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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MUTB F164L MUTANT FROM CRYSTALS SOAKED WITH THE SUBSTRATE SUCROSE
 
Authors :  A. Lipski, R. Haser, N. Aghajari
Date :  08 Aug 12  (Deposition) - 13 Feb 13  (Release) - 03 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Mutant Enzyme, Tim-Barrel(Beta/Alpha)8, Sucrose Isomerase, Glycoside Hydrolase, Trehalulose Synthase, Gh13 Family(Cazy Database), Calcium Binding, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Lipski, H. Watzlawick, S. Ravaud, X. Robert, M. Rhimi, R. Haser, R. Mattes, N. Aghajari
Mutations Inducing An Active-Site Aperture In Rhizobium Sp. Sucrose Isomerase Confer Hydrolytic Activity
Acta Crystallogr. , Sect. D V. 69 298 2013
PubMed-ID: 23385465  |  Reference-DOI: 10.1107/S0907444912045532

(-) Compounds

Molecule 1 - SUCROSE ISOMERASE
    Chains: A, B
    EC Number: 5.4.11.99
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHWG660.12
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: MUTB FRAGMENT, UNP RESIDUES 28-584
    Gene: MUTB
    Mutation: YES
    Organism Scientific: RHIZOBIUM
    Organism Taxid: 1071045
    Strain: MX-45
    Synonym: TREHALULOSE SYNTHASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 17)

Asymmetric Unit (3, 17)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2GOL14Ligand/IonGLYCEROL
3TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GOL7Ligand/IonGLYCEROL
3TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 2 (1, 7)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GOL7Ligand/IonGLYCEROL
3TRS-1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:22 , ASN A:24 , ASP A:26 , ILE A:28 , ASP A:30 , HOH A:4185 , HOH A:4477BINDING SITE FOR RESIDUE CA A 601
02AC2SOFTWAREGLN A:218 , GLN A:228 , HOH A:4120 , HOH A:4141BINDING SITE FOR RESIDUE GOL A 602
03AC3SOFTWAREASP A:61 , TYR A:64 , HIS A:104 , PHE A:145 , ASP A:200 , HIS A:326 , ASP A:327 , ARG A:414 , HOH A:4016 , HOH A:4104BINDING SITE FOR RESIDUE GOL A 603
04AC4SOFTWAREASN A:221 , PHE A:222 , ALA A:223 , LEU A:289 , ARG A:291 , HOH A:4175 , HOH A:4416BINDING SITE FOR RESIDUE GOL A 604
05AC5SOFTWAREGLU A:526 , THR A:527 , PRO A:537 , ALA A:539BINDING SITE FOR RESIDUE GOL A 605
06AC6SOFTWAREGLY A:229 , GLN A:262 , HOH A:4069 , HOH A:4122BINDING SITE FOR RESIDUE GOL A 606
07AC7SOFTWAREGLY A:257 , PHE A:280 , ARG A:284 , HOH A:4029BINDING SITE FOR RESIDUE GOL A 607
08AC8SOFTWAREILE A:306 , VAL A:309 , ASP A:310 , PHE A:321 , GLN A:357 , ARG A:358 , TYR A:481 , HOH A:4107 , HOH A:4363 , HOH A:4514BINDING SITE FOR RESIDUE GOL A 608
09AC9SOFTWAREPHE A:144 , GLU A:254 , PHE A:256 , ARG A:284 , ASP A:327 , HOH A:4109 , HOH A:4116 , HOH A:4506BINDING SITE FOR RESIDUE TRS A 609
10BC1SOFTWAREASP B:22 , ASN B:24 , ASP B:26 , ILE B:28 , ASP B:30 , HOH B:876 , HOH B:910BINDING SITE FOR RESIDUE CA B 601
11BC2SOFTWAREASN B:221 , PHE B:222 , ALA B:223 , LEU B:289 , ARG B:291 , HOH B:816 , HOH B:972 , HOH B:1098BINDING SITE FOR RESIDUE GOL B 602
12BC3SOFTWAREGLU B:254 , PHE B:256 , ASP B:327 , HOH B:767 , HOH B:913 , HOH B:915BINDING SITE FOR RESIDUE GOL B 603
13BC4SOFTWAREASP B:61 , TYR B:64 , HIS B:104 , PHE B:145 , ASP B:200 , HIS B:326 , ASP B:327 , ARG B:414 , HOH B:711BINDING SITE FOR RESIDUE GOL B 604
14BC5SOFTWAREGLN B:218 , GLN B:228 , HOH B:724 , HOH B:894 , HOH B:1032BINDING SITE FOR RESIDUE GOL B 605
15BC6SOFTWAREGLN B:228 , GLY B:229 , GLN B:262 , HOH B:712 , HOH B:799BINDING SITE FOR RESIDUE GOL B 606
16BC7SOFTWAREILE B:524 , GLU B:526 , THR B:527 , PRO B:537BINDING SITE FOR RESIDUE GOL B 607
17BC8SOFTWAREILE B:306 , ASP B:310 , PHE B:321 , GLN B:357 , ARG B:358 , TYR B:481 , HOH B:1136BINDING SITE FOR RESIDUE GOL B 608

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4GI8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4GI8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4GI8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GI8)

(-) Exons   (0, 0)

(no "Exon" information available for 4GI8)

