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(-) Description

Title :  CRYSTAL STRUCTURE OF THERMOCOCCUS LITORALIS ADP-DEPENDENT GLUCOKINASE (GK)
 
Authors :  A. Herrera-Morande, J. A. Rivas-Pardo, F. J. Fernandez, V. Guixe, M. C.
Date :  30 Aug 12  (Deposition) - 10 Jul 13  (Release) - 17 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A
Keywords :  Transferase, Ribokinase Superfamily (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. A. Rivas-Pardo, A. Herrera-Morande, V. Castro-Fernandez, F. J. Fernandez, M. C. Vega, V. Guixe
Crystal Structure, Saxs And Kinetic Mechanism Of Hyperthermophilic Adp-Dependent Glucokinase From Thermococcus Litoralis Reveal A Conserved Mechanism For Catalysis.
Plos One V. 8 66687 2013
PubMed-ID: 23818958  |  Reference-DOI: 10.1371/JOURNAL.PONE.0066687

(-) Compounds

Molecule 1 - ADP-DEPENDENT GLUCOKINASE
    Chains: A
    EC Number: 2.7.1.147
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: PLYSS
    Expression System Vector: PET-17B
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMOCOCCUS LITORALIS
    Organism Taxid: 2265
    Synonym: ADP-GK, ADPGK

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 33)

Asymmetric/Biological Unit (6, 33)
No.NameCountTypeFull Name
1DTT2Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
2GOL15Ligand/IonGLYCEROL
3PEG5Ligand/IonDI(HYDROXYETHYL)ETHER
4PGE3Ligand/IonTRIETHYLENE GLYCOL
5SO46Ligand/IonSULFATE ION
6TRS2Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (33, 33)

