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(-) Description

Title :  1-DEOXY-D-XYLULOSE 5-PHOSPHATE SYNTHASE (DXS) FROM ESCHERICHIA COLI
 
Authors :  S. Xiang, G. Usunow, G. Lange, M. Busch, L. Tong
Date :  29 Nov 06  (Deposition) - 26 Dec 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Dxs, Thiamine, Isoprenoid, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Xiang, G. Usunow, G. Lange, M. Busch, L. Tong
Crystal Structure Of 1-Deoxy-D-Xylulose 5-Phosphate Synthase, A Crucial Enzyme For Isoprenoids Biosynthesis.
J. Biol. Chem. V. 282 2676 2007
PubMed-ID: 17135236  |  Reference-DOI: 10.1074/JBC.M610235200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 1-DEOXY-D-XYLULOSE-5-PHOSPHATE SYNTHASE
    Chains: A, B, C, D
    EC Number: 2.2.1.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET26B
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: DXS
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: 1-DEOXYXYLULOSE-5-PHOSPHATE SYNTHASE, DXP SYNTHASE, DXPS

 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  (5, 84)

Asymmetric Unit (5, 84)
No.NameCountTypeFull Name
1DPO2Ligand/IonDIPHOSPHATE
2K4Ligand/IonPOTASSIUM ION
3MG4Ligand/IonMAGNESIUM ION
4MSE72Mod. Amino AcidSELENOMETHIONINE
5TDP2Ligand/IonTHIAMIN DIPHOSPHATE
Biological Unit 1 (3, 38)
No.NameCountTypeFull Name
1DPO1Ligand/IonDIPHOSPHATE
2K-1Ligand/IonPOTASSIUM ION
3MG-1Ligand/IonMAGNESIUM ION
4MSE36Mod. Amino AcidSELENOMETHIONINE
5TDP1Ligand/IonTHIAMIN DIPHOSPHATE
Biological Unit 2 (3, 38)
No.NameCountTypeFull Name
1DPO1Ligand/IonDIPHOSPHATE
2K-1Ligand/IonPOTASSIUM ION
3MG-1Ligand/IonMAGNESIUM ION
4MSE36Mod. Amino AcidSELENOMETHIONINE
5TDP1Ligand/IonTHIAMIN DIPHOSPHATE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:152 , ASN A:181 , TDP A:3001 , HOH A:3137 , HOH A:3138BINDING SITE FOR RESIDUE MG A 1001
02AC2SOFTWAREPRO A:413 , GLY A:464 , TYR A:465 , TYR A:467BINDING SITE FOR RESIDUE K A 2001
03AC3SOFTWAREASP B:152 , ASN B:179 , ASN B:181 , DPO B:4001 , HOH B:4130BINDING SITE FOR RESIDUE MG B 1002
04AC4SOFTWAREPRO B:413 , GLY B:464 , TYR B:465 , TYR B:467BINDING SITE FOR RESIDUE K B 2002
05AC5SOFTWAREASP C:152 , ASN C:181 , LYS C:284 , TDP C:3002 , HOH C:3121BINDING SITE FOR RESIDUE MG C 1003
06AC6SOFTWAREPRO C:413 , GLY C:464 , TYR C:465 , TYR C:467BINDING SITE FOR RESIDUE K C 2003
07AC7SOFTWAREASP D:152 , ASN D:181 , DPO D:4002 , HOH D:4113BINDING SITE FOR RESIDUE MG D 1004
08AC8SOFTWAREPRO D:413 , GLY D:464 , TYR D:465 , TYR D:467BINDING SITE FOR RESIDUE K D 2004
09AC9SOFTWARESER A:52 , HIS A:80 , GLY A:121 , HIS A:122 , SER A:123 , GLY A:151 , ASP A:152 , GLY A:153 , ALA A:154 , ASN A:181 , TYR A:288 , ALA A:345 , MSE A:346 , ILE A:368 , GLU A:370 , PHE A:395 , ARG A:398 , MG A:1001 , HOH A:3100 , HOH A:3141 , HOH A:3158BINDING SITE FOR RESIDUE TDP A 3001
10BC1SOFTWAREHIS B:80 , GLY B:151 , ASP B:152 , GLY B:153 , ALA B:154 , ASN B:181 , MG B:1002BINDING SITE FOR RESIDUE DPO B 4001
11BC2SOFTWAREHIS C:80 , GLY C:121 , HIS C:122 , SER C:123 , GLY C:151 , ASP C:152 , GLY C:153 , ALA C:154 , ASN C:181 , LYS C:284 , TYR C:288 , ALA C:345 , MSE C:346 , ILE C:368 , GLU C:370 , PHE C:395 , ARG C:398 , MG C:1003 , HOH C:3121 , HOH C:3129BINDING SITE FOR RESIDUE TDP C 3002
12BC3SOFTWAREHIS D:80 , GLY D:151 , ASP D:152 , GLY D:153 , ALA D:154 , ASN D:181 , MG D:1004BINDING SITE FOR RESIDUE DPO D 4002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2O1S)

