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(-) Description

Title :  CRYSTAL STRUCTURE OF D-TAGATOSE 3-EPIMERASE FROM PSEUDOMONAS CICHORII WITH D-TAGATOSE
 
Authors :  H. Yoshida, M. Yamada, T. Nishitani, G. Takada, K. Izumori, S. Kamitori
Date :  06 Aug 07  (Deposition) - 25 Dec 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.28
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Beta/Alpha Barrel, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Yoshida, M. Yamada, T. Nishitani, G. Takada, K. Izumori, S. Kamitori
Crystal Structures Of D-Tagatose 3-Epimerase From Pseudomonas Cichorii And Its Complexes With D-Tagatose And D-Fructose
J. Mol. Biol. V. 374 443 2007
PubMed-ID: 17936787  |  Reference-DOI: 10.1016/J.JMB.2007.09.033
(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: PTRC99A
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: PSEUDOMONAS CICHORII
    Organism Taxid: 36746
    Strain: ST-24

 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  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1MN4Ligand/IonMANGANESE (II) ION
2TAG4Ligand/IonD-TAGATOSE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2TAG2Ligand/IonD-TAGATOSE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2TAG2Ligand/IonD-TAGATOSE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:7 , CYS A:66 , TRP A:113 , GLU A:152 , GLU A:158 , ASP A:185 , HIS A:188 , ARG A:217 , GLU A:246 , MN A:292BINDING SITE FOR RESIDUE TAG A 291
2AC2SOFTWAREPHE B:7 , CYS B:66 , ILE B:67 , 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:292 , HOH B:458BINDING SITE FOR RESIDUE TAG B 291
3AC3SOFTWAREPHE C:7 , CYS C:66 , ILE C:67 , GLU C:152 , GLU C:158 , ASP C:185 , HIS C:188 , HIS C:211 , ARG C:217 , GLU C:246 , MN C:292BINDING SITE FOR RESIDUE TAG C 291
4AC4SOFTWAREPHE D:7 , CYS D:66 , 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:292 , HOH D:306BINDING SITE FOR RESIDUE TAG D 291
5AC5SOFTWAREGLU A:152 , ASP A:185 , HIS A:211 , GLU A:246 , TAG A:291BINDING SITE FOR RESIDUE MN A 292
6AC6SOFTWAREGLU B:152 , ASP B:185 , HIS B:211 , GLU B:246 , TAG B:291BINDING SITE FOR RESIDUE MN B 292
7AC7SOFTWAREGLU C:152 , ASP C:185 , HIS C:211 , GLU C:246 , TAG C:291BINDING SITE FOR RESIDUE MN C 292
8AC8SOFTWAREGLU D:152 , ASP D:185 , HIS D:211 , GLU D:246 , TAG D:291BINDING SITE FOR RESIDUE MN D 292

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2QUM)

(-) 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 2QUM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2QUM)

(-) Exons   (0, 0)

(no "Exon" information available for 2QUM)

(-) 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:290
 aligned with DT3E_PSECI | O50580 from UniProtKB/Swiss-Prot  Length:290

    Alignment length: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
           DT3E_PSECI     1 MNKVGMFYTYWSTEWMVDFPATAKRIAGLGFDLMEISLGEFHNLSDAKKRELKAVADDLGLTVMCCIGLKSEYDFASPDKSVRDAGTEYVKRLLDDCHLLGAPVFAGLTFCAWPQSPPLDMKDKRPYVDRAIESVRRVIKVAEDYGIIYALEVVNRFEQWLCNDAKEAIAFADAVDSPACKVQLDTFHMNIEETSFRDAILACKGKMGHFHLGEANRLPPGEGRLPWDEIFGALKEIGYDGTIVMEPFMRKGGSVSRAVGVWRDMSNGATDEEMDERARRSLQFVRDKLA 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.hhhhhhhh....eeeeee.............hhhhhhhhhhhh.....eee.......hhhhhhh..........hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qum A   1 MNKVGMFYTYWSTEWMVDFPATAKRIAGLGFDLMEISLGEFHNLSDAKKRELKAVADDLGLTVMCCIGLKSEYDFASPDKSVRDAGTEYVKRLLDDCHLLGAPVFAGLTFCAWPQSPPLDMKDKRPYVDRAIESVRRVIKVAEDYGIIYALEVVNRFEQWLCNDAKEAIAFADAVDSPACKVQLDTFHMNIEETSFRDAILACKGKMGHFHLGEANRLPPGEGRLPWDEIFGALKEIGYDGTIVMEPFMRKGGSVSRAVGVWRDMSNGATDEEMDERARRSLQFVRDKLA 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 B from PDB  Type:PROTEIN  Length:290
 aligned with DT3E_PSECI | O50580 from UniProtKB/Swiss-Prot  Length:290

