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(-) Description

Title :  CRYSTAL STRUCTURE OF ENGINEERED D-TAGATOSE 3-EPIMERASE PCDTE-ILS6
 
Authors :  C. S. Hee, A. Bosshart, T. Schirmer
Date :  02 May 14  (Deposition) - 22 Oct 14  (Release) - 04 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Epimerase, Tim-Barrel, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Bosshart, C. S. Hee, M. Bechtold, T. Schirmer, S. Panke
Directed Divergent Evolution Of A Thermostable D-Tagatose Epimerase Towards Improved Activity For Two Hexose Substrates.
Chembiochem V. 16 592 2015
PubMed-ID: 25655925  |  Reference-DOI: 10.1002/CBIC.201402620

(-) Compounds

Molecule 1 - D-TAGATOSE 3-EPIMERASE
    Chains: A, B, C, D
    EC Number: 5.3.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKTS-C6H
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: PSEUDOMONAS CICHORII
    Organism Taxid: 36746

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 18)

Asymmetric Unit (4, 18)
No.NameCountTypeFull Name
1LTG4Ligand/IonL-TAGATOSE
2MN5Ligand/IonMANGANESE (II) ION
3SOE5Ligand/IonALPHA-L-SORBOPYRANOSE
4SOL4Ligand/IonL-SORBOSE
Biological Unit 1 (3, 7)
No.NameCountTypeFull Name
1LTG2Ligand/IonL-TAGATOSE
2MN-1Ligand/IonMANGANESE (II) ION
3SOE3Ligand/IonALPHA-L-SORBOPYRANOSE
4SOL2Ligand/IonL-SORBOSE
Biological Unit 2 (3, 6)
No.NameCountTypeFull Name
1LTG2Ligand/IonL-TAGATOSE
2MN-1Ligand/IonMANGANESE (II) ION
3SOE2Ligand/IonALPHA-L-SORBOPYRANOSE
4SOL2Ligand/IonL-SORBOSE