(-) Cis Peptide Bonds  (11, 11)

Asymmetric Unit
No.Residues
1Thr A:69 -Pro A:70
2Gly A:252 -Pro A:253
3Lys A:536 -Pro A:537
4Thr B:69 -Pro B:70
5Gly B:252 -Pro B:253
6Lys B:536 -Pro B:537
7Thr C:69 -Pro C:70
8Lys C:536 -Pro C:537
9Thr D:69 -Pro D:70
10Gly D:252 -Pro D:253
11Lys D:536 -Pro D:537

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2O1S)

(-) PROSITE Motifs  (2, 8)

Asymmetric Unit (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRANSKETOLASE_1PS00801 Transketolase signature 1.DXS_ECOLI36-55
 
 
 		  4A:36-55
B:36-55
C:36-55
D:36-55
2TRANSKETOLASE_2PS00802 Transketolase signature 2.DXS_ECOLI425-441
 
 
 		  4A:425-441
B:425-441
C:425-441
D:425-441
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRANSKETOLASE_1PS00801 Transketolase signature 1.DXS_ECOLI36-55
 
 
 		  2A:36-55
B:36-55
-
-
2TRANSKETOLASE_2PS00802 Transketolase signature 2.DXS_ECOLI425-441
 
 
 		  2A:425-441
B:425-441
-
-
Biological Unit 2 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRANSKETOLASE_1PS00801 Transketolase signature 1.DXS_ECOLI36-55
 
 
 		  2-
-
C:36-55
D:36-55
2TRANSKETOLASE_2PS00802 Transketolase signature 2.DXS_ECOLI425-441
 
 
 		  2-
-
C:425-441
D:425-441

(-) Exons   (0, 0)

(no "Exon" information available for 2O1S)

(-) 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:536
 aligned with DXS_ECOLI | P77488 from UniProtKB/Swiss-Prot  Length:620

