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(-) Description

Title :  CRYSTAL STRUCTURE OF D-TAGATOSE 3-EPIMERASE C66S FROM PSEUDOMONAS CICHORII IN COMPLEX WITH 1-DEOXY L-TAGATOSE
 
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 :  1.90
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 L-Tagatose
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, 14)

Asymmetric Unit (3, 14)
No.NameCountTypeFull Name
1MN4Ligand/IonMANGANESE (II) ION
2TGJ1Ligand/Ion1-DEOXY-L-TAGATOSE
3TGK9Ligand/Ion1-DEOXY-BETA-L-TAGATOPYRANOSE
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2TGJ-1Ligand/Ion1-DEOXY-L-TAGATOSE
3TGK3Ligand/Ion1-DEOXY-BETA-L-TAGATOPYRANOSE
Biological Unit 2 (2, 7)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2TGJ1Ligand/Ion1-DEOXY-L-TAGATOSE
3TGK6Ligand/Ion1-DEOXY-BETA-L-TAGATOPYRANOSE

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:152 , ASP A:185 , HIS A:211 , GLU A:246 , HOH A:669binding site for residue MN A 401
02AC2SOFTWAREGLU A:158 , ARG A:257 , ALA A:258 , TRP A:262 , SER B:116 , PHE B:157 , HOH B:532binding site for residue TGK B 401
03AC3SOFTWAREGLU B:152 , ASP B:185 , HIS B:211 , GLU B:246 , HOH B:702binding site for residue MN B 402
04AC4SOFTWARESER A:116 , PHE A:157 , HOH A:511 , PRO B:114 , ARG B:257 , ALA B:258 , TRP B:262binding site for residue TGK B 403
05AC5SOFTWARETRP B:11 , VAL B:17 , ASP B:18 , ALA B:21 , THR B:22 , ARG B:25 , HOH B:585 , HOH B:712binding site for residue TGK B 404
06AC6SOFTWAREGLU C:152 , ASP C:185 , HIS C:211 , GLU C:246 , TGJ C:402binding site for residue MN C 401
07AC7SOFTWAREILE C:67 , 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:401 , HOH C:504 , HOH C:522 , HOH C:650binding site for residue TGJ C 402
08AC8SOFTWAREGLU C:158 , ARG C:257 , ALA C:258 , TRP C:262 , HOH C:518 , SER D:116 , PHE D:157 , HOH D:521binding site for residue TGK C 403
09AC9SOFTWAREGLY C:221 , GLU C:222 , ARG C:280 , HOH C:547 , HOH C:646 , HOH C:654 , THR D:270binding site for residue TGK C 404
10AD1SOFTWAREASP C:57 , GLY C:60 , THR C:62 , HOH C:525binding site for residue TGK C 405
11AD2SOFTWAREGLU D:152 , ASP D:185 , HIS D:211 , GLU D:246 , HOH D:721binding site for residue MN D 401
12AD3SOFTWARESER C:116 , PHE C:157 , HOH C:530 , ARG D:257 , ALA D:258 , TRP D:262binding site for residue TGK D 402
13AD4SOFTWARETRP D:11 , ASP D:18 , THR D:22 , ARG D:25 , HOH D:523 , HOH D:529 , HOH D:561 , HOH D:724binding site for residue TGK D 403
14AD5SOFTWAREGLY D:221 , GLU D:222 , ARG D:280 , HOH D:516 , HOH D:652binding site for residue TGK D 404

(-) SS Bonds  (0, 0)

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

(-) 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 4YTR)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YTR)

(-) 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..........hhhhhhhhhhhh...eeeeehhhhh..hhhhhhhhhhhhhhhh.eeeeeeeehhhhh....hhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee...........hhhhhhhhhhhhhhhhhhhhhhh.eeeee...........hhhhhhhhhhhhh...eeeeeehhhhhhhh.hhhhhhhhh...eeeeee.............hhhhhhhhhhhh....eeee.......hhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ytr 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:296
                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..........hhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhhhh.eeeeeeeehhhhh....hhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee...........hhhhhhhhhhhhhhhhhhhhhhh.eeeee...........hhhhhhhhhhhhh...eeeeeehhhhhhhh.hhhhhhhhh...eeeeee.............hhhhhhhhhhhh....eeee.......hhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ytr B   1 MNKVGMFYTYWSTEWMVDFPATAKRIAGLGFDLMEISLGEFHNLSDAKKRELKAVADDLGLTVMCSIGLKSEYDFASPDKSVRDAGTEYVKRLLDDCHLLGAPVFAGLTFCAWPQSPPLDMKDKRPYVDRAIESVRRVIKVAEDYGIIYALEVVNRFEQWLCNDAKEAIAFADAVDSPACKVQLDTFHMNIEETSFRDAILACKGKMGHFHLGEANRLPPGEGRLPWDEIFGALKEIGYDGTIVMEPFMRKGGSVSRAVGVWRDMSNGATDEEMDERARRSLQFVRDKLAGSRSHH 296
                                    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..hhhhhhhhhhhhhhhhhhhh..eeeeeeeehhhhh....hhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee...........hhhhhhhhhhhhhhhhhhhhhhh.eeeee...........hhhhhhhhhhhhh...eeeeeehhhhhhhh.hhhhhhhhh...eeeeee.............hhhhhhhhhhhh....eeee.......hhhhhhh..........hhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ytr 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...eeeee..hhhhhhhhhhhhhhhhhhhhh.eeeeeeeehhhhh....hhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee...........hhhhhhhhhhhhhhhhhhhhhhh.eeeee...........hhhhhhhhhhhhh...eeeeeehhhhhhhh.hhhhhhhhh...eeeeee.............hhhhhhhhhhhh....eeee.......hhhhhhh..........hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ytr 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 4YTR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 4yts 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.
4yts THE SAME PROTEIN COMPLEXED WITH 1-DEOXY 3-KETO D-GALACTITOL.
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.