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(-) Description

Title :  CRYSTAL STRUCTURE OF B. MEGATERIUM LEVANSUCRASE MUTANT D257A
 
Authors :  C. P. Strube, A. Homann, M. Gamer, D. Jahn, J. Seibel, D. W. Heinz
Date :  26 Aug 10  (Deposition) - 23 Mar 11  (Release) - 01 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Five Fold Beta-Propeller, Levansucrase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. P. Strube, A. Homann, M. Gamer, D. Jahn, J. Seibel, D. W. Heinz
Polysaccharide Synthesis Of The Levansucrase Sacb From Bacillus Megaterium Is Controlled By Distinct Surface Motifs.
J. Biol. Chem. V. 286 17593 2011
PubMed-ID: 21454585  |  Reference-DOI: 10.1074/JBC.M110.203166

(-) Compounds

Molecule 1 - LEVANSUCRASE
    Chains: A
    EC Number: 2.4.1.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: LEVANSUCRASE SACB, UNP RESIDUES 29-484
    Gene: SACB
    Mutation: YES
    Organism Common: BACILLUS FRUCTOSUS
    Organism Scientific: BACILLUS MEGATERIUM
    Organism Taxid: 1404

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2CIT2Ligand/IonCITRIC ACID
3MG2Ligand/IonMAGNESIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:251 , GLN A:282 , LEU A:318 , ASN A:320 , ASP A:349 , HOH A:658BINDING SITE FOR RESIDUE CA A 1
2AC2SOFTWAREPRO A:163 , HIS A:164 , SER A:226 , ILE A:227 , PHE A:228 , ASP A:229 , LEU A:334 , MG A:486 , HOH A:491 , HOH A:533 , HOH A:543 , HOH A:545 , HOH A:546 , HOH A:561 , HOH A:596 , HOH A:795BINDING SITE FOR RESIDUE CIT A 485
3AC3SOFTWAREASP A:229 , CIT A:485 , HOH A:533 , HOH A:543BINDING SITE FOR RESIDUE MG A 486
4AC4SOFTWAREASP A:61 , LYS A:64 , PRO A:66 , ALA A:67 , GLY A:294 , GLY A:295 , LYS A:470 , MG A:488 , HOH A:539 , HOH A:605 , HOH A:652 , HOH A:653 , HOH A:655 , HOH A:656 , HOH A:810 , HOH A:991BINDING SITE FOR RESIDUE CIT A 487
5AC5SOFTWARECIT A:487 , HOH A:653 , HOH A:655 , HOH A:656BINDING SITE FOR RESIDUE MG A 488

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3OM2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3OM2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3OM2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3OM2)

(-) Exons   (0, 0)

(no "Exon" information available for 3OM2)

(-) 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:448
 aligned with D5DC07_BACMD | D5DC07 from UniProtKB/TrEMBL  Length:484

    Alignment length:448
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473        
         D5DC07_BACMD    34 SKDFNNSYGISHITRDNMVKIPQQQNSDQFKVPAFDESTIKNIASAKGKNASGNTIDLDVWDSWPLQNADGTVATYHGYQIVFALAGDPKDSNDTSVYLFYKKAGDKSIDSWKNAGRVFKDSDKFVPNDPHLKNQTQEWSGSGTLTKDGKVRLFYTDYSGKQYGKQTLTTAQVNMSQPNDNTLKVDGVEDYKSIFDGDGKIYQTVQQFIDEGGYDTGDNHTLRDPHYIEDNGHKYLVFEANTGTEDGYQGEDSLYNRAYYGGNNPFFQSEKKKLLEGSNKEKASLANGALGIIELNDDYTLKKVMKPLITSNTVTDEIERANIFKKDGKWYLFTDSRGSKMTIDGIGQDDVYMLGYVSNTLTGKYKPLNDTGLVLHMDLDPNDKTFTYSHFAVPQTKGDNVVITSYMTNRGFYEDNHSTFAPSFLVNIDGSKTSVVKDRVLEQGQLTV 481
               SCOP domains d3om2a_ A: Levansucrase                                                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -Glyco_hydro_68-3om2A01 A:35-480                                                                                                                                                                                                                                                                                                                                                                                                                               - Pfam domains
         Sec.struct. author ..........ee.hhhhhhhhhhhh..........hhhhh......eee.....eee.eeeeeeeee...........eeeeeeeee........eeeeeeee....hhhhheeeee..hhhhhhh....hhhhh.eeeeeeeee.....eeeeeeeee.....eeeeeeeeeeeeeee..eeeeeeeeeeeeee........hhhhhhhhhhhhhh.....eeeeeeee..eeeeeeeee........hhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhh.eeeeeeee.....eeee....ee........eeeeeeee..eeeeeeeee.hhh.........eeeeeeee.......ee.....eeeee.........eeeeeee......eeeeeeee...........ee...eeeeee..eeee............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3om2 A  34 SKDFNNSYGISHITRDNMVKIPQQQNSDQFKVPAFDESTIKNIASAKGKNASGNTIDLDVWDSWPLQNADGTVATYHGYQIVFALAGDPKDSNDTSVYLFYKKAGDKSIDSWKNAGRVFKDSDKFVPNDPHLKNQTQEWSGSGTLTKDGKVRLFYTDYSGKQYGKQTLTTAQVNMSQPNDNTLKVDGVEDYKSIFDGDGKIYQTVQQFIDEGGYDTGDNHTLRAPHYIEDNGHKYLVFEANTGTEDGYQGEDSLYNRAYYGGNNPFFQSEKKKLLEGSNKEKASLANGALGIIELNDDYTLKKVMKPLITSNTVTDEIERANIFKKDGKWYLFTDSRGSKMTIDGIGQDDVYMLGYVSNTLTGKYKPLNDTGLVLHMDLDPNDKTFTYSHFAVPQTKGDNVVITSYMTNRGFYEDNHSTFAPSFLVNIDGSKTSVVKDRVLEQGQLTV 481
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473
   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: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3OM2)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: B_Fructosidase (34)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (D5DC07_BACMD | D5DC07)
molecular function
    GO:0050053    levansucrase activity    Catalysis of the reaction: sucrose + 2,6-beta-D-fructosyl(n) = glucose + 2,6-beta-D-fructosyl(n+1).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
biological process
    GO:0009758    carbohydrate utilization    A series of processes that forms an integrated mechanism by which a cell or an organism detects the depletion of primary carbohydrate sources,usually glucose, and then activates genes to scavenge the last traces of the primary carbohydrate source and to transport and metabolize alternate carbohydrate sources. The utilization process begins when the cell or organism detects carbohydrate levels, includes the activation of genes whose products detect, transport or metabolize carbohydrates, and ends when the carbohydrate is incorporated into the cell or organism's metabolism.

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        D5DC07_BACMD | D5DC07: 3om4 3om5 3om6 3om7

(-) Related Entries Specified in the PDB File

3om4 3om5 3om6 3om7