    Alignment length:618
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612        
            DXS_ECOLI     3 FDIAKYPTLALVDSTQELRLLPKESLPKLCDELRRYLLDSVSRSSGHFASGLGTVELTVALHYVYNTPFDQLIWDVGHQAYPHKILTGRRDKIGTIRQKGGLHPFPWRGESEYDVLSVGHSSTSISAGIGIAVAAEKEGKNRRTVCVIGDGAITAGMAFEAMNHAGDIRPDMLVILNDNEMSISENVGALNNHLAQLLSGKLYSSLREGGKKVFSGVPPIKELLKRTEEHIKGMVVPGTLFEELGFNYIGPVDGHDVLGLITTLKNMRDLKGPQFLHIMTKKGRGYEPAEKDPITFHAVPKFDPSSGCLPKSSGGLPSYSKIFGDWLCETAAKDNKLMAITPAMREGSGMVEFSRKFPDRYFDVAIAEQHAVTFAAGLAIGGYKPIVAIYSTFLQRAYDQVLHDVAIQKLPVLFAIDRAGIVGADGQTHQGAFDLSYLRCIPEMVIMTPSDENECRQMLYTGYHYNDGPSAVRYPRGNAVGVELTPLEKLPIGKGIVKRRGEKLAILNFGTLMPEAAKVAESLNATLVDMRFVKPLDEALILEMAASHEALVTVEENAIMGGAGSGVNEVLMAHRKPVPVLNIGLPDFFIPQGTQEEMRAELGLDAAGMEAKIKAWLA 620
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee.....hhhhhhh..hhhhhhhh..........................hhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhhhh..eeeeeee..--------------------------------------------------------hhhhhhhh..eeeeeee..hhhhhhhhhhhhhhh..eeeeeee..........--------------------------..hhhhhhhhhhhhhhhhh..eeeee........hhhhhhhh...eee...hhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhh........eeeee........hhhhh..hhhhhh......eee...hhhhhhhhhhhhhhh....eeee......................eeee....eeeeee..hhhhhhhhhhhhh.eeee..eee..hhhhhhhhhhhh.eeeeeeeee...hhhhhhhhhhhhh.....eeeeee........hhhhhhhhh..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------TRANSKETOLASE_1     ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TRANSKETOLASE_2  ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2o1s A   3 FDIAKYPTLALVDSTQELRLLPKESLPKLCDELRRYLLDSVSRSSGHFASGLGTVELTVALHYVYNTPFDQLIWDVGHQAYPHKILTGRRDKIGTIRQKGGLHPFPWRGESEYDVLSVGHSSTSISAGIGIAVAAEKEGKNRRTVCVIGDGAITAGmAFEAmNHAGDIRPDmLVILNDNE--------------------------------------------------------PGTLFEELGFNYIGPVDGHDVLGLITTLKNmRDLKGPQFLHImTKKGRGYEPA--------------------------LPSYSKIFGDWLCETAAKDNKLmAITPAmREGSGmVEFSRKFPDRYFDVAIAEQHAVTFAAGLAIGGYKPIVAIYSTFLQRAYDQVLHDVAIQKLPVLFAIDRAGIVGADGQTHQGAFDLSYLRCIPEmVImTPSDENECRQmLYTGYHYNDGPSAVRYPRGNAVGVELTPLEKLPIGKGIVKRRGEKLAILNFGTLmPEAAKVAESLNATLVDmRFVKPLDEALILEmAASHEALVTVEENAImGGAGSGVNEVLmAHRKPVPVLNIGLPDFFIPQGTQEEmRAELGLDAAGmEAKIKAWLA 620
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152      |162 |     172 |     182         -         -         -         -         -      |242       252       262      |272       282        |-         -         -     | 322       332       342   |   352       362       372       382       392       402       412       422       432       442   |  |452       462       472       482       492       502       512  |    522       532       542   |   552       562       572 |     582       592       602       612        
                                                                                                                                                                                      159-MSE|       174-MSE 182                                                      239                           269-MSE     281-MSE   291                        318                   340-MSE |     |                                                                                           446-MSE       460-MSE                                                515-MSE          532-MSE       546-MSE         562-MSE     574-MSE                   600-MSE    611-MSE     
                                                                                                                                                                                           164-MSE                                                                                                                                                                               346-MSE |                                                                                              449-MSE                                                                                                                                                                       
                                                                                                                                                                                                                                                                                                                                                                                       352-MSE                                                                                                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:493
 aligned with DXS_ECOLI | P77488 from UniProtKB/Swiss-Prot  Length:620

