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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ISOMALTULOSE SYNTHASE SMUA FROM PROTAMINOBACTER RUBRUM IN COMPLEX WITH THE INHIBITOR DEOXYNOJIRIMYCIN
 
Authors :  S. Ravaud, X. Robert, R. Haser, N. Aghajari
Date :  19 Feb 09  (Deposition) - 26 May 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Sucrose Isomerase, Glycoside Hydrolase, Protaminobacter Rubrum, Deoxynojirimycin Complex, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Ravaud, X. Robert, H. Watzlawick, R. Haser, R. Mattes, N. Aghajari
Structural Determinants Of Product Specificity Of Sucrose Isomerases
Febs Lett. V. 583 1964 2009
PubMed-ID: 19427862  |  Reference-DOI: 10.1016/J.FEBSLET.2009.05.002

(-) Compounds

Molecule 1 - SUCROSE ISOMERASE SMUA FROM PROTAMINOBACTER RUBRUM
    Chains: A
    EC Number: 5.4.99.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHWG314
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SMUA
    Organism Scientific: PROTAMINOBACTER RUBRUM
    Organism Taxid: 126825
    Strain: CBS 547.77

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric/Biological Unit (3, 10)
No.NameCountTypeFull Name
1EDO8Ligand/Ion1,2-ETHANEDIOL
2FLC1Ligand/IonCITRATE ANION
3NOJ1Ligand/Ion1-DEOXYNOJIRIMYCIN

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:178 , PHE A:270 , ARG A:306 , GLU A:401 , HOH A:1734 , HOH A:1743 , HOH A:1765 , HOH A:1799 , NOJ A:8000BINDING SITE FOR RESIDUE EDO A 8002
02AC2SOFTWARELYS A:51 , TRP A:438 , HOH A:1452 , HOH A:1814 , EDO A:8009BINDING SITE FOR RESIDUE EDO A 8005
03AC3SOFTWAREASP A:353 , ASN A:388 , TYR A:389 , PRO A:390 , HOH A:1206 , HOH A:1210 , HOH A:1593BINDING SITE FOR RESIDUE EDO A 8006
04AC4SOFTWAREILE A:222 , PRO A:223 , ASP A:224 , PHE A:225BINDING SITE FOR RESIDUE EDO A 8007
05AC5SOFTWARETRP A:312 , LYS A:313 , LYS A:525 , HOH A:1231 , HOH A:1282BINDING SITE FOR RESIDUE EDO A 8008
06AC6SOFTWARELYS A:51 , TRP A:438 , ASP A:439 , VAL A:465 , HOH A:1046 , EDO A:8005BINDING SITE FOR RESIDUE EDO A 8009
07AC7SOFTWARESER A:348 , GLY A:351 , ASP A:352 , ASP A:353 , HOH A:1205BINDING SITE FOR RESIDUE EDO A 8010
08AC8SOFTWAREASP A:311 , TRP A:312BINDING SITE FOR RESIDUE EDO A 8011
09AC9SOFTWARELYS A:169 , PRO A:244 , ASN A:245 , ILE A:246 , HIS A:247 , ARG A:248 , LYS A:279 , ARG A:285 , HOH A:1134 , HOH A:1493 , HOH A:1495 , HOH A:1751BINDING SITE FOR RESIDUE FLC A 9000
10BC1SOFTWAREASP A:75 , TYR A:78 , HIS A:118 , PHE A:159 , PHE A:178 , ARG A:212 , ASP A:214 , GLU A:268 , HIS A:341 , ASP A:342 , ARG A:429 , HOH A:1024 , HOH A:1743 , EDO A:8002BINDING SITE FOR RESIDUE NOJ A 8000

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3GBE)

(-) 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:558
 aligned with D0VX20_SERPL | D0VX20 from UniProtKB/TrEMBL  Length:558

