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(-) Description

Title :  CRYSTAL STRUCTURE OF SULFOLOBUS SOLFATARICUS 2-KETO-3-DEOXYGLUCONATE KINASE COMPLEXED WITH 2-KETO-3-DEOXYGLUCONATE
 
Authors :  J. A. Potter, A. Theodossis, M. Kerou, H. J. Lamble, S. D. Bull, D. W. Hough, M. J. Danson, G. L. Taylor
Date :  04 Sep 07  (Deposition) - 02 Oct 07  (Release) - 10 Nov 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Kinase, Transferase, Sulfolobus Solfataricus, Pfkb Family Carbohydrate Kinase, 2- Keto-3-Deoxygluconate Kinasekinase, 2- Keto-3-Deoxygluconate Kinase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. A. Potter, M. Kerou, H. J. Lamble, S. D. Bull, D. W. Hough, M. J. Danson, G. L. Taylor
The Structure Of Sulfolobus Solfataricus 2-Keto-3- Deoxygluconate Kinase.
Acta Crystallogr. , Sect. D V. 64 1283 2008
PubMed-ID: 19018105  |  Reference-DOI: 10.1107/S0907444908036111

(-) Compounds

Molecule 1 - FRUCTOKINASE
    Chains: A, B, C
    EC Number: 2.7.1.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: SULFOLOBUS SOLFATARICUS
    Organism Taxid: 2287
    Synonym: 2-KETO-3-DEOXYGLUCONATE KINASE

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric Unit (4, 12)
No.NameCountTypeFull Name
1AMP3Ligand/IonADENOSINE MONOPHOSPHATE
2ANP3Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
3KDF3Ligand/Ion3-DEOXY-ALPHA-D-ERYTHRO-HEX-2-ULOFURANOSONICACID
4KDG3Ligand/Ion2-KETO-3-DEOXYGLUCONATE
Biological Unit 1 (4, 24)
No.NameCountTypeFull Name
1AMP6Ligand/IonADENOSINE MONOPHOSPHATE
2ANP6Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
3KDF6Ligand/Ion3-DEOXY-ALPHA-D-ERYTHRO-HEX-2-ULOFURANOSONICACID
4KDG6Ligand/Ion2-KETO-3-DEOXYGLUCONATE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:11 , GLY A:34 , SER A:35 , TYR A:90 , LEU A:104 , TYR A:106 , ARG A:108 , ILE A:137 , ARG A:166 , GLY A:255 , ASP A:258 , ASP A:294 , KDF A:1314 , ANP A:1315BINDING SITE FOR RESIDUE KDG A1313
02AC2SOFTWARELEU A:11 , ALA A:33 , GLY A:34 , SER A:35 , TYR A:90 , TYR A:106 , ARG A:108 , ILE A:137 , ARG A:166 , GLY A:255 , ASP A:258 , ASP A:294 , KDG A:1313 , ANP A:1315 , HOH A:2002BINDING SITE FOR RESIDUE KDF A1314
03AC3SOFTWAREASN A:164 , ARG A:166 , LYS A:226 , GLY A:228 , SER A:229 , GLY A:231 , TYR A:246 , GLY A:255 , ALA A:256 , GLY A:257 , ASP A:258 , MET A:260 , ILE A:282 , SER A:285 , ILE A:289 , KDG A:1313 , KDF A:1314 , AMP A:1316 , HOH A:2137 , HOH A:2138 , HOH A:2139BINDING SITE FOR RESIDUE ANP A1315
04AC4SOFTWARELYS A:226 , GLY A:228 , GLY A:231 , TYR A:246 , VAL A:250 , ALA A:256 , MET A:260 , ILE A:282 , SER A:285 , ILE A:289 , ANP A:1315 , HOH A:2048 , HOH A:2137 , HOH A:2139BINDING SITE FOR RESIDUE AMP A1316
05AC5SOFTWARELEU B:11 , GLY B:34 , SER B:35 , ASN B:38 , TYR B:90 , LEU B:104 , TYR B:106 , ARG B:108 , ILE B:137 , ARG B:166 , GLY B:255 , ASP B:258 , ASP B:294 , KDF B:1314 , ANP B:1315 , HOH B:2004BINDING SITE FOR RESIDUE KDG B1313
06AC6SOFTWARELEU B:11 , ALA B:33 , GLY B:34 , SER B:35 , ASN B:38 , TYR B:90 , LEU B:104 , TYR B:106 , ARG B:108 , ILE B:137 , ARG B:166 , GLY B:255 , ASP B:258 , ASP B:294 , KDG B:1313 , ANP B:1315 , HOH B:2004BINDING SITE FOR RESIDUE KDF B1314
07AC7SOFTWAREASN B:164 , ARG B:166 , LYS B:226 , GLY B:228 , SER B:229 , GLY B:231 , ALA B:245 , TYR B:246 , PRO B:253 , GLY B:255 , ALA B:256 , GLY B:257 , ASP B:258 , MET B:260 , ILE B:282 , SER B:285 , ILE B:289 , KDG B:1313 , KDF B:1314 , AMP B:1316 , HOH B:2160 , HOH B:2161 , HOH B:2162 , HOH B:2163 , HOH B:2164BINDING SITE FOR RESIDUE ANP B1315
08AC8SOFTWARELYS B:226 , GLY B:228 , GLY B:231 , TYR B:246 , VAL B:250 , ALA B:256 , MET B:260 , ILE B:282 , SER B:285 , ILE B:289 , ANP B:1315 , HOH B:2054 , HOH B:2163 , HOH B:2164BINDING SITE FOR RESIDUE AMP B1316
09AC9SOFTWARELEU C:11 , GLY C:34 , SER C:35 , TYR C:90 , LEU C:104 , TYR C:106 , ARG C:108 , ILE C:137 , ARG C:166 , GLY C:255 , ASP C:258 , ASP C:294 , KDF C:1314 , ANP C:1315BINDING SITE FOR RESIDUE KDG C1313
10BC1SOFTWAREALA C:33 , GLY C:34 , SER C:35 , ASN C:38 , TYR C:90 , LEU C:104 , TYR C:106 , ARG C:108 , ARG C:166 , GLY C:255 , ASP C:258 , ASP C:294 , KDG C:1313 , ANP C:1315BINDING SITE FOR RESIDUE KDF C1314
11BC2SOFTWAREASN C:164 , ARG C:166 , LYS C:226 , GLY C:228 , GLY C:231 , TYR C:246 , GLY C:255 , ALA C:256 , GLY C:257 , ASP C:258 , MET C:260 , ILE C:282 , SER C:285 , ILE C:289 , KDG C:1313 , KDF C:1314 , AMP C:1316 , HOH C:2049 , HOH C:2153 , HOH C:2154BINDING SITE FOR RESIDUE ANP C1315
12BC3SOFTWARELYS C:226 , GLY C:228 , SER C:229 , GLY C:231 , ALA C:245 , TYR C:246 , ALA C:256 , MET C:260 , ILE C:282 , SER C:285 , ILE C:289 , ANP C:1315 , HOH C:2153 , HOH C:2154BINDING SITE FOR RESIDUE AMP C1316