    Alignment length:614
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              620 
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617  | 
            DXS_ECOLI     8 YPTLALVDSTQELRLLPKESLPKLCDELRRYLLDSVSRSSGHFASGLGTVELTVALHYVYNTPFDQLIWDVGHQAYPHKILTGRRDKIGTIRQKGGLHPFPWRGESEYDVLSVGHSSTSISAGIGIAVAAEKEGKNRRTVCVIGDGAITAGMAFEAMNHAGDIRPDMLVILNDNEMSISENVGALNNHLAQLLSGKLYSSLREGGKKVFSGVPPIKELLKRTEEHIKGMVVPGTLFEELGFNYIGPVDGHDVLGLITTLKNMRDLKGPQFLHIMTKKGRGYEPAEKDPITFHAVPKFDPSSGCLPKSSGGLPSYSKIFGDWLCETAAKDNKLMAITPAMREGSGMVEFSRKFPDRYFDVAIAEQHAVTFAAGLAIGGYKPIVAIYSTFLQRAYDQVLHDVAIQKLPVLFAIDRAGIVGADGQTHQGAFDLSYLRCIPEMVIMTPSDENECRQMLYTGYHYNDGPSAVRYPRGNAVGVELTPLEKLPIGKGIVKRRGEKLAILNFGTLMPEAAKVAESLNATLVDMRFVKPLDEALILEMAASHEALVTVEENAIMGGAGSGVNEVLMAHRKPVPVLNIGLPDFFIPQGTQEEMRAELGLDAAGMEAKIKAWLA-   -
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh------------hhhhhhhhhhhhhhh.....eeee.....hhhhhhh.---------------....................hhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhhhh..eeeeeee.------------------------------------------------------------hhhhhh.eeeeeee..hhhhhhhhhhhh.....eeeeeee..----------------------------------..hhhhhhhhhhhhhhh....eeeee........hhhhhhhh...eee...hhhhhhhhhhhhhhh..eeeeeeehhhhh.hhhhhhhhh.......eeeee........hhhhh..hhhhhh......eee...hhhhhhhhhhhhhh.....eeee......................eeee....eeeeee..hhhhhhhhhhhhh.eeee..eee..hhhhhhhhhhhh.eeeeeeeee...hhhhhhhhhhhhh.....eeeeee........hhhhhhhhhh.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------TRANSKETOLASE_1     ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TRANSKETOLASE_2  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o1s B   8 YPTLALVDSTQELRLLPKESLPKLCDELRRYLL------------GLGTVELTVALHYVYNTPFDQLIWDVGHQAYPHKILT---------------HPFPWRGESEYDVLSVGHSSTSISAGIGIAVAAEKEGKNRRTVCVIGDGAITAGmAFEAmNHAGDIRPDmLVILNDN------------------------------------------------------------LFEELGFNYIGPVDGHDVLGLITTLKNmRDLKGPQFLHImTK----------------------------------LPSYSKIFGDWLCETAAKDNKLmAITPAmREGSGmVEFSRKFPDRYFDVAIAEQHAVTFAAGLAIGGYKPIVAIYSTFLQRAYDQVLHDVAIQKLPVLFAIDRAGIVGADGQTHQGAFDLSYLRCIPEmVImTPSDENECRQmLYTGYHYNDGPSAVRYPRGNAVGVELTPLEKLPIGKGIVKRRGEKLAILNFGTLmPEAAKVAESLNATLVDmRFVKPLDEALILEmAASHEALVTVEENAImGGAGSGVNEVLmAHRKPVPVLNIGLPDFFIPQGTQEEmRAELGLDAAGmEAKIKAWLAL 621
                                    17        27        37  |      -     |  57        67        77        87 |       -       107       117       127       137       147       157 |    |167      |177   |     -         -         -         -         -         -    |  247       257       267 |     277   | |   -         -         -         -|      327       337  |    347    |  357       367       377       387       397       407       417       427       437       447 |     457  |    467       477       487       497       507       517       527    |  537       547       557    |  567      |577       587       597  |    607   |   617    
                                                           40           53                                  89             105                                                   159-MSE|       174-MSE181                                                          242                        269-MSE     281-MSE                              318                   340-MSE |     |                                                                                           446-MSE       460-MSE                                                515-MSE          532-MSE       546-MSE         562-MSE     574-MSE                   600-MSE    611-MSE      
                                                                                                                                                                                      164-MSE                                                                                                                283                                                            346-MSE |                                                                                              449-MSE                                                                                                                                                                        
                                                                                                                                                                                                                                                                                                                                                                                  352-MSE                                                                                                                                                                                                                                                                         


Chain C from PDB  Type:PROTEIN  Length:536
 aligned with DXS_ECOLI | P77488 from UniProtKB/Swiss-Prot  Length:620

