atp Analogues Reveal A Putative Active Conformation Of The Enzyme As A Result Of Domain Motion.
Biochemistry V. 38 3508 1999
PubMed-ID: 10090737  |  Reference-DOI: 10.1021/BI982460Z

(-) Compounds

Molecule 1 - GLYCEROL KINASE
    Chains: Y, O
    EC Number: 2.7.1.30
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: GLPK
    Expression System Strain: DG1 (DE3)
    Expression System Taxid: 562
    Expression System Vector: PET28B
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organ: SEED
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: CLONED GENE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : OY

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1ACP2Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2GOL2Ligand/IonGLYCEROL
3MG2Ligand/IonMAGNESIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1UNKNOWNASP O:245PUTATIVE PROTON ACCEPTOR FROM NUCLEOPHILIC O3 POSITION OF GLYCEROL, CHAIN Y.
2AC2UNKNOWNASP Y:245PUTATIVE PROTON ACCEPTOR FROM NUCLEOPHILIC O3 POSITION OF GLYCEROL, CHAIN O.
3AC3SOFTWAREACP Y:601BINDING SITE FOR RESIDUE MG Y 602
4AC4SOFTWAREASP O:245 , ACP O:601BINDING SITE FOR RESIDUE MG O 602
5AC5SOFTWAREGLY Y:12 , THR Y:13 , THR Y:14 , GLY Y:266 , THR Y:267 , GLY Y:310 , ALA Y:311 , ILE Y:313 , GLN Y:314 , ALA Y:326 , TYR Y:327 , SER Y:329 , GLY Y:411 , ALA Y:412 , ASN Y:415 , MG Y:602BINDING SITE FOR RESIDUE ACP Y 601
6AC6SOFTWAREGLY O:12 , THR O:13 , THR O:14 , GLY O:266 , THR O:267 , GLY O:310 , ALA O:311 , ILE O:313 , GLN O:314 , GLY O:411 , ASN O:415 , MG O:602BINDING SITE FOR RESIDUE ACP O 601
7AC7SOFTWAREGLN Y:82 , ARG Y:83 , GLU Y:84 , TYR Y:135 , ASP Y:245 , GLN Y:246 , PHE Y:270BINDING SITE FOR RESIDUE GOL Y 600
8AC8SOFTWARETHR O:13 , ASN O:81 , GLN O:82 , ARG O:83 , GLU O:84 , TYR O:135 , ASP O:245 , GLN O:246BINDING SITE FOR RESIDUE GOL O 600

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala Y:353 -Pro Y:354
2Ala O:353 -Pro O:354

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FGGY_KINASES_1PS00933 FGGY family of carbohydrate kinases signature 1.GLPK_ECOLI136-148
 		  2O:135-147
Y:135-147
2FGGY_KINASES_2PS00445 FGGY family of carbohydrate kinases signature 2.GLPK_ECOLI363-383
 		  2O:362-382
Y:362-382

(-) Exons   (0, 0)

(no "Exon" information available for 1GLL)

(-) 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:494
 aligned with GLPK_ECOLI | P0A6F3 from UniProtKB/Swiss-Prot  Length:502

    Alignment length:498
                                    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_ECOLI     3 EKKYIVALDQGTTSSRAVVMDHDANIISVSQREFEQIYPKPGWVEHDPMEIWATQSSTLVEVLAKADISSDQIAAIGITNQRETTIVWEKETGKPIYNAIVWQCRRTAEICEHLKRDGLEDYIRSNTGLVIDPYFSGTKVKWILDHVEGSRERARRGELLFGTVDTWLIWKMTQGRVHVTDYTNASRTMLFNIHTLDWDDKMLEVLDIPREMLPEVRRSSEVYGQTNIGGKGGTRIPISGIAGDQQAALFGQLCVKEGMAKNTYGTGCFMLMNTGEKAVKSENGLLTTIACGPTGEVNYALEGAVFMAGASIQWLRDEMKLINDAYDSEYFATKVQNTNGVYVVPAFTGLGAPYWDPYARGAIFGLTRGVNANHIIRATLESIAYQTRDVLEAMQADSGIRLHALRVDGGAVANNFLMQFQSDILGTRVERPEVREVTALGAAYLAGLAVGFWQNLDELQEKAVIEREFRPGIETTERNYRYAGWKKAVKRAMAWEEH 500
               SCOP domains d1gllo1 O:2-253 Glycerol kinase                                                                                                                                                                                                                             d1gllo2 O:254-499 Glycerol kinase                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee...eeeeeee.....eeeeeeee..............hhhhhhhhhhhhhhhhhhh...hhh...eeeee....eeeee..................hhhhhhhhh...hhhhhhhh........hhhhhhhhhhh....hhhhh...eeeeehhhhhhhhh......eeehhhhhhh...........hhhhhh.........eee......eeee..----.eeee.....hhhhhhhh........eeeee...eeeeeeee..........eeeeeee...eeeeeeeeee...hhhhhhhhh.......hhhhhhhh.........eee.hhh.............eee.......hhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee.hhhh.hhhhhhhhhhh..eeeee....hhhhhhhhhhhhhh........hhh...eeeee.....hhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------FGGY_KINASES_----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FGGY_KINASES_2       --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1gll O   2 EKKYIVALDQGTTSSRAVVMDHDANIISVSQREFEQIYPKPGWVEHDPMEIWATQSWTLVEVLAKADISSDQIAAIGITNQRETTIVWEKETGKPIYNAIVWQCRRTAEICEHLKRDGLEDYIRSNTGLVIDPYFSGTKVKWILDHVEGSRERARRGELLFGTVDTWLIWKMTQGRVHVTDYTNASRTMLFNIHTLDWDDKMLEVLDIPREMLPEVRRSSEVYGQTNIG----TRIPISGIAGDQQAALFGQLCVKEGMAKNTYGTGCFMLMNTGEKAVKSENGLLTTIACGPTGEVNYALEGAVFMAGASIQWLRDEMKLINDAYDSEYFATKVQNTNGVYVVPAFTGLGAPYWDPYARGAIFGLTRGVNANHIIRATLESIAYQTRDVLEAMQADSGIRLHALRVDGGAVANNFLMQFQSDILGTRVERPEVREVTALGAAYLAGLAVGFWQNLDELQEKAVIEREFRPGIETTERNYRYAGWKKAVKRAMAWEEH 499
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221        |-   |   241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491        
                                                                                                                                                                                                                                                              230  235                                                                                                                                                                                                                                                                        