    Alignment length:558
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550        
         D0VX20_SERPL     1 TIPKWWKEAVFYQVYPRSFKDTNGDGIGDINGIIEKLDYLKALGIDAIWINPHYDSPNTDNGYDIRDYRKIMKEYGTMEDFDRLISEMKKRNMRLMIDVVINHTSDQNEWFVKSKSSKDNPYRGYYFWKDAKEGQAPNNYPSFFGGSAWQKDEKTNQYYLHYFAKQQPDLNWDNPKVRQDLYAMLRFWLDKGVSGLRFDTVATYSKIPDFPNLTQQQLKNFAAEYTKGPNIHRYVNEMNKEVLSHYDIATAGEIFGVPLDQSIKFFDRRRDELNIAFTFDLIRLDRDSDQRWRRKDWKLSQFRQIIDNVDRTAGEYGWNAFFLDNHDNPRAVSHFGDDRPQWREPSAKALATLTLTQRATPFIYQGSELGMTNYPFKAIDEFDDIEVKGFWHDYVETGKVKADEFLQNVRLTSRDNSRTPFQWDGSKNAGFTSGKPWFKVNPNYQEINAVSQVTQPDSVFNYYRQLIKIRHDIPALTYGTYTDLDPANDSVYAYTRSLGAEKYLVVVNFKEQMMRYKLPDNLSIEKVIIDSNSKNVVKKNDSLLELKPWQSGVYKLNQ 558
               SCOP domains d3gbea1 A:16-493 automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                            d3gbea2 A:494-573 automated matches                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhh.eeeehhhhh.........hhhhhhhhhhhhhhhh..eeee...ee...........eeeee.hhhhhhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhh....hhhhh.ee...................eeee....eeee.............hhhhhhhhhhhhhhhhh....eeee.hhhhh.........hhhhhhhhhhhh....hhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhh...eee....................hhhhhhhhhhhhhhhhh.....ee........hhhhhhh.....hhhhhhhhhhhhhh....eeeee.hhhhh.......hhhhh.hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhh.........hhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhhhhhhheeee.......eeeeeeee..eeeeeeee.....eeee......eeeeeeee...........eeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3gbe A  16 TIPKWWKEAVFYQVYPRSFKDTNGDGIGDINGIIEKLDYLKALGIDAIWINPHYDSPNTDNGYDIRDYRKIMKEYGTMEDFDRLISEMKKRNMRLMIDVVINHTSDQNEWFVKSKSSKDNPYRGYYFWKDAKEGQAPNNYPSFFGGSAWQKDEKTNQYYLHYFAKQQPDLNWDNPKVRQDLYAMLRFWLDKGVSGLRFDTVATYSKIPDFPNLTQQQLKNFAAEYTKGPNIHRYVNEMNKEVLSHYDIATAGEIFGVPLDQSIKFFDRRRDELNIAFTFDLIRLDRDSDQRWRRKDWKLSQFRQIIDNVDRTAGEYGWNAFFLDNHDNPRAVSHFGDDRPQWREPSAKALATLTLTQRATPFIYQGSELGMTNYPFKAIDEFDDIEVKGFWHDYVETGKVKADEFLQNVRLTSRDNSRTPFQWDGSKNAGFTSGKPWFKVNPNYQEINAVSQVTQPDSVFNYYRQLIKIRHDIPALTYGTYTDLDPANDSVYAYTRSLGAEKYLVVVNFKEQMMRYKLPDNLSIEKVIIDSNSKNVVKKNDSLLELKPWQSGVYKLNQ 573
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       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
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3GBE)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (D0VX20_SERPL | D0VX20)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0050006    isomaltulose synthase activity    Catalysis of the reaction: sucrose = 6-O-alpha-D-glucopyranosyl-D-fructofuranose.
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.

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        D0VX20_SERPL | D0VX20: 3gbd

(-) Related Entries Specified in the PDB File

3gbd CRYSTAL STRUCTURE OF SUCROSE ISOMERASE SMUA FROM PROTAMINOBACTER RUBRUM