    Alignment length: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
           DT3E_PSECI     1 MNKVGMFYTYWSTEWMVDFPATAKRIAGLGFDLMEISLGEFHNLSDAKKRELKAVADDLGLTVMCCIGLKSEYDFASPDKSVRDAGTEYVKRLLDDCHLLGAPVFAGLTFCAWPQSPPLDMKDKRPYVDRAIESVRRVIKVAEDYGIIYALEVVNRFEQWLCNDAKEAIAFADAVDSPACKVQLDTFHMNIEETSFRDAILACKGKMGHFHLGEANRLPPGEGRLPWDEIFGALKEIGYDGTIVMEPFMRKGGSVSRAVGVWRDMSNGATDEEMDERARRSLQFVRDKLA 290
               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.......hhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qum B   1 MNKVGMFYTYWSTEWMVDFPATAKRIAGLGFDLMEISLGEFHNLSDAKKRELKAVADDLGLTVMCCIGLKSEYDFASPDKSVRDAGTEYVKRLLDDCHLLGAPVFAGLTFCAWPQSPPLDMKDKRPYVDRAIESVRRVIKVAEDYGIIYALEVVNRFEQWLCNDAKEAIAFADAVDSPACKVQLDTFHMNIEETSFRDAILACKGKMGHFHLGEANRLPPGEGRLPWDEIFGALKEIGYDGTIVMEPFMRKGGSVSRAVGVWRDMSNGATDEEMDERARRSLQFVRDKLA 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:290
 aligned with DT3E_PSECI | O50580 from UniProtKB/Swiss-Prot  Length:290

    Alignment length: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
           DT3E_PSECI     1 MNKVGMFYTYWSTEWMVDFPATAKRIAGLGFDLMEISLGEFHNLSDAKKRELKAVADDLGLTVMCCIGLKSEYDFASPDKSVRDAGTEYVKRLLDDCHLLGAPVFAGLTFCAWPQSPPLDMKDKRPYVDRAIESVRRVIKVAEDYGIIYALEVVNRFEQWLCNDAKEAIAFADAVDSPACKVQLDTFHMNIEETSFRDAILACKGKMGHFHLGEANRLPPGEGRLPWDEIFGALKEIGYDGTIVMEPFMRKGGSVSRAVGVWRDMSNGATDEEMDERARRSLQFVRDKLA 290
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..........hhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhhh..eeeeeeeehhhhh....hhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee...........hhhhhhhhhhhhhhhhhhhhhhh.eeeee...........hhhhhhhhhhhhh...eeeeeehhhhhhhh.hhhhhhhhh...eeeeee.............hhhhhhhhhhhh....eeee.......hhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qum C   1 MNKVGMFYTYWSTEWMVDFPATAKRIAGLGFDLMEISLGEFHNLSDAKKRELKAVADDLGLTVMCCIGLKSEYDFASPDKSVRDAGTEYVKRLLDDCHLLGAPVFAGLTFCAWPQSPPLDMKDKRPYVDRAIESVRRVIKVAEDYGIIYALEVVNRFEQWLCNDAKEAIAFADAVDSPACKVQLDTFHMNIEETSFRDAILACKGKMGHFHLGEANRLPPGEGRLPWDEIFGALKEIGYDGTIVMEPFMRKGGSVSRAVGVWRDMSNGATDEEMDERARRSLQFVRDKLA 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 D from PDB  Type:PROTEIN  Length:290
 aligned with DT3E_PSECI | O50580 from UniProtKB/Swiss-Prot  Length:290

    Alignment length: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
           DT3E_PSECI     1 MNKVGMFYTYWSTEWMVDFPATAKRIAGLGFDLMEISLGEFHNLSDAKKRELKAVADDLGLTVMCCIGLKSEYDFASPDKSVRDAGTEYVKRLLDDCHLLGAPVFAGLTFCAWPQSPPLDMKDKRPYVDRAIESVRRVIKVAEDYGIIYALEVVNRFEQWLCNDAKEAIAFADAVDSPACKVQLDTFHMNIEETSFRDAILACKGKMGHFHLGEANRLPPGEGRLPWDEIFGALKEIGYDGTIVMEPFMRKGGSVSRAVGVWRDMSNGATDEEMDERARRSLQFVRDKLA 290
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------AP_endonuc_2-2qumD01 D:23-225                                                                                                                                                                              ----------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----------------------AP_endonuc_2-2qumD02 D:23-225                                                                                                                                                                              ----------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) ----------------------AP_endonuc_2-2qumD03 D:23-225                                                                                                                                                                              ----------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) ----------------------AP_endonuc_2-2qumD04 D:23-225                                                                                                                                                                              ----------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author ...eeee..........hhhhhhhhhhhh...eeeeehhhhh..hhhhhhhhhhhhhhhh.eeeeeeeehhhhh....hhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee...........hhhhhhhhhhhhhhhhhhhhhhh.eeeee...........hhhhhhhhhhhhh...eeeeeehhhhhhhh.hhhhhhhhh...eeeeee.............hhhhhhhhhhhh.....eee.......hhhhhhh..........hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qum D   1 MNKVGMFYTYWSTEWMVDFPATAKRIAGLGFDLMEISLGEFHNLSDAKKRELKAVADDLGLTVMCCIGLKSEYDFASPDKSVRDAGTEYVKRLLDDCHLLGAPVFAGLTFCAWPQSPPLDMKDKRPYVDRAIESVRRVIKVAEDYGIIYALEVVNRFEQWLCNDAKEAIAFADAVDSPACKVQLDTFHMNIEETSFRDAILACKGKMGHFHLGEANRLPPGEGRLPWDEIFGALKEIGYDGTIVMEPFMRKGGSVSRAVGVWRDMSNGATDEEMDERARRSLQFVRDKLA 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 2QUM)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2QUM)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (DT3E_PSECI | O50580)
molecular function
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

2qul THE SAME PROTEIN WITHOUT SUBSTRATE
2qun