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:152 , ASP A:185 , HIS A:211 , GLU A:246 , SOL A:502 , LTG A:505binding site for residue MN A 501
02AC2SOFTWARECYS A:66 , ILE A:67 , LEU A:108 , TRP A:113 , GLU A:152 , GLU A:158 , ASP A:185 , HIS A:188 , HIS A:211 , ARG A:217 , GLU A:246 , MN A:501 , LTG A:505 , HOH A:651binding site for residue SOL A 502
03AC3SOFTWARETHR A:251 , HOH A:615 , HOH A:665binding site for residue SOE A 503
04AC4SOFTWARETHR A:251 , GLY A:252 , SER A:256 , VAL A:261 , TRP A:262 , MET B:121 , VAL B:122 , ASP B:123 , LYS B:124binding site for residue SOE A 504
05AC5SOFTWARECYS A:66 , ILE A:67 , LEU A:108 , TRP A:113 , GLU A:152 , GLU A:158 , ASP A:185 , HIS A:188 , HIS A:211 , ARG A:217 , GLU A:246 , MN A:501 , SOL A:502 , HOH A:651binding site for residue LTG A 505
06AC6SOFTWAREHIS A:98 , HIS A:293 , HIS A:297 , HIS C:98 , HIS C:293 , HIS C:297binding site for residue MN A 506
07AC7SOFTWAREGLU B:152 , ASP B:185 , HIS B:211 , GLU B:246 , LTG B:503 , SOL B:504binding site for residue MN B 501
08AC8SOFTWAREVAL B:17 , ASP B:18 , ALA B:21 , THR B:22 , ARG B:25 , HOH B:621binding site for residue SOE B 502
09AC9SOFTWAREPHE B:7 , CYS B:66 , ILE B:67 , GLY B:68 , LEU B:108 , TRP B:113 , GLU B:152 , GLU B:158 , ASP B:185 , HIS B:188 , HIS B:211 , ARG B:217 , GLU B:246 , MN B:501 , SOL B:504 , HOH B:656binding site for residue LTG B 503
10AD1SOFTWAREPHE B:7 , TRP B:15 , ILE B:67 , GLY B:107 , LEU B:108 , GLU B:152 , GLU B:158 , ASP B:185 , HIS B:188 , HIS B:211 , ARG B:217 , GLU B:246 , MN B:501 , LTG B:503 , HOH B:656binding site for residue SOL B 504
11AD2SOFTWAREGLU C:152 , ASP C:185 , HIS C:211 , GLU C:246 , LTG C:303 , SOL C:304binding site for residue MN C 301
12AD3SOFTWAREHIS A:296 , HIS A:298 , ASP C:46 , ARG C:50 , ASP C:95 , HIS C:98 , HIS C:293binding site for residue SOE C 302
13AD4SOFTWARECYS C:66 , ILE C:67 , GLY C:68 , LEU C:108 , TRP C:113 , GLU C:152 , GLU C:158 , ASP C:185 , HIS C:188 , HIS C:211 , ARG C:217 , GLU C:246 , MN C:301 , SOL C:304 , HOH C:458binding site for residue LTG C 303
14AD5SOFTWARECYS C:66 , GLY C:107 , LEU C:108 , TRP C:113 , GLU C:152 , GLU C:158 , ASP C:185 , HIS C:188 , HIS C:211 , ARG C:217 , GLU C:246 , MN C:301 , LTG C:303 , HOH C:430 , HOH C:458binding site for residue SOL C 304
15AD6SOFTWAREGLU D:152 , ASP D:185 , HIS D:211 , GLU D:246 , LTG D:503 , SOL D:504binding site for residue MN D 501
16AD7SOFTWAREARG D:280 , HOH D:607binding site for residue SOE D 502
17AD8SOFTWARECYS D:66 , ILE D:67 , GLY D:68 , TRP D:113 , GLU D:152 , GLU D:158 , ASP D:185 , HIS D:188 , HIS D:211 , ARG D:217 , GLU D:246 , MN D:501 , SOL D:504 , HOH D:661binding site for residue LTG D 503
18AD9SOFTWARECYS D:66 , GLY D:107 , LEU D:108 , TRP D:113 , GLU D:152 , GLU D:158 , ASP D:185 , HIS D:188 , HIS D:211 , ARG D:217 , GLU D:246 , MN D:501 , LTG D:503 , HOH D:660 , HOH D:661binding site for residue SOL D 504

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Trp A:113 -Pro A:114
2Trp B:113 -Pro B:114
3Trp C:113 -Pro C:114
4Trp D:113 -Pro D:114

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4PGL)

(-) 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:298
                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..........hhhhhhhhhhhh...eeeeehhhhh..hhhhhhhhhhhhhhhh.eeeeeeeehhhhh....hhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee...........hhhhhhhhhhhhhhhhhhhhhhh.eeeee...........hhhhhhhhhhhhh...eeeeeehhhhhhhh.hhhhhhhhh...eeeeee.............hhhhhhhhhhhh.....eee.......hhhhhhh..........hhhhhhhhhhhhhhhhhhhhh.hhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pgl A   1 MNKVGMFYSYWSTEWMVDFPATAKRIAGLGFDLMEISLSEFHNLSDAKKRELKAVADDLGLTVMCCIGLKSEYDFASPDKSVRDAGTEYVKRLLDDCHLLGAPVFAGLNFCAWPQHPPLDMVDKRPYVDRAIESVRRVIKVAEDYGIIYALEAVNRYEQWLCNDAKEAIAFADAVDSPACKVHLDTFHMNIEENSFRDAILACKGKMGHFHLGEQNRLPPGEGRLPWDEIFGALKEIGYDGTIVIEPFMRTGGSVSRAVCVWRDLSNGATDEEMDERARRSLQFVRDKLALEHHHHHH 298
                                    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        


