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(-) Description

Title :  CRYSTAL STRUCTURE OF INULOSUCRASE FROM LACTOBACILLUS JOHNSONII NCC533
 
Authors :  T. Pijning, M. A. Anwar, H. Leemhuis, S. Kralj, L. Dijkhuizen, B. W. Dijk
Date :  07 Apr 11  (Deposition) - 03 Aug 11  (Release) - 31 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Fructosyltransferase, Glycoside Hydrolase Family Gh68, Transferase, Sugar Utilization (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Pijning, M. A. Anwar, M. Boger, J. M. Dobruchowska, H. Leemhuis, S. Kralj, L. Dijkhuizen, B. W. Dijkstra
Crystal Structure Of Inulosucrase From Lactobacillus: Insights Into The Substrate Specificity And Product Specificity Of Gh68 Fructansucrases.
J. Mol. Biol. V. 412 80 2011
PubMed-ID: 21801732  |  Reference-DOI: 10.1016/J.JMB.2011.07.031

(-) Compounds

Molecule 1 - LEVANSUCRASE
    Chains: A
    EC Number: 2.4.1.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETINUJ
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET15B
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 145-708
    Organism Scientific: LACTOBACILLUS JOHNSONII
    Organism Taxid: 33959
    Strain: NCC533
    Synonym: INULOSUCRASE

 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  (5, 23)

Asymmetric Unit (5, 23)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2CA1Ligand/IonCALCIUM ION
3CL1Ligand/IonCHLORIDE ION
4GOL9Ligand/IonGLYCEROL
5SO49Ligand/IonSULFATE ION
Biological Unit 1 (3, 21)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2CA-1Ligand/IonCALCIUM ION
3CL-1Ligand/IonCHLORIDE ION
4GOL9Ligand/IonGLYCEROL
5SO49Ligand/IonSULFATE ION
Biological Unit 2 (3, 42)
No.NameCountTypeFull Name
1ACT6Ligand/IonACETATE ION
2CA-1Ligand/IonCALCIUM ION
3CL-1Ligand/IonCHLORIDE ION
4GOL18Ligand/IonGLYCEROL
5SO418Ligand/IonSULFATE ION

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:419 , GLN A:450 , TRP A:487 , ASN A:489 , ASP A:521 , HOH A:2276BINDING SITE FOR RESIDUE CA A1709
02AC2SOFTWAREGLN A:338 , TYR A:355 , LYS A:357BINDING SITE FOR RESIDUE CL A1710
03AC3SOFTWARELYS A:250 , ASN A:320 , SO4 A:1721 , HOH A:2497BINDING SITE FOR RESIDUE ACT A1711
04AC4SOFTWAREASP A:500 , ASN A:503 , HOH A:2336BINDING SITE FOR RESIDUE ACT A1712
05AC5SOFTWAREARG A:545BINDING SITE FOR RESIDUE ACT A1713
06AC6SOFTWAREGLU A:625 , LYS A:629 , GLY A:630 , HIS A:632 , HOH A:2088 , HOH A:2498BINDING SITE FOR RESIDUE SO4 A1714
07AC7SOFTWARELYS A:264 , VAL A:265 , HOH A:2079 , HOH A:2499 , HOH A:2501BINDING SITE FOR RESIDUE SO4 A1715
08AC8SOFTWAREASN A:364 , HIS A:390 , ASP A:392 , LYS A:678 , PRO A:687 , GLY A:688 , HOH A:2240 , HOH A:2502 , HOH A:2503BINDING SITE FOR RESIDUE SO4 A1716
09AC9SOFTWARETYR A:376 , ASP A:392 , ASN A:393 , LYS A:502 , HOH A:2470BINDING SITE FOR RESIDUE SO4 A1717
10BC1SOFTWAREASP A:318 , ASN A:320 , HIS A:321BINDING SITE FOR RESIDUE SO4 A1718
11BC2SOFTWARELYS A:248 , ASN A:669 , ASP A:671 , SO4 A:1721 , HOH A:2504BINDING SITE FOR RESIDUE SO4 A1719
12BC3SOFTWARESER A:211 , LYS A:212 , GLU A:213BINDING SITE FOR RESIDUE SO4 A1720
13BC4SOFTWARESER A:247 , LYS A:248 , GLU A:380 , ASP A:382 , ACT A:1711 , SO4 A:1719 , HOH A:2051 , HOH A:2505 , HOH A:2506 , HOH A:2507BINDING SITE FOR RESIDUE SO4 A1721
14BC5SOFTWAREARG A:238 , HOH A:2508BINDING SITE FOR RESIDUE SO4 A1722
15BC6SOFTWAREASP A:272 , TRP A:339 , SER A:340 , ARG A:424 , ASP A:425 , GLU A:441 , GLU A:524 , GOL A:1730 , GOL A:1731BINDING SITE FOR RESIDUE GOL A1723
16BC7SOFTWAREASP A:480 , ARG A:484 , MET A:553 , ASN A:556 , LYS A:557 , ASP A:695 , LEU A:698BINDING SITE FOR RESIDUE GOL A1724
17BC8SOFTWAREARG A:610 , LYS A:654 , TRP A:663 , HOH A:2447 , HOH A:2509BINDING SITE FOR RESIDUE GOL A1725
18BC9SOFTWAREASP A:431 , ASP A:432 , TYR A:535 , LEU A:573 , HOH A:2510BINDING SITE FOR RESIDUE GOL A1726
19CC1SOFTWAREASP A:318 , ASN A:657 , HOH A:2511 , HOH A:2512BINDING SITE FOR RESIDUE GOL A1727
20CC2SOFTWAREASN A:556 , LYS A:557 , ALA A:558 , VAL A:559 , GLY A:560 , PRO A:592 , VAL A:694 , LEU A:698 , ILE A:699 , GLY A:700 , GLY A:701 , TYR A:702 , ASN A:703 , LEU A:704BINDING SITE FOR RESIDUE GOL A1728
21CC3SOFTWARELYS A:534 , VAL A:569 , SER A:570 , ASP A:571 , ASN A:647 , HOH A:2513 , HOH A:2514BINDING SITE FOR RESIDUE GOL A1729
22CC4SOFTWARETRP A:271 , MET A:296 , ASN A:305 , ARG A:623 , GOL A:1723BINDING SITE FOR RESIDUE GOL A1730
23CC5SOFTWAREASP A:272 , GLU A:524 , ARG A:542 , TYR A:600 , SER A:601 , TYR A:619 , ARG A:623 , GOL A:1723BINDING SITE FOR RESIDUE GOL A1731