    Alignment length:619
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   620 
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       | 
            DXS_ECOLI     3 FDIAKYPTLALVDSTQELRLLPKESLPKLCDELRRYLLDSVSRSSGHFASGLGTVELTVALHYVYNTPFDQLIWDVGHQAYPHKILTGRRDKIGTIRQKGGLHPFPWRGESEYDVLSVGHSSTSISAGIGIAVAAEKEGKNRRTVCVIGDGAITAGMAFEAMNHAGDIRPDMLVILNDNEMSISENVGALNNHLAQLLSGKLYSSLREGGKKVFSGVPPIKELLKRTEEHIKGMVVPGTLFEELGFNYIGPVDGHDVLGLITTLKNMRDLKGPQFLHIMTKKGRGYEPAEKDPITFHAVPKFDPSSGCLPKSSGGLPSYSKIFGDWLCETAAKDNKLMAITPAMREGSGMVEFSRKFPDRYFDVAIAEQHAVTFAAGLAIGGYKPIVAIYSTFLQRAYDQVLHDVAIQKLPVLFAIDRAGIVGADGQTHQGAFDLSYLRCIPEMVIMTPSDENECRQMLYTGYHYNDGPSAVRYPRGNAVGVELTPLEKLPIGKGIVKRRGEKLAILNFGTLMPEAAKVAESLNATLVDMRFVKPLDEALILEMAASHEALVTVEENAIMGGAGSGVNEVLMAHRKPVPVLNIGLPDFFIPQGTQEEMRAELGLDAAGMEAKIKAWLA-   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee.....hhhhhhhh.hhhhhhhh..........................hhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhhhh..eeeeeee..---------------------------------------------------------hhhhhhh..eeeeeee..hhhhhhhhhhhhhhh..eeeeeee..........--------------------------..hhhhhhhhhhhhhhhhh..eeeee........hhhhhhhh...eee...hhhhhhhhhhhhhhh..eeeeeeehhhhh.hhhhhhhhh.......eeeee........hhhhh..hhhhhh......eee...hhhhhhhhhhhhhh.....eeee......................eeee....eeeeee..hhhhhhhhhhhhh.eeee..eee..hhhhhhhhhhhh.eeeeeeeee...hhhhhhhhhhhhh.....eeeeee........hhhhhhhhh..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------TRANSKETOLASE_1     ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TRANSKETOLASE_2  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o1s C   3 FDIAKYPTLALVDSTQELRLLPKESLPKLCDELRRYLLDSVSRSSGHFASGLGTVELTVALHYVYNTPFDQLIWDVGHQAYPHKILTGRRDKIGTIRQKGGLHPFPWRGESEYDVLSVGHSSTSISAGIGIAVAAEKEGKNRRTVCVIGDGAITAGmAFEAmNHAGDIRPDmLVILNDNE---------------------------------------------------------GTLFEELGFNYIGPVDGHDVLGLITTLKNmRDLKGPQFLHImTKKGRGYEPA--------------------------LPSYSKIFGDWLCETAAKDNKLmAITPAmREGSGmVEFSRKFPDRYFDVAIAEQHAVTFAAGLAIGGYKPIVAIYSTFLQRAYDQVLHDVAIQKLPVLFAIDRAGIVGADGQTHQGAFDLSYLRCIPEmVImTPSDENECRQmLYTGYHYNDGPSAVRYPRGNAVGVELTPLEKLPIGKGIVKRRGEKLAILNFGTLmPEAAKVAESLNATLVDmRFVKPLDEALILEmAASHEALVTVEENAImGGAGSGVNEVLmAHRKPVPVLNIGLPDFFIPQGTQEEmRAELGLDAAGmEAKIKAWLAL 621
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152      |162 |     172 |     182         -         -         -         -         -       242       252       262      |272       282        |-         -         -     | 322       332       342   |   352       362       372       382       392       402       412       422       432       442   |  |452       462       472       482       492       502       512  |    522       532       542   |   552       562       572 |     582       592       602       612         
                                                                                                                                                                                      159-MSE|       174-MSE 182                                                       240                          269-MSE     281-MSE   291                        318                   340-MSE |     |                                                                                           446-MSE       460-MSE                                                515-MSE          532-MSE       546-MSE         562-MSE     574-MSE                   600-MSE    611-MSE      
                                                                                                                                                                                           164-MSE                                                                                                                                                                               346-MSE |                                                                                              449-MSE                                                                                                                                                                        
                                                                                                                                                                                                                                                                                                                                                                                       352-MSE                                                                                                                                                                                                                                                                         


