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(-) Description

Title :  CRYSTAL STRUCTURE OF D-TAGATOSE 3-EPIMERASE C66S FROM PSEUDOMONAS CICHORII IN COMPLEX WITH 1-DEOXY 3-KETO D-GALACTITOL
 
Authors :  H. Yoshida, A. Yoshihara, T. Ishii, K. Izumori, S. Kamitori
Date :  18 Mar 15  (Deposition) - 23 Mar 16  (Release) - 23 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.14
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Epimerase, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Yoshida, A. Yoshihara, T. Ishii, K. Izumori, S. Kamitori
Crystal Structure Of D-Tagatose 3-Epimerase C66S From Pseudomonas Cichorii In Complex With 1-Deoxy 3-Keto D-Galactitol
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) 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: PQE60
    Expression System Strain: JM109
    Expression System Taxid: 562
    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  (3, 16)

Asymmetric Unit (3, 16)
No.NameCountTypeFull Name
1MN4Ligand/IonMANGANESE (II) ION
2TGR3Ligand/Ion1-DEOXY-ALPHA-D-XYLO-HEX-3-ULOFURANOSE
3TGS9Ligand/Ion1-DEOXY-D-XYLO-HEX-3-ULOSE
Biological Unit 1 (2, 7)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2TGR2Ligand/Ion1-DEOXY-ALPHA-D-XYLO-HEX-3-ULOFURANOSE
3TGS5Ligand/Ion1-DEOXY-D-XYLO-HEX-3-ULOSE
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2TGR1Ligand/Ion1-DEOXY-ALPHA-D-XYLO-HEX-3-ULOFURANOSE
3TGS4Ligand/Ion1-DEOXY-D-XYLO-HEX-3-ULOSE

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:152 , ASP A:185 , HIS A:211 , GLU A:246 , TGS A:402binding site for residue MN A 401
02AC2SOFTWARELEU 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 , VAL A:259 , MN A:401 , HOH A:525binding site for residue TGS A 402
03AC3SOFTWARETRP A:15 , SER A:37 , ILE A:67 , GLY A:68 , TRP A:113 , HOH A:525binding site for residue TGS A 403
04AC4SOFTWARETRP A:11 , ARG A:25 , ASP A:271binding site for residue TGR A 404
05AC5SOFTWARESER A:116 , PHE A:157 , ARG B:257 , TGS B:401binding site for residue TGS A 405
06AC6SOFTWAREARG A:257 , ALA A:258 , TRP A:262 , TGS A:405 , SER B:116 , PHE B:157 , HOH B:550 , HOH B:586binding site for residue TGS B 401
07AC7SOFTWAREGLU B:152 , ASP B:185 , HIS B:211 , GLU B:246 , TGS B:403binding site for residue MN B 402
08AC8SOFTWARELEU 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:402 , HOH B:508 , HOH B:518binding site for residue TGS B 403
09AC9SOFTWARETRP B:11 , THR B:22 , ARG B:25 , ASP B:271 , HOH B:521binding site for residue TGR B 404
10AD1SOFTWAREGLU C:152 , ASP C:185 , HIS C:211 , GLU C:246 , TGS C:402binding site for residue MN C 401
11AD2SOFTWARELEU C:108 , GLU C:152 , GLU C:158 , ASP C:185 , HIS C:188 , HIS C:211 , ARG C:217 , GLU C:246 , MN C:401 , HOH C:502 , HOH C:507binding site for residue TGS C 402
12AD3SOFTWARETRP C:15 , SER C:37 , GLY C:39 , ILE C:67 , GLY C:68 , TRP C:113 , HOH C:502binding site for residue TGS C 403
13AD4SOFTWAREARG C:257 , ALA C:258 , SER D:116 , PHE D:157 , HOH D:506binding site for residue TGS D 401
14AD5SOFTWAREGLU D:152 , ASP D:185 , HIS D:211 , GLU D:246 , TGS D:403binding site for residue MN D 402
15AD6SOFTWARETRP D:113 , GLU D:152 , GLU D:158 , ASP D:185 , HIS D:188 , HIS D:211 , ARG D:217 , GLU D:246 , VAL D:259 , MN D:402 , HOH D:505binding site for residue TGS D 403
16AD7SOFTWARESER C:116 , PHE C:157 , PRO D:114 , PHE D:157 , GLU D:158 , ARG D:257 , ALA D:258 , TRP D:262binding site for residue TGR D 404

(-) SS Bonds  (0, 0)

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

(-) 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 4YTS)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YTS)

