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(-) Description

Title :  STRUCTURE OF A PUTATIVE FRUCTOKINASE FROM BACILLUS SUBTILIS
 
Authors :  M. E. Cuff, P. Quartey, L. Lezondra, A. Joachimiak, Midwest Center Fo Structural Genomics (Mcsg)
Date :  31 Aug 04  (Deposition) - 12 Oct 04  (Release) - 10 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Reductively Methylated, Fructokinase, Zn-Coordiation, Structural Genomics, Protein Structure Initiative, Mcsg, Psi, Midwest Center For Structural Genomics, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. Nocek, A. J. Stein, R. Jedrzejczak, M. E. Cuff, H. Li, L. Volkart, A. Joachimiak
Structural Studies Of Rok Fructokinase Ydhr From Bacillus Subtilis: Insights Into Substrate Binding And Fructose Specificity.
J. Mol. Biol. V. 406 325 2011
PubMed-ID: 21185308  |  Reference-DOI: 10.1016/J.JMB.2010.12.021

(-) Compounds

Molecule 1 - PUTATIVE FRUCTOKINASE
    ChainsA
    EC Number2.7.1.4
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPMCSG7
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneYDHR
    Organism ScientificBACILLUS SUBTILIS
    Organism Taxid1423

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (1x)A
Biological Unit 2 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2PT2Ligand/IonPLATINUM (II) ION
3ZN1Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2PT-1Ligand/IonPLATINUM (II) ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2PT-1Ligand/IonPLATINUM (II) ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:33BINDING SITE FOR RESIDUE PT A 301
2AC2SOFTWAREHIS A:153 , CYS A:168 , HIS A:171 , CYS A:174BINDING SITE FOR RESIDUE ZN A 302
3AC3SOFTWAREMET A:94BINDING SITE FOR RESIDUE PT A 303
4AC4SOFTWAREGLY A:59 , PRO A:60 , ASP A:103 , HIS A:148 , PRO A:149 , GLU A:150 , GOL A:306 , HOH A:310 , HOH A:315 , HOH A:333BINDING SITE FOR RESIDUE GOL A 305
5AC5SOFTWAREASP A:103 , GLY A:131 , ILE A:132 , GLY A:133 , GOL A:305 , HOH A:333 , HOH A:373BINDING SITE FOR RESIDUE GOL A 306

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1XC3)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly A:59 -Pro A:60

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1XC3)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ROKPS01125 ROK family signature.SCRK_BACSU128-153  1A:128-153
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ROKPS01125 ROK family signature.SCRK_BACSU128-153  1A:128-153
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ROKPS01125 ROK family signature.SCRK_BACSU128-153  2A:128-153

(-) Exons   (0, 0)

(no "Exon" information available for 1XC3)

(-) 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:295
 aligned with SCRK_BACSU | O05510 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:295
                             1                                                                                                                                                                                                                                                                                                     
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289     
           SCRK_BACSU     - -MLGGIEAGGTKFVCAVGREDGTIIDRIEFPTKMPDETIEKVIQYFSQFSLQAIGIGSFGPVDNDKTSQTYGTITATPKAGWRHYPFLQTVKNEMKIPVGFSTDVNAAALGEFLFGEAKGLDSCLYITIGTGIGAGAIVEGRLLQGLSHPEMGHIYIRRHPDDVYQGKCPYHGDCFEGLASGPAIEARWGKKAADLSDIAQVWELEGYYIAQALAQYILILAPKKIILGGGVMQQKQVFSYIYQYVPKIMNSYLDFSELSDDISDYIVPPRLGSNAGIIGTLVLAHQALQAEAAS 294
               SCOP domains -d1xc3a1 A:1-118 Putative fructokinase YhdR                                                                            d1xc3a2 A:119-294 Putative fructokinase YhdR                                                                                                                                     SCOP domains
               CATH domains 1xc3A01 A:0-102  [code=3.30.420.40, no name defined]                                                   1xc3A02 A:103-294  [code=3.30.420.40, no name defined]                                                                                                                                           CATH domains
               Pfam domains ----ROK-1xc3A01 A:4-184                                                                                                                                                                  -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...eeeeeee.....eeeeeeee..hhhhhhhhhhhhhh.....eeeeee...........................hhhhhhhhhhh..eeeeehhhhhhhhhhhhh.......eeeeee...eeeeeee..ee.......hhhhh...................hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhhhhh....hhhhh.hhhh.ee...hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------ROK  PDB: A:128-153       --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xc3 A   0 AMLGGIEAGGTKFVCAVGREDGTIIDRIEFPTKMPDETIEKVIQYFSQFSLQAIGIGSFGPVDNDKTSQTYGTITATPKAGWRHYPFLQTVKNEMKIPVGFSTDVNAAALGEFLFGEAKGLDSCLYITIGTGIGAGAIVEGRLLQGLSHPEMGHIYIRRHPDDVYQGKCPYHGDCFEGLASGPAIEARWGKKAADLSDIAQVWELEGYYIAQALAQYILILAPKKIILGGGVMQQKQVFSYIYQYVPKIMNSYLDFSELSDDISDYIVPPRLGSNAGIIGTLVLAHQALQAEAAS 294
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289     

   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, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (SCRK_BACSU | O05510)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0008865    fructokinase activity    Catalysis of the reaction: ATP + D-fructose = ADP + D-fructose 6-phosphate.
    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: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.
    GO:0000272    polysaccharide catabolic process    The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.

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 Related Entries

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

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        SCRK_BACSU | O055103lm9 3ohr

(-) Related Entries Specified in the PDB File

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