Chain D from PDB  Type:PROTEIN  Length:487
 aligned with DXS_ECOLI | P77488 from UniProtKB/Swiss-Prot  Length:620

    Alignment length:613
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             620 
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618 | 
            DXS_ECOLI     9 PTLALVDSTQELRLLPKESLPKLCDELRRYLLDSVSRSSGHFASGLGTVELTVALHYVYNTPFDQLIWDVGHQAYPHKILTGRRDKIGTIRQKGGLHPFPWRGESEYDVLSVGHSSTSISAGIGIAVAAEKEGKNRRTVCVIGDGAITAGMAFEAMNHAGDIRPDMLVILNDNEMSISENVGALNNHLAQLLSGKLYSSLREGGKKVFSGVPPIKELLKRTEEHIKGMVVPGTLFEELGFNYIGPVDGHDVLGLITTLKNMRDLKGPQFLHIMTKKGRGYEPAEKDPITFHAVPKFDPSSGCLPKSSGGLPSYSKIFGDWLCETAAKDNKLMAITPAMREGSGMVEFSRKFPDRYFDVAIAEQHAVTFAAGLAIGGYKPIVAIYSTFLQRAYDQVLHDVAIQKLPVLFAIDRAGIVGADGQTHQGAFDLSYLRCIPEMVIMTPSDENECRQMLYTGYHYNDGPSAVRYPRGNAVGVELTPLEKLPIGKGIVKRRGEKLAILNFGTLMPEAAKVAESLNATLVDMRFVKPLDEALILEMAASHEALVTVEENAIMGGAGSGVNEVLMAHRKPVPVLNIGLPDFFIPQGTQEEMRAELGLDAAGMEAKIKAWLA-   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --DXP_synthase_N-2o1sD01 D:11-282                                                                                                                                                                                                                                                 -                                  Transket_pyr-2o1sD05 D:318-482                                                                                                                                       ------------Transketolase_C-2o1sD09 D:495-611                                                                                    ---------- Pfam domains (1)
           Pfam domains (2) --DXP_synthase_N-2o1sD02 D:11-282                                                                                                                                                                                                                                                 -                                  Transket_pyr-2o1sD06 D:318-482                                                                                                                                       ------------Transketolase_C-2o1sD10 D:495-611                                                                                    ---------- Pfam domains (2)
           Pfam domains (3) --DXP_synthase_N-2o1sD03 D:11-282                                                                                                                                                                                                                                                 -                                  Transket_pyr-2o1sD07 D:318-482                                                                                                                                       ------------Transketolase_C-2o1sD11 D:495-611                                                                                    ---------- Pfam domains (3)
           Pfam domains (4) --DXP_synthase_N-2o1sD04 D:11-282                                                                                                                                                                                                                                                 -                                  Transket_pyr-2o1sD08 D:318-482                                                                                                                                       ------------Transketolase_C-2o1sD12 D:495-611                                                                                    ---------- Pfam domains (4)
         Sec.struct. author .hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.-----------hhhhhhhhhhhhhhh.....eeee.....hhhhhhhh.----------------------............hhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhhhh..eeeeeee.-----------------------------------------------------------hhhhhh..eeeeeee..hhhhhhhhhhhhhhh..eeeeeee..----------------------------------..hhhhhhhhhhhhhhh....eeeee........hhhhhhhh...eee...hhhhhhhhhhhhhhh..eeeeeeehhhhh.hhhhhhhhh.......eeeee........hhhhh..hhhhhh......eee...hhhhhhhhhhhhhh.....eeee......................eeee....eeeeee..hhhhhhhhhhhhh.eeee..eee..hhhhhhhhhhh..eeeeeeeee...hhhhhhhhhhhhh.....eeeeee........hhhhhhhhh..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------TRANSKETOLASE_1     ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TRANSKETOLASE_2  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o1s D   9 PTLALVDSTQELRLLPKESLPKLCDELRRYLLD-----------GLGTVELTVALHYVYNTPFDQLIWDVGHQAYPHKILTG----------------------SEYDVLSVGHSSTSISAGIGIAVAAEKEGKNRRTVCVIGDGAITAGmAFEAmNHAGDIRPDmLVILNDN-----------------------------------------------------------TLFEELGFNYIGPVDGHDVLGLITTLKNmRDLKGPQFLHImTK----------------------------------LPSYSKIFGDWLCETAAKDNKLmAITPAmREGSGmVEFSRKFPDRYFDVAIAEQHAVTFAAGLAIGGYKPIVAIYSTFLQRAYDQVLHDVAIQKLPVLFAIDRAGIVGADGQTHQGAFDLSYLRCIPEmVImTPSDENECRQmLYTGYHYNDGPSAVRYPRGNAVGVELTPLEKLPIGKGIVKRRGEKLAILNFGTLmPEAAKVAESLNATLVDmRFVKPLDEALILEmAASHEALVTVEENAImGGAGSGVNEVLmAHRKPVPVLNIGLPDFFIPQGTQEEmRAELGLDAAGmEAKIKAWLAL 621
                                    18        28        38  |      -    |   58        68        78        88 |       -         -    |  118       128       138       148       158|    | 168     | 178  |      -         -         -         -         -         -  |    248       258       268|      278  | |    -         -         -       318       328       338 |     348   |   358       368       378       388       398       408       418       428       438       448|      458 |     468       478       488       498       508      |518       528   |   538       548       558   |   568     | 578       588       598 |     608  |    618   
                                                           41          53                                   90                    113                                           159-MSE|       174-MSE181                                                         241                         269-MSE     281-MSE                              318                   340-MSE |     |                                                                                           446-MSE       460-MSE                                                515-MSE          532-MSE       546-MSE         562-MSE     574-MSE                   600-MSE    611-MSE      
                                                                                                                                                                                     164-MSE                                                                                                                283                                                            346-MSE |                                                                                              449-MSE                                                                                                                                                                        
                                                                                                                                                                                                                                                                                                                                                                                 352-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)
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  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 2O1S)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2O1S)