Chain Y from PDB  Type:PROTEIN  Length:494
 aligned with GLPK_ECOLI | P0A6F3 from UniProtKB/Swiss-Prot  Length:502

    Alignment length:498
                                    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_ECOLI     3 EKKYIVALDQGTTSSRAVVMDHDANIISVSQREFEQIYPKPGWVEHDPMEIWATQSSTLVEVLAKADISSDQIAAIGITNQRETTIVWEKETGKPIYNAIVWQCRRTAEICEHLKRDGLEDYIRSNTGLVIDPYFSGTKVKWILDHVEGSRERARRGELLFGTVDTWLIWKMTQGRVHVTDYTNASRTMLFNIHTLDWDDKMLEVLDIPREMLPEVRRSSEVYGQTNIGGKGGTRIPISGIAGDQQAALFGQLCVKEGMAKNTYGTGCFMLMNTGEKAVKSENGLLTTIACGPTGEVNYALEGAVFMAGASIQWLRDEMKLINDAYDSEYFATKVQNTNGVYVVPAFTGLGAPYWDPYARGAIFGLTRGVNANHIIRATLESIAYQTRDVLEAMQADSGIRLHALRVDGGAVANNFLMQFQSDILGTRVERPEVREVTALGAAYLAGLAVGFWQNLDELQEKAVIEREFRPGIETTERNYRYAGWKKAVKRAMAWEEH 500
               SCOP domains d1glly1 Y:2-253 Glycerol kinase                                                                                                                                                                                                                             d1glly2 Y:254-499 Glycerol kinase                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeee...eeeeeeee....eeeeeeee..............hhhhhhhhhhhhhhhhhhh...hhh...eeeee....eeeee..................hhhhhhhhhh..hhhhh...........hhhhhhhhhhh....hhhhh...eeeeehhhhhhhhh......eeehhhhhhh...........hhhhhh.........eee......eeee..----.eeee.....hhhhhhh..........eeee...eee...............eeeeee.....eeeeee......hhhhhhhhh.......hhhhhhhhh........eee.hhh.............eee.......hhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee.hhhh.hhhhhhhhhhh..eeeee....hhhhhhhhhhhhhh........hhhh..eeeee.....hhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------FGGY_KINASES_----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FGGY_KINASES_2       --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1gll Y   2 EKKYIVALDQGTTSSRAVVMDHDANIISVSQREFEQIYPKPGWVEHDPMEIWATQSWTLVEVLAKADISSDQIAAIGITNQRETTIVWEKETGKPIYNAIVWQCRRTAEICEHLKRDGLEDYIRSNTGLVIDPYFSGTKVKWILDHVEGSRERARRGELLFGTVDTWLIWKMTQGRVHVTDYTNASRTMLFNIHTLDWDDKMLEVLDIPREMLPEVRRSSEVYGQTNIG----TRIPISGIAGDQQAALFGQLCVKEGMAKNTYGTGCFMLMNTGEKAVKSENGLLTTIACGPTGEVNYALEGAVFMAGASIQWLRDEMKLINDAYDSEYFATKVQNTNGVYVVPAFTGLGAPYWDPYARGAIFGLTRGVNANHIIRATLESIAYQTRDVLEAMQADSGIRLHALRVDGGAVANNFLMQFQSDILGTRVERPEVREVTALGAAYLAGLAVGFWQNLDELQEKAVIEREFRPGIETTERNYRYAGWKKAVKRAMAWEEH 499
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221        |-   |   241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491        
                                                                                                                                                                                                                                                              230  235
   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 1GLL)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1GLL)

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain O,Y   (GLPK_ECOLI | P0A6F3)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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: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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
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:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    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:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    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.
cellular component
    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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 Related Entries

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UniProtKB/Swiss-Prot
        GLPK_ECOLI | P0A6F3: 1bo5 1bot 1bu6 1bwf 1gla 1glb 1glc 1gld 1gle 1glf 1glj 3ezw

(-) Related Entries Specified in the PDB File

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