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(-) Description

Title :  CRYSTAL STRUCTURE OF FRUCTOKINASE FROM BACILLUS SUBTILIS COMPLEXED WITH ADP
 
Authors :  B. Nocek, L. Volkart, M. Cuff, A. Joachimiak, Midwest Center For Str Genomics (Mcsg)
Date :  17 Aug 10  (Deposition) - 15 Sep 10  (Release) - 10 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.66
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Metal Dependent, Adp Binding, D-Fructose Binding, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Rok Family, Fructokinase, Reductive Methylation, 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
    Chains: A
    EC Number: 2.7.1.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21DE3
    Expression System Taxid: 469008
    Expression System Vector: PMCSG7
    Gene: GMUE, YDHR, BSU05860
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: GLUCOMANNAN UTILIZATION PROTEIN E

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 22)

Asymmetric Unit (6, 22)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MLY12Mod. Amino AcidN-DIMETHYL-LYSINE
3MLZ1Mod. Amino AcidN-METHYL-LYSINE
4MSE6Mod. Amino AcidSELENOMETHIONINE
5SO41Ligand/IonSULFATE ION
6ZN1Ligand/IonZINC ION
Biological Unit 1 (5, 42)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MLY24Mod. Amino AcidN-DIMETHYL-LYSINE
3MLZ2Mod. Amino AcidN-METHYL-LYSINE
4MSE12Mod. Amino AcidSELENOMETHIONINE
5SO42Ligand/IonSULFATE ION
6ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:129 , THR A:130 , GLY A:181 , PRO A:182 , ALA A:192 , ALA A:193 , GLY A:229 , GLY A:230 , GLN A:233 , GLN A:234 , HOH A:351 , HOH A:352 , HOH A:366 , HOH A:371 , HOH A:376 , HOH A:397 , HOH A:420 , HOH A:441 , HOH A:443 , HOH A:518 , HOH A:537 , HOH A:567 , HOH A:632 , HOH A:640 , HOH A:642BINDING SITE FOR RESIDUE ADP A 300
2AC2SOFTWAREHIS A:153 , CYS A:168 , HIS A:171 , CYS A:174BINDING SITE FOR RESIDUE ZN A 302
3AC3SOFTWAREMLY A:78 , ALA A:79 , ASN A:274 , HOH A:586 , HOH A:618BINDING SITE FOR RESIDUE SO4 A 303

(-) SS Bonds  (0, 0)

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

(-) 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 3OHR)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3OHR)

(-) 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:294
 aligned with SCRK_BACSU | O05510 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:294
                             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     - -MLGGIEAGGTKFVCAVGREDGTIIDRIEFPTKMPDETIEKVIQYFSQFSLQAIGIGSFGPVDNDKTSQTYGTITATPKAGWRHYPFLQTVKNEMKIPVGFSTDVNAAALGEFLFGEAKGLDSCLYITIGTGIGAGAIVEGRLLQGLSHPEMGHIYIRRHPDDVYQGKCPYHGDCFEGLASGPAIEARWGKKAADLSDIAQVWELEGYYIAQALAQYILILAPKKIILGGGVMQQKQVFSYIYQYVPKIMNSYLDFSELSDDISDYIVPPRLGSNAGIIGTLVLAHQALQAEAA 293
               SCOP domains d3ohra1 A:0-118 Putative fructokinase YhdR                                                                             d3ohra2 A:119-293 Putative fructokinase YhdR                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ----ROK-3ohrA01 A:4-184                                                                                                                                                                  ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...eeeeeee.....eeeeeeee..hhhhhhhhhhhhhh.....eeeeee...........................hhhhhhhhhhh..eeeeehhhhhhhhhhhhh.......eeeeee...eeeeeee..ee.......hhhhh...................hhhhhhhhhhhhhhhh.hhhhhh.hhhhhhhhhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhh....hhhhh.hhhh.ee...hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------ROK  PDB: A:128-153       -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ohr A   0 AmLGGIEAGGTkFVCAVGREDGTIIDRIEFPTkmPDETIEkVIQYFSQFSLQAIGIGSFGPVDNDkTSQTYGTITATPkAGWRHYPFLQTVkNEmkIPVGFSTDVNAAALGEFLFGEAkGLDSCLYITIGTGIGAGAIVEGRLLQGLSHPEmGHIYIRRHPDDVYQGkCPYHGDCFEGLASGPAIEARWGkKAADLSDIAQVWELEGYYIAQALAQYILILAPkkIILGGGVmQQkQVFSYIYQYVPKImNSYLDFSELSDDISDYIVPPRLGSNAGIIGTLVLAHQALQAEAA 293
                             |       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    
                             |        11-MLY               32-MLY  40-MLY                   65-MLY       78-MLY       91-MLY                    118-MLY                          151-MSE         167-MLY                190-MLY                          223-MLY  232-MSE          249-MSE                                        
                             1-MSE                          33-MSE                                                       94-MSE                                                                                                                           224-MLY    235-MLY                                                      
                                                                                                                          95-MLZ
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0 ; only for superseded entry 3EPQ: 1,2)

(no "CATH Domain" information available for 3OHR, only for superseded entry 3EPQ replaced by 3OHR)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Actin_ATPase (173)

(-) 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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  3ohr
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  2.7.1.4
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 Related Entries

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

UniProtKB/Swiss-Prot
        SCRK_BACSU | O05510: 1xc3 3lm9

(-) Related Entries Specified in the PDB File

1xc3 RELATED ID: APC1098 RELATED DB: TARGETDB
3lm9