(-) 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:294
                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee..........hhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhhhh.eeeeeeeehhhhh....hhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee...........hhhhhhhhhhhhhhhhhhhhhhh.eeeee...........hhhhhhhhhhhhh...eeeeeehhhhhhhh.hhhhhhhhh...eeeeee.............hhhhhhhhhhhh....eeee.......hhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4yts A   1 MNKVGMFYTYWSTEWMVDFPATAKRIAGLGFDLMEISLGEFHNLSDAKKRELKAVADDLGLTVMCSIGLKSEYDFASPDKSVRDAGTEYVKRLLDDCHLLGAPVFAGLTFCAWPQSPPLDMKDKRPYVDRAIESVRRVIKVAEDYGIIYALEVVNRFEQWLCNDAKEAIAFADAVDSPACKVQLDTFHMNIEETSFRDAILACKGKMGHFHLGEANRLPPGEGRLPWDEIFGALKEIGYDGTIVMEPFMRKGGSVSRAVGVWRDMSNGATDEEMDERARRSLQFVRDKLAGSRS 294
                                    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:292
                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..........hhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhhhh.eeeeeeeehhhhh....hhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee...........hhhhhhhhhhhhhhhhhhhhhhh.eeeee...........hhhhhhhhhhhhh...eeeeeehhhhhhhh.hhhhhhhhh...eeeeee.............hhhhhhhhhhhh.....eee.......hhhhhhh..........hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yts B   1 MNKVGMFYTYWSTEWMVDFPATAKRIAGLGFDLMEISLGEFHNLSDAKKRELKAVADDLGLTVMCSIGLKSEYDFASPDKSVRDAGTEYVKRLLDDCHLLGAPVFAGLTFCAWPQSPPLDMKDKRPYVDRAIESVRRVIKVAEDYGIIYALEVVNRFEQWLCNDAKEAIAFADAVDSPACKVQLDTFHMNIEETSFRDAILACKGKMGHFHLGEANRLPPGEGRLPWDEIFGALKEIGYDGTIVMEPFMRKGGSVSRAVGVWRDMSNGATDEEMDERARRSLQFVRDKLAGS 292
                                    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:297
                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..........hhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhhhh.eeeeeee.hhhhh....hhhhhhhhhhhhhhhhhhhhhhh..eeeee...............hhhhhhhhhhhhhhhhhhhhhhh.eeeee...........hhhhhhhhhhhhh...eeeeeehhhhhhhh.hhhhhhhh....eeeeee.............hhhhhhhhhhhh....eeee.......hhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yts C   1 MNKVGMFYTYWSTEWMVDFPATAKRIAGLGFDLMEISLGEFHNLSDAKKRELKAVADDLGLTVMCSIGLKSEYDFASPDKSVRDAGTEYVKRLLDDCHLLGAPVFAGLTFCAWPQSPPLDMKDKRPYVDRAIESVRRVIKVAEDYGIIYALEVVNRFEQWLCNDAKEAIAFADAVDSPACKVQLDTFHMNIEETSFRDAILACKGKMGHFHLGEANRLPPGEGRLPWDEIFGALKEIGYDGTIVMEPFMRKGGSVSRAVGVWRDMSNGATDEEMDERARRSLQFVRDKLAGSRSHHH 297
                                    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 ..eeeee..........hhhhhhhhhhhh...eeeeehhhhh..hhhhhhhhhhhhhhhh.eeeeeee.hhhhh....hhhhhhhhhhhhhhhhhhhhhhh..eeeee...............hhhhhhhhhhhhhhhhhhhhhhh.eeeee...........hhhhhhhhhhhhh...eeeeeehhhhhhhh.hhhhhhhh....eeeeee.............hhhhhhhhhhhh....eeee.......hhhhhhh..........hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yts D   1 MNKVGMFYTYWSTEWMVDFPATAKRIAGLGFDLMEISLGEFHNLSDAKKRELKAVADDLGLTVMCSIGLKSEYDFASPDKSVRDAGTEYVKRLLDDCHLLGAPVFAGLTFCAWPQSPPLDMKDKRPYVDRAIESVRRVIKVAEDYGIIYALEVVNRFEQWLCNDAKEAIAFADAVDSPACKVQLDTFHMNIEETSFRDAILACKGKMGHFHLGEANRLPPGEGRLPWDEIFGALKEIGYDGTIVMEPFMRKGGSVSRAVGVWRDMSNGATDEEMDERARRSLQFVRDKLA 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)
  - → 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 4YTS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

4xsl 4XSL CONTAINS THE SAME PROTEIN COMPLEXED WITH GLYCEROL.
4xsm 4XSM CONTAINS THE SAME PROTEIN COMPLEXED WITH D-TALITOL.
4ytq 4YTQ CONTAINS THE SAME PROTEIN COMPLEXED WITH 1-DEOXY D-TAGATOSE.
4ytr 4YTR CONTAINS THE SAME PROTEIN COMPLEXED WITH 1-DEOXY L-TAGATOSE.
4ytt THE SAME PROTEIN COMPLEXED WITH 6-DEOXY L-PSICOSE.
4ytu THE SAME PROTEIN COMPLEXED WITH L-ERYTHRULOSE.
4yvl THE SAME PROTEIN COMPLEX WITH 1-DEOXY L-TAGATOSE, USING A CRYSTAL GROWN IN MICROGRAVITY.