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Tyr A:96 -Pro A:97
2Tyr B:96 -Pro B:97
3Tyr C:96 -Pro C:97

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VAR)

(-) Exons   (0, 0)

(no "Exon" information available for 2VAR)

(-) Sequences/Alignments

Asymmetric 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:311
 aligned with KDGK_SULSO | Q97U29 from UniProtKB/Swiss-Prot  Length:313

    Alignment length:311
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311 
           KDGK_SULSO     2 VDVIALGEPLIQFNSFNPGPLRFVNYFEKHVAGSELNFCIAVVRNHLSCSLIARVGNDEFGKNIIEYSRAQGIDTSHIKVDNESFTGIYFIQRGYPIPMKSELVYYRKGSAGSRLSPEDINENYVRNSRLVHSTGITLAISDNAKEAVIKAFELAKSRSLDTNIRPKLWSSLEKAKETILSILKKYDIEVLITDPDDTKILLDVTDPDEAYRKYKELGVKVLLYKLGSKGAIAYKDNVKAFKDAYKVPVEDPTGAGDAMAGTFVSLYLQGKDIEYSLAHGIAASTLVITVRGDNELTPTLEDAERFLNEFK 312
               SCOP domains d2vara_ A: automated matches                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eeeeee....hhhhh.eeeeeeehhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhhh......eeee......eeeeee.......eeeeee...hhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhhhh..eeee...hhhhh.hhhhhhhhhhhhhhhh.eeeeeehhhhhhhhhh..hhhhhhhhhhh..eeeeeee.hhh.eeeee..eeeee...........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2var A   2 VDVIALGEPLIQFNSFNPGPLRFVNYFEKHVAGSELNFCIAVVRNHLSCSLIARVGNDEFGKNIIEYSRAQGIDTSHIKVDNESFTGIYFIQRGYPIPMKSELVYYRKGSAGSRLSPEDINENYVRNSRLVHSTGITLAISDNAKEAVIKAFELAKSRSLDTNIRPKLWSSLEKAKETILSILKKYDIEVLITDPDDTKILLDVTDPDEAYRKYKELGVKVLLYKLGSKGAIAYKDNVKAFKDAYKVPVEDPTGAGDAMAGTFVSLYLQGKDIEYSLAHGIAASTLVITVRGDNELTPTLEDAERFLNEFK 312
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311 


Chain B from PDB  Type:PROTEIN  Length:311
 aligned with KDGK_SULSO | Q97U29 from UniProtKB/Swiss-Prot  Length:313