(-) 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:554
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh.eeeehhhhh.........hhhhhhhhhhhhhhhh..eeee...ee...........eeeee.....hhhhhhhhhhhhhhh..eeeeee........hhhhhhhh......hhhhh.ee...................eee......eee.............hhhhhhhhhhhhhhhhh....eeee.hhhhh.........hhhhhhhhhhhh....hhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhh...eee...................hhhhhhhhhhhhhhhhh.....ee........hhhhhhh.....hhhhhhhhhhhhhh....eeeee.hhhhh.......hhhhh.hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhh.........hhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhhhhhhheeee.......eeeeeeee..eeeeeeee.....eeee........eeeeee...........eeee....eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gi8 A   3 GAPWWKSAVFYQVYPRSFKDTNGDGIGDFKGLTEKLDYLKGLGIDAIWINPHYASPNTDNGYDISDYREVMKEYGTMEDFDRLMAELKKRGMRLMVDVVINHSSDQHEWFKSSRASKDNPYRDYYFWRDGKDGHEPNNYPSFFGGSAWEKDPVTGQYYLHYLGRQQPDLNWDTPKLREELYAMLRFWLDKGVSGMRFDTVATYSKTPGFPDLTPEQMKNFAEAYTQGPNLHRYLQEMHEKVFDHYDAVTAGEIFGAPLNQVPLFIDSRRKELDMAFTFDLIRYDRALDRWHTIPRTLADFRQTIDKVDAIAGEYGWNTFFLGNHDNPRAVSHFGDDRPQWREASAKALATVTLTQRGTPFIFQGDELGMTNYPFKTLQDFDDIEVKGFFQDYVETGKATAEELLTNVALTSRDNARTPFQWDDSANAGFTTGKPWLKVNPNYTEINAAREIGDPKSVYSFYRNLISIRHETPALSTGSYRDIDPSNADVYAYTRSQDGETYLVVVNFKAEPRSFTLPDGMHIAETLIESSSPAAPAAGAASLELQPWQSGIYKV 556
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552    


Chain B from PDB  Type:PROTEIN  Length:555
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh..eeeehhhhh.........hhhhhhhhhhhhhhhh..eeee...ee...........eeeee.....hhhhhhhhhhhhhhh..eeeeee........hhhhhhhh......hhhhh.ee...................eee......eee.............hhhhhhhhhhhhhhhhh....eeee.hhhhh.........hhhhhhhhhhhh....hhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhh...eee...................hhhhhhhhhhhhhhhhh.....ee........hhhhhhh.....hhhhhhhhhhhhhh....eeeee.hhhhh.......hhhhh.hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhh.........hhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhhhhhhheeee.......eeeeeeee..eeeeeeee.....eeee.....eeeeeeeee...........eeee....eeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gi8 B   3 GAPWWKSAVFYQVYPRSFKDTNGDGIGDFKGLTEKLDYLKGLGIDAIWINPHYASPNTDNGYDISDYREVMKEYGTMEDFDRLMAELKKRGMRLMVDVVINHSSDQHEWFKSSRASKDNPYRDYYFWRDGKDGHEPNNYPSFFGGSAWEKDPVTGQYYLHYLGRQQPDLNWDTPKLREELYAMLRFWLDKGVSGMRFDTVATYSKTPGFPDLTPEQMKNFAEAYTQGPNLHRYLQEMHEKVFDHYDAVTAGEIFGAPLNQVPLFIDSRRKELDMAFTFDLIRYDRALDRWHTIPRTLADFRQTIDKVDAIAGEYGWNTFFLGNHDNPRAVSHFGDDRPQWREASAKALATVTLTQRGTPFIFQGDELGMTNYPFKTLQDFDDIEVKGFFQDYVETGKATAEELLTNVALTSRDNARTPFQWDDSANAGFTTGKPWLKVNPNYTEINAAREIGDPKSVYSFYRNLISIRHETPALSTGSYRDIDPSNADVYAYTRSQDGETYLVVVNFKAEPRSFTLPDGMHIAETLIESSSPAAPAAGAASLELQPWQSGIYKVK 557
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552
   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 4GI8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4GI8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4GI8)

(-) Gene Ontology  (4, 7)

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 Related Entries

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

UniProtKB/Swiss-Prot
        Q2PS28_9BURK | Q2PS28: 4gi6 4gi9 4gia 4gin 4h2c 4h7v 4h8h 4h8u 4h8v 4ha1
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        M1E1F3_9RHIZ | M1E1F3: 4gi6 4gi9 4gia
        Q2PS28_9BURK | Q2PS28: 1zja 1zjb 2pwd 2pwe 2pwf 2pwg 2pwh 4go8 4go9

(-) Related Entries Specified in the PDB File

1zja TREHALULOSE SYNTHASE, MUTB, IN COMPLEX WITH TRIS (P1 FORM)
1zjb TREHALULOSE SYNTHASE, MUTB, IN COMPLEX WITH TRIS (P21 FORM)
2pwd MUTB IN COMPLEX WITH DEOXYNOJIRIMYCIN
2pwe AN INACTIVE MUTANT OF MUTB IN COMPLEX WITH SUCROSE
2pwf AN INACTIVE MUTANT OF MUTB IN COMPLEX WITH GLUCOSE
2pwg MUTB IN COMPLEX WITH CASTANOSPERMINE
2pwh MUTB IN THE NATIVE STATE
4gi6 MUTB F164L MUTANT FROM CRYSTALS SOAKED WITH GLUCOSE
4gi9 MUTB F164L MUTANT FROM CRYSTALS SOAKED WITH TREHALULOSE
4gia MUTB F164L MUTANT FROM CRYSTALS SOAKED WITH ISOMALTULOSE
4gin MUTB R284C MUTANT FROM CRYSTALS SOAKED WITH DEOXYNOJIRIMYCIN
4h2c MUTB MUTANT R284C FROM CRYSTALS SOAKED WITH TREHALULOSE