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2YFR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2YFR)

(-) 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:534
 aligned with INUS_LACJO | Q74K42 from UniProtKB/Swiss-Prot  Length:797

    Alignment length:534
                                   185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705    
           INUS_LACJO   176 KAELKGQVKDIVEESGVDTSKLTNDQINELNKINFSKEAKSGTQLTYNDFKKIAKTLIEQDARYAIPFFNASKIKNMPAAKTLDAQSGKVEDLEIWDSWPVQDAKTGYVSNWNGYQLVIGMMGVPNVNDNHIYLLYNKYGDNDFNHWKNAGPIFGLGTPVIQQWSGSATLNKDGSIQLYYTKVDTSDNNTNHQKLASATVYLNLEKDQDKISIAHVDNDHIVFEGDGYHYQTYDQWKETNKGADNIAMRDAHVIDDDNGNRYLVFEASTGTENYQGDDQIYQWLNYGGTNKDNLGDFFQILSNSDIKDRAKWSNAAIGIIKLNDDVKNPSVAKVYSPLISAPMVSDEIERPDVVKLGNKYYLFAATRLNRGSNDDAWMATNKAVGDNVAMIGYVSDNLTHGYVPLNESGVVLTASVPANWRTATYSYYAVPVEGRDDQLLITSYITNRGEVAGKGMHATWAPSFLLQINPDNTTTVLAKMTNQGDWIWDDSSENPDMMGVLEKDAPNSAALPGEWGKPVDWDLIGGYNLKPHQP 709
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhh..hhhhhhhhhhhhhh...........ee.hhhhhhhhhhhhhhh.........hhhhh..hhh.eee......eee.eeeeeee..............eeeeeeeee.......eeeeeeee....hhhhheeeee........eeeeeeeeee.....eeeeeeeee.......eeeeeeeeeeeeeehhhheeeeeeeeeeeeee........hhhhhhhhh........eeeeeee.....eeeeeeee.......hhhhhh.hhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee........eeee....ee........eeeeeeee..eeeeeeeee.....hhhhhhhhhhhhh..eeeeeeee.......ee.....eeee..........eeeeeeeee..eeeeeeeeeee.............ee.eeeeeeee...eeeeeeeeeee..........hhhh....................ee...ee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2yfr A 176 KAELKGQVKDIVEESGVDTSKLTNDQINELNKINFSKEAKSGTQLTYNDFKKIAKTLIEQDARYAIPFFNASKIKNMPAAKTLDAQSGKVEDLEIWDSWPVQDAKTGYVSNWNGYQLVIGMMGVPNVNDNHIYLLYNKYGDNDFNHWKNAGPIFGLGTPVIQQWSGSATLNKDGSIQLYYTKVDTSDNNTNHQKLASATVYLNLEKDQDKISIAHVDNDHIVFEGDGYHYQTYDQWKETNKGADNIAMRDAHVIDDDNGNRYLVFEASTGTENYQGDDQIYQWLNYGGTNKDNLGDFFQILSNSDIKDRAKWSNAAIGIIKLNDDVKNPSVAKVYSPLISAPMVSDEIERPDVVKLGNKYYLFAATRLNRGSNDDAWMATNKAVGDNVAMIGYVSDNLTHGYVPLNESGVVLTASVPANWRTATYSYYAVPVEGRDDQLLITSYITNRGEVAGKGMHATWAPSFLLQINPDNTTTVLAKMTNQGDWIWDDSSENPDMMGVLEKDAPNSAALPGEWGKPVDWDLIGGYNLKPHQH 709
                                   185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705
   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  (0, 0)

(no "SCOP Domain" information available for 2YFR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (INUS_LACJO | Q74K42)
molecular function
    GO:0047725    inulosucrase activity    Catalysis of the reaction: sucrose + 2,1-beta-D-fructosyl(n) = glucose + 2,1-beta-D-fructosyl(n+1).
    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: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: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.
cellular component
    GO:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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        INUS_LACJO | Q74K42: 2yfs 2yft

(-) Related Entries Specified in the PDB File

2yfs CRYSTAL STRUCTURE OF INULOSUCRASE FROM LACTOBACILLUS JOHNSONII NCC533 IN COMPLEX WITH SUCROSE
2yft CRYSTAL STRUCTURE OF INULOSUCRASE FROM LACTOBACILLUS JOHNSONII NCC533 IN COMPLEX WITH 1-KESTOSE