Asymmetric Unit (33, 33)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:233BINDING SITE FOR RESIDUE GOL A1468
02AC2SOFTWARELYS A:45 , TYR A:46 , ASP A:51 , TRP A:111 , ASP A:114 , HOH A:2044 , HOH A:2046 , HOH A:2081BINDING SITE FOR RESIDUE GOL A1469
03AC3SOFTWAREALA A:281 , TYR A:282 , ASN A:305 , VAL A:307 , GLU A:308BINDING SITE FOR RESIDUE GOL A1470
04AC4SOFTWAREMET A:341 , ASP A:342 , GLN A:362 , ASP A:429 , ARG A:430 , GOL A:1475BINDING SITE FOR RESIDUE GOL A1471
05AC5SOFTWARETYR A:354 , ASN A:403 , ARG A:405 , PGE A:1494 , SO4 A:1498 , HOH A:2227BINDING SITE FOR RESIDUE GOL A1472
06AC6SOFTWAREALA A:379 , ALA A:380 , LYS A:438 , ILE A:439 , VAL A:440 , ILE A:449 , HOH A:2228 , HOH A:2272 , HOH A:2282BINDING SITE FOR RESIDUE GOL A1473
07AC7SOFTWAREGLU A:102 , ARG A:106 , ARG A:109 , PHE A:420 , GLU A:421 , HOH A:2068 , HOH A:2078BINDING SITE FOR RESIDUE GOL A1474
08AC8SOFTWAREASP A:342 , GLU A:343 , GOL A:1471BINDING SITE FOR RESIDUE GOL A1475
09AC9SOFTWAREVAL A:159 , PRO A:160 , ALA A:175 , ARG A:220 , GLU A:222 , SO4 A:1500 , HOH A:2101 , HOH A:2283BINDING SITE FOR RESIDUE GOL A1476
10BC1SOFTWAREPRO A:71 , ARG A:87 , LYS A:93 , MET A:95 , TRP A:97 , HOH A:2053 , HOH A:2065BINDING SITE FOR RESIDUE GOL A1477
11BC2SOFTWAREASP A:260 , ARG A:261 , SER A:264 , GLU A:327 , HIS A:329 , HOH A:2183 , HOH A:2189BINDING SITE FOR RESIDUE GOL A1478
12BC3SOFTWAREPHE A:162 , GLY A:164 , ASP A:174 , ILE A:176 , ARG A:221 , HOH A:2123 , HOH A:2133BINDING SITE FOR RESIDUE GOL A1479
13BC4SOFTWARESER A:101 , GLU A:102 , GLU A:103BINDING SITE FOR RESIDUE GOL A1480
14BC5SOFTWARETHR A:446 , VAL A:447 , GLY A:448 , ILE A:449 , GLY A:450 , HOH A:2274 , HOH A:2285BINDING SITE FOR RESIDUE GOL A1481
15BC6SOFTWARESER A:264 , ASN A:267 , ARG A:271 , HOH A:2189 , HOH A:2193BINDING SITE FOR RESIDUE GOL A1482
16BC7SOFTWARETYR A:282 , ARG A:286 , ARG A:289 , SER A:311 , GLU A:314 , PEG A:1487BINDING SITE FOR RESIDUE TRS A1483
17BC8SOFTWAREGLU A:279 , GLY A:303 , LEU A:304 , ASN A:305 , GLU A:308 , HIS A:352 , GLY A:450 , ASP A:451BINDING SITE FOR RESIDUE TRS A1484
18BC9SOFTWAREASN A:40 , ASP A:42 , GLU A:96 , GLY A:119 , GLY A:120 , ILE A:124 , HIS A:184 , ILE A:207BINDING SITE FOR RESIDUE DTT A1485
19CC1SOFTWAREARG A:369 , GLU A:421 , ASN A:422 , HOH A:2018 , HOH A:2287BINDING SITE FOR RESIDUE DTT A1486
20CC2SOFTWAREALA A:310 , GLU A:314 , TRS A:1483BINDING SITE FOR RESIDUE PEG A1487
21CC3SOFTWARELYS A:2 , ARG A:8 , PRO A:142 , TYR A:213 , TYR A:218 , MET A:219 , ARG A:220 , VAL A:408 , GLU A:411 , HOH A:2105BINDING SITE FOR RESIDUE PEG A1488
22CC4SOFTWAREARG A:117 , ILE A:118 , ASN A:127 , GLU A:150 , LEU A:151 , PHE A:152BINDING SITE FOR RESIDUE PEG A1489
23CC5SOFTWAREGLU A:247 , TYR A:248 , ASN A:285BINDING SITE FOR RESIDUE PEG A1490
24CC6SOFTWAREARG A:271 , TYR A:272BINDING SITE FOR RESIDUE PEG A1491
25CC7SOFTWAREGLU A:347 , TYR A:363 , GLU A:461 , ARG A:465 , SO4 A:1495 , HOH A:2196 , HOH A:2288BINDING SITE FOR RESIDUE PGE A1492
26CC8SOFTWAREASN A:270 , ASN A:273 , VAL A:274 , LYS A:275 , PRO A:297 , THR A:300 , GLU A:347 , HOH A:2207BINDING SITE FOR RESIDUE PGE A1493
27CC9SOFTWAREARG A:224 , ARG A:261 , GLY A:328 , HIS A:329 , ILE A:330 , GLU A:412 , GOL A:1472 , HOH A:2217BINDING SITE FOR RESIDUE PGE A1494
28DC1SOFTWAREASN A:273 , LYS A:275 , PGE A:1492 , HOH A:2195BINDING SITE FOR RESIDUE SO4 A1495
29DC2SOFTWARELYS A:385 , ARG A:390 , GLN A:393BINDING SITE FOR RESIDUE SO4 A1496
30DC3SOFTWAREARG A:117 , GLU A:188 , ARG A:205 , LYS A:444 , SER A:445 , THR A:446 , VAL A:447BINDING SITE FOR RESIDUE SO4 A1497
31DC4SOFTWAREARG A:224 , ARG A:405 , GOL A:1472 , HOH A:2256 , HOH A:2257 , HOH A:2290 , HOH A:2291BINDING SITE FOR RESIDUE SO4 A1498
32DC5SOFTWAREARG A:134BINDING SITE FOR RESIDUE SO4 A1499
33DC6SOFTWAREARG A:220 , ARG A:221 , GLU A:222 , LYS A:415 , GOL A:1476 , HOH A:2122 , HOH A:2156 , HOH A:2283 , HOH A:2284BINDING SITE FOR RESIDUE SO4 A1500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4B8R)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala A:36 -Tyr A:37

