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(-) Description

Title :  CRYSTAL STRUCTURE OF D-PSICOSE 3-EPIMERASE (DPEASE) IN THE ABSENCE OF SUBSTRATE
 
Authors :  K. Kim, H. J. Kim, D. K. Oh, S. S. Cha, S. Rhee
Date :  03 Jul 06  (Deposition) - 29 Aug 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Tim-Barrel, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Kim, H. J. Kim, D. K. Oh, S. S. Cha, S. Rhee
Crystal Structure Of D-Psicose 3-Epimerase From Agrobacterium Tumefaciens And Its Complex With True Substrate D-Fructose: A Pivotal Role Of Metal In Catalysis, An Active Site For The Non-Phosphorylated Substrate, And Its Conformational Changes
J. Mol. Biol. V. 361 920 2006
PubMed-ID: 16876192  |  Reference-DOI: 10.1016/J.JMB.2006.06.069
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - D-PSICOSE 3-EPIMERASE
    Chains: A, B, C, D
    EC Number: 5.3.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: AGROBACTERIUM TUMEFACIENS
    Organism Taxid: 358
    Synonym: D-TAGATOSE 3-EPIMERASE, DTEASE, AGR_L_260P

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 24)

Asymmetric/Biological Unit (1, 24)
No.NameCountTypeFull Name
1MSE24Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2HK0)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2HK0)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Trp A:112 -Pro A:113
2Trp B:112 -Pro B:113
3Trp C:112 -Pro C:113
4Trp D:112 -Pro D:113

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2HK0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2HK0)

(-) Exons   (0, 0)

(no "Exon" information available for 2HK0)

(-) Sequences/Alignments

Asymmetric/Biological 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:289
 aligned with DPES_AGRFC | A9CH28 from UniProtKB/Swiss-Prot  Length:289

    Alignment length:289
                                    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         
           DPES_AGRFC     1 MKHGIYYSYWEHEWSAKFGPYIEKVAKLGFDIIEVAAHHINEYSDAELATIRKSAKDNGIILTAGIGPSKTKNLSSEDAAVRAAGKAFFERTLSNVAKLDIHTIGGALHSYWPIDYSQPVDKAGDYARGVEGINGIADFANDLGINLCIEVLNRFENHVLNTAAEGVAFVKDVGKNNVKVMLDTFHMNIEEDSFGDAIRTAGPLLGHFHTGESNRRVPGKGRMPWHEIGLALRDINYTGAVIMEPFVKTGGTIGSDIKVWRDLSGGADIAKMDEDARNALAFSRFVLGG 289
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhh........hhhhhhhhh...eeeeehhhhh..hhhhhhhhhhhhhhh..eeeee............hhhhhhhhhhhhhhhhhhhhhh...eeee..............hhhhhhhhhhhhhhhhhhhhhhh..eeeee...........hhhhhhhhhhhhh...eeeeeehhhhhhhh.hhhhhhhhhh..eeeeee.............hhhhhhhhhhhh....eeee......hhhhhhhh..........hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hk0 A   1 mKHGIYYSYWEHEWSAKFGPYIEKVAKLGFDIIEVAAHHINEYSDAELATIRKSAKDNGIILTAGIGPSKTKNLSSEDAAVRAAGKAFFERTLSNVAKLDIHTIGGALHSYWPIDYSQPVDKAGDYARGVEGINGIADFANDLGINLCIEVLNRFENHVLNTAAEGVAFVKDVGKNNVKVmLDTFHmNIEEDSFGDAIRTAGPLLGHFHTGESNRRVPGKGRmPWHEIGLALRDINYTGAVImEPFVKTGGTIGSDIKVWRDLSGGADIAKmDEDARNALAFSRFVLGG 289
                            |       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         
                            |                                                                                                                                                                                 181-MSE |                                 223-MSE             243-MSE                      272-MSE             
                            1-MSE                                                                                                                                                                                   187-MSE                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:289
 aligned with DPES_AGRFC | A9CH28 from UniProtKB/Swiss-Prot  Length:289

    Alignment length:289
                                    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         
           DPES_AGRFC     1 MKHGIYYSYWEHEWSAKFGPYIEKVAKLGFDIIEVAAHHINEYSDAELATIRKSAKDNGIILTAGIGPSKTKNLSSEDAAVRAAGKAFFERTLSNVAKLDIHTIGGALHSYWPIDYSQPVDKAGDYARGVEGINGIADFANDLGINLCIEVLNRFENHVLNTAAEGVAFVKDVGKNNVKVMLDTFHMNIEEDSFGDAIRTAGPLLGHFHTGESNRRVPGKGRMPWHEIGLALRDINYTGAVIMEPFVKTGGTIGSDIKVWRDLSGGADIAKMDEDARNALAFSRFVLGG 289
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhh........hhhhhhhhh...eeeeehhhhh..hhhhhhhhhhhhhhh..eeeee............hhhhhhhhhhhhhhhhhhhhh....eeee..............hhhhhhhhhhhhhhhhhhhhhhh..eeeee...........hhhhhhhhhhhhh...eeeeeehhhhhhhh.hhhhhhhhhh..eeeeee.............hhhhhhhhhhhh....eeee......hhhhhhhh..........hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hk0 B   1 mKHGIYYSYWEHEWSAKFGPYIEKVAKLGFDIIEVAAHHINEYSDAELATIRKSAKDNGIILTAGIGPSKTKNLSSEDAAVRAAGKAFFERTLSNVAKLDIHTIGGALHSYWPIDYSQPVDKAGDYARGVEGINGIADFANDLGINLCIEVLNRFENHVLNTAAEGVAFVKDVGKNNVKVmLDTFHmNIEEDSFGDAIRTAGPLLGHFHTGESNRRVPGKGRmPWHEIGLALRDINYTGAVImEPFVKTGGTIGSDIKVWRDLSGGADIAKmDEDARNALAFSRFVLGG 289
                            |       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         
                            1-MSE                                                                                                                                                                             181-MSE |                                 223-MSE             243-MSE                      272-MSE             
                                                                                                                                                                                                                    187-MSE                                                                                                  