    Alignment length:311
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311 
           KDGK_SULSO     2 VDVIALGEPLIQFNSFNPGPLRFVNYFEKHVAGSELNFCIAVVRNHLSCSLIARVGNDEFGKNIIEYSRAQGIDTSHIKVDNESFTGIYFIQRGYPIPMKSELVYYRKGSAGSRLSPEDINENYVRNSRLVHSTGITLAISDNAKEAVIKAFELAKSRSLDTNIRPKLWSSLEKAKETILSILKKYDIEVLITDPDDTKILLDVTDPDEAYRKYKELGVKVLLYKLGSKGAIAYKDNVKAFKDAYKVPVEDPTGAGDAMAGTFVSLYLQGKDIEYSLAHGIAASTLVITVRGDNELTPTLEDAERFLNEFK 312
               SCOP domains d2varb_ B: automated matches                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eeeeee....hhhhh.eeeeeeehhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhhh......eeee......eeeeee.......eeeeee....hhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhhhh..eeee...hhhhh.hhhhhhhhhhhhhhhh.eeeeeehhhhhhhhhh..hhhhhhhhhhhh.eeeeeee.hhh.eeeee..eeeee...........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..........hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2var B   2 VDVIALGEPLIQFNSFNPGPLRFVNYFEKHVAGSELNFCIAVVRNHLSCSLIARVGNDEFGKNIIEYSRAQGIDTSHIKVDNESFTGIYFIQRGYPIPMKSELVYYRKGSAGSRLSPEDINENYVRNSRLVHSTGITLAISDNAKEAVIKAFELAKSRSLDTNIRPKLWSSLEKAKETILSILKKYDIEVLITDPDDTKILLDVTDPDEAYRKYKELGVKVLLYKLGSKGAIAYKDNVKAFKDAYKVPVEDPTGAGDAMAGTFVSLYLQGKDIEYSLAHGIAASTLVITVRGDNELTPTLEDAERFLNEFK 312
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311 


Chain C from PDB  Type:PROTEIN  Length:311
 aligned with KDGK_SULSO | Q97U29 from UniProtKB/Swiss-Prot  Length:313

    Alignment length:311
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311 
           KDGK_SULSO     2 VDVIALGEPLIQFNSFNPGPLRFVNYFEKHVAGSELNFCIAVVRNHLSCSLIARVGNDEFGKNIIEYSRAQGIDTSHIKVDNESFTGIYFIQRGYPIPMKSELVYYRKGSAGSRLSPEDINENYVRNSRLVHSTGITLAISDNAKEAVIKAFELAKSRSLDTNIRPKLWSSLEKAKETILSILKKYDIEVLITDPDDTKILLDVTDPDEAYRKYKELGVKVLLYKLGSKGAIAYKDNVKAFKDAYKVPVEDPTGAGDAMAGTFVSLYLQGKDIEYSLAHGIAASTLVITVRGDNELTPTLEDAERFLNEFK 312
               SCOP domains d2varc_ C: automated matches                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eeeeee....hhhhh..eeeeeehhhhhhhhhhhhh...eeeeeeee.hhhhhhhhhhhhhh......eeee......eeeeee.......eeeeee....hhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhhhh..eeee...hhhhh.hhhhhhhhhhhhhhhh.eeeeeehhhhhhhhhh..hhhhhhhhhhhh.eeeeeee.hhh.eeeee..eeeee...........hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..........hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2var C   2 VDVIALGEPLIQFNSFNPGPLRFVNYFEKHVAGSELNFCIAVVRNHLSCSLIARVGNDEFGKNIIEYSRAQGIDTSHIKVDNESFTGIYFIQRGYPIPMKSELVYYRKGSAGSRLSPEDINENYVRNSRLVHSTGITLAISDNAKEAVIKAFELAKSRSLDTNIRPKLWSSLEKAKETILSILKKYDIEVLITDPDDTKILLDVTDPDEAYRKYKELGVKVLLYKLGSKGAIAYKDNVKAFKDAYKVPVEDPTGAGDAMAGTFVSLYLQGKDIEYSLAHGIAASTLVITVRGDNELTPTLEDAERFLNEFK 312
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311
   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, 3)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (KDGK_SULSO | Q97U29)
molecular function
    GO:0008671    2-dehydro-3-deoxygalactonokinase activity    Catalysis of the reaction: 2-dehydro-3-deoxy-D-galactonate + ATP = 6-phospho-2-dehydro-3-deoxy-D-galactonate + ADP + 2 H(+).
    GO:0008673    2-dehydro-3-deoxygluconokinase activity    Catalysis of the reaction: 2-dehydro-3-deoxy-D-gluconate + ATP = 2-dehydro-3-deoxy-6-phospho-D-gluconate + ADP + 2 H(+).
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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: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:0046835    carbohydrate phosphorylation    The process of introducing a phosphate group into a carbohydrate, any organic compound based on the general formula Cx(H2O)y.
    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
        KDGK_SULSO | Q97U29: 2v78

(-) Related Entries Specified in the PDB File

2v78 CRYSTAL STRUCTURE OF SULFOLOBUS SOLFATARICUS 2 -KETO-3-DEOXYGLUCONATE KINASE