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4B8R)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADPKPS51255 ADP-dependent kinase (ADPK) domain profile.GLKA_THELN10-467  1A:10-467

(-) Exons   (0, 0)

(no "Exon" information available for 4B8R)

(-) 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:467
 aligned with GLKA_THELN | Q7M537 from UniProtKB/Swiss-Prot  Length:467

    Alignment length:467
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       
           GLKA_THELN     1 MKESLKDRIRLWKRLYVNAFENALNAIPNVKGVLLAYNTNIDAIKYLDKDDLEKRVTEIGKEKVFEIIENPPEKISSIEELLGGILRSIKLGKAMEWFVESEEVRRYLREWGWDELRIGGQAGIMANLLGGVYRIPTIVHVPQNPKLQAELFVDGPIYVPVFEGNKLKLVHPKDAIAEEEELIHYIYEFPRGFQVFDVQAPRENRFIANADDYNARVYMRREFREGFEEITRNVELAIISGLQVLKEYYPDGTTYRDVLDRVESHLNILNRYNVKSHFEFAYTANRRVREALVELLPKFTSVGLNEVELASIMEIIGDEELAKEVLEGHIFSVIDAMNVLMDETGIERIHFHTYGYYLALTQYRGEEVRDALLFASLAAAAKAMKGNLERIEQIRDALSVPTNERAIVLEEELEKEFTEFENGLIDMVDRQLAFVPTKIVASPKSTVGIGDTISSSAFVSEFGMRKR 467
               SCOP domains d4b8ra_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee...eeeeeee.hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhh..eeeeehhhhhhhhhhh......eee.....hhhhhh......eeeeeee..eeeeehhhhhh......eeeeeee....ee..ee....eeeeeee.........hhhhhhhhhhhhh...eeee.hhhhh.........hhhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..eeeee...eeeeee....hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh..hhhhhhhhhhhhhhh.eee..eee....eeeeee...........hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------ADPK  PDB: A:10-467 UniProt: 10-467                                                                                                                                                                                                                                                                                                                                                                                                                                        PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b8r A   1 MKESLKDRIRLWKRLYVNAFENALNAIPNVKGVLLAYNTNIDAIKYLDKDDLEKRVTEIGKEKVFEIIENPPEKISSIEELLGGILRSIKLGKAMEWFVESEEVRRYLREWGWDELRIGGQAGIMANLLGGVYRIPTIVHVPQNPKLQAELFVDGPIYVPVFEGNKLKLVHPKDAIAEEEELIHYIYEFPRGFQVFDVQAPRENRFIANADDYNARVYMRREFREGFEEITRNVELAIISGLQVLKEYYPDGTTYRDVLDRVESHLNILNRYNVKSHFEFAYTANRRVREALVELLPKFTSVGLNEVELASIMEIIGDEELAKEVLEGHIFSVIDAMNVLMDETGIERIHFHTYGYYLALTQYRGEEVRDALLFASLAAAAKAMKGNLERIEQIRDALSVPTNERAIVLEEELEKEFTEFENGLIDMVDRQLAFVPTKIVASPKSTVGIGDTISSSAFVSEFGMRKR 467
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460
   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  (0, 0)

(no "CATH Domain" information available for 4B8R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4B8R)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GLKA_THELN | Q7M537)
molecular function
    GO:0043843    ADP-specific glucokinase activity    Catalysis of the reaction: ADP + D-glucose = AMP + D-glucose 6-phosphate.
    GO:0004340    glucokinase activity    Catalysis of the reaction: ATP + D-glucose = ADP + D-glucose-6-phosphate.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0051156    glucose 6-phosphate metabolic process    The chemical reactions and pathways involving glucose 6-phosphate, a monophosphorylated derivative of glucose with the phosphate group attached to C-6.
    GO:0006006    glucose metabolic process    The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides.
    GO:0006096    glycolytic process    The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  Cis Peptide Bonds
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 Related Entries

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

UniProtKB/Swiss-Prot
        GLKA_THELN | Q7M537: 1gc5 4b8s

(-) Related Entries Specified in the PDB File

4b8s CRYSTAL STRUCTURE OF THERMOCOCCUS LITORALIS ADP-DEPENDENT GLUCOKINASE (GK)