Chain C from PDB  Type:PROTEIN  Length:289
 aligned with DPES_AGRFC | A9CH28 from UniProtKB/Swiss-Prot  Length:289

    Alignment length:289
                                    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         
           DPES_AGRFC     1 MKHGIYYSYWEHEWSAKFGPYIEKVAKLGFDIIEVAAHHINEYSDAELATIRKSAKDNGIILTAGIGPSKTKNLSSEDAAVRAAGKAFFERTLSNVAKLDIHTIGGALHSYWPIDYSQPVDKAGDYARGVEGINGIADFANDLGINLCIEVLNRFENHVLNTAAEGVAFVKDVGKNNVKVMLDTFHMNIEEDSFGDAIRTAGPLLGHFHTGESNRRVPGKGRMPWHEIGLALRDINYTGAVIMEPFVKTGGTIGSDIKVWRDLSGGADIAKMDEDARNALAFSRFVLGG 289
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhh........hhhhhhhhh...eeeeehhhhh..hhhhhhhhhhhhhhh..eeeee............hhhhhhhhhhhhhhhhhhhhh....eeee..............hhhhhhhhhhhhhhhhhhhhhhh..eeeee...........hhhhhhhhhhhhh...eeeeeehhhhhhhh.hhhhhhhhhh..eeeeee.............hhhhhhhhhhhh....eeee......hhhhhhhh..........hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hk0 C   1 mKHGIYYSYWEHEWSAKFGPYIEKVAKLGFDIIEVAAHHINEYSDAELATIRKSAKDNGIILTAGIGPSKTKNLSSEDAAVRAAGKAFFERTLSNVAKLDIHTIGGALHSYWPIDYSQPVDKAGDYARGVEGINGIADFANDLGINLCIEVLNRFENHVLNTAAEGVAFVKDVGKNNVKVmLDTFHmNIEEDSFGDAIRTAGPLLGHFHTGESNRRVPGKGRmPWHEIGLALRDINYTGAVImEPFVKTGGTIGSDIKVWRDLSGGADIAKmDEDARNALAFSRFVLGG 289
                            |       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         
                            1-MSE                                                                                                                                                                             181-MSE |                                 223-MSE             243-MSE                      272-MSE             
                                                                                                                                                                                                                    187-MSE                                                                                                  


Chain D from PDB  Type:PROTEIN  Length:289
 aligned with DPES_AGRFC | A9CH28 from UniProtKB/Swiss-Prot  Length:289

    Alignment length:289
                                    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         
           DPES_AGRFC     1 MKHGIYYSYWEHEWSAKFGPYIEKVAKLGFDIIEVAAHHINEYSDAELATIRKSAKDNGIILTAGIGPSKTKNLSSEDAAVRAAGKAFFERTLSNVAKLDIHTIGGALHSYWPIDYSQPVDKAGDYARGVEGINGIADFANDLGINLCIEVLNRFENHVLNTAAEGVAFVKDVGKNNVKVMLDTFHMNIEEDSFGDAIRTAGPLLGHFHTGESNRRVPGKGRMPWHEIGLALRDINYTGAVIMEPFVKTGGTIGSDIKVWRDLSGGADIAKMDEDARNALAFSRFVLGG 289
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhh........hhhhhhhhh...eeeeehhhhh..hhhhhhhhhhhhhhh..eeeee............hhhhhhhhhhhhhhhhhhhhhh...eeee..............hhhhhhhhhhhhhhhhhhhhhhh..eeeee...........hhhhhhhhhhhhh...eeeeeehhhhhhhh.hhhhhhhhhh..eeeeee.............hhhhhhhhhhhh....eeee......hhhhhhhh..........hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hk0 D   1 mKHGIYYSYWEHEWSAKFGPYIEKVAKLGFDIIEVAAHHINEYSDAELATIRKSAKDNGIILTAGIGPSKTKNLSSEDAAVRAAGKAFFERTLSNVAKLDIHTIGGALHSYWPIDYSQPVDKAGDYARGVEGINGIADFANDLGINLCIEVLNRFENHVLNTAAEGVAFVKDVGKNNVKVmLDTFHmNIEEDSFGDAIRTAGPLLGHFHTGESNRRVPGKGRmPWHEIGLALRDINYTGAVImEPFVKTGGTIGSDIKVWRDLSGGADIAKmDEDARNALAFSRFVLGG 289
                            |       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         
                            1-MSE                                                                                                                                                                             181-MSE |                                 223-MSE             243-MSE                      272-MSE             
                                                                                                                                                                                                                    187-MSE
   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 2HK0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2HK0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2HK0)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (DPES_AGRFC | A9CH28)
molecular function
    GO:0050897    cobalt ion binding    Interacting selectively and non-covalently with a cobalt (Co) ion.
    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:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016857    racemase and epimerase activity, acting on carbohydrates and derivatives    Catalysis of a reaction that alters the configuration of one or more chiral centers in a carbohydrate molecule.

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  Cis Peptide Bonds
    Trp A:112 - Pro A:113   [ RasMol ]  
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  2hk0
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 Related Entries

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

UniProtKB/Swiss-Prot
        DPES_AGRFC | A9CH28: 2hk1

(-) Related Entries Specified in the PDB File

2hk1 THE SAME PROTEIN IN THE PRESENCE OF D-FRUCTOSE.