Chain B from PDB  Type:PROTEIN  Length:290
                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..........hhhhhhhhhhhh...eeeeehhhhh..hhhhhhhhhhhhhhhh.eeeeeeeehhhhh....hhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee...........hhhhhhhhhhhhhhhhhhhhhhh.eeeee...........hhhhhhhhhhhhh...eeeeeehhhhhhhh.hhhhhhhhh...eeeeee.............hhhhhhhhhhhh.....eee.......hhhhhhh..........hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pgl B   1 MNKVGMFYSYWSTEWMVDFPATAKRIAGLGFDLMEISLSEFHNLSDAKKRELKAVADDLGLTVMCCIGLKSEYDFASPDKSVRDAGTEYVKRLLDDCHLLGAPVFAGLNFCAWPQHPPLDMVDKRPYVDRAIESVRRVIKVAEDYGIIYALEAVNRYEQWLCNDAKEAIAFADAVDSPACKVHLDTFHMNIEENSFRDAILACKGKMGHFHLGEQNRLPPGEGRLPWDEIFGALKEIGYDGTIVIEPFMRTGGSVSRAVCVWRDLSNGATDEEMDERARRSLQFVRDKLA 290
                                    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


Chain C from PDB  Type:PROTEIN  Length:298
                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..........hhhhhhhhhhhh...eeeeehhhhh..hhhhhhhhhhhhhhhh.eeeeeeeehhhhh....hhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee...........hhhhhhhhhhhhhhhhhhhhhhh.eeeee...........hhhhhhhhhhhhh...eeeeeehhhhhhhh.hhhhhhhhh...eeeeee.............hhhhhhhhhhhh.....eee.......hhhhhhh..........hhhhhhhhhhhhhhhhhhhhh.hhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pgl C   1 MNKVGMFYSYWSTEWMVDFPATAKRIAGLGFDLMEISLSEFHNLSDAKKRELKAVADDLGLTVMCCIGLKSEYDFASPDKSVRDAGTEYVKRLLDDCHLLGAPVFAGLNFCAWPQHPPLDMVDKRPYVDRAIESVRRVIKVAEDYGIIYALEAVNRYEQWLCNDAKEAIAFADAVDSPACKVHLDTFHMNIEENSFRDAILACKGKMGHFHLGEQNRLPPGEGRLPWDEIFGALKEIGYDGTIVIEPFMRTGGSVSRAVCVWRDLSNGATDEEMDERARRSLQFVRDKLALEHHHHHH 298
                                    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        


Chain D from PDB  Type:PROTEIN  Length:290
                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..........hhhhhhhhhhhh...eeeeehhhhh..hhhhhhhhhhhhhhhh.eeeeeeeehhhhh....hhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee...........hhhhhhhhhhhhhhhhhhhhhhh.eeeee...........hhhhhhhhhhhhh...eeeeeehhhhhhhh.hhhhhhhhh...eeeeee.............hhhhhhhhhhhh.....eee.......hhhhhhh..........hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pgl D   1 MNKVGMFYSYWSTEWMVDFPATAKRIAGLGFDLMEISLSEFHNLSDAKKRELKAVADDLGLTVMCCIGLKSEYDFASPDKSVRDAGTEYVKRLLDDCHLLGAPVFAGLNFCAWPQHPPLDMVDKRPYVDRAIESVRRVIKVAEDYGIIYALEAVNRYEQWLCNDAKEAIAFADAVDSPACKVHLDTFHMNIEENSFRDAILACKGKMGHFHLGEQNRLPPGEGRLPWDEIFGALKEIGYDGTIVIEPFMRTGGSVSRAVCVWRDLSNGATDEEMDERARRSLQFVRDKLA 290
                                    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
   Legend:   → Mismatch (orange background)
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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  (0, 0)

(no "SCOP Domain" information available for 4PGL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

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 Related Entries

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UniProtKB/Swiss-Prot
        DT3E_PSECI | O50580: 2ou4 2qul 2qum 2qun 4pfh 4xsl 4xsm 4ytq 4ytr 4yts 4ytt 4ytu 5j8l

(-) Related Entries Specified in the PDB File

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