(-) Pfam Domains  (3, 12)

Asymmetric Unit
(-)
Clan: THDP-binding (106)
(-)
Clan: no clan defined [family: Transketolase_C] (40)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (DXS_ECOLI | P77488)
molecular function
    GO:0008661    1-deoxy-D-xylulose-5-phosphate synthase activity    Catalysis of the reaction: D-glyceraldehyde 3-phosphate + H(+) + pyruvate = 1-deoxy-D-xylulose 5-phosphate + CO(2).
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0030976    thiamine pyrophosphate binding    Interacting selectively and non-covalently with thiamine pyrophosphate, the diphosphoric ester of thiamine. Acts as a coenzyme of several (de)carboxylases, transketolases, and alpha-oxoacid dehydrogenases.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0052865    1-deoxy-D-xylulose 5-phosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of 1-deoxy-D-xylulose 5-phosphate, the 5-phospho derivative of 1-deoxy-D-xylulose. 1-deoxy-D-xylulose 5-phosphate is an intermediate in the non-mevalonate pathway and a common precursor for isoprenoid, thiamin, and pyridoxol biosynthesis.
    GO:0019288    isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway    The chemical reactions and pathways resulting in the formation of isopentenyl diphosphate by the mevalonate-independent pathway. Isopentenyl diphosphate (IPP) is the fundamental unit in isoprenoid biosynthesis and is biosynthesized from pyruvate and glyceraldehyde 3-phosphate via intermediates, including 1-deoxy-D-xylulose 5-phosphate.
    GO:0008299    isoprenoid biosynthetic process    The chemical reactions and pathways resulting in the formation of any isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0008615    pyridoxine biosynthetic process    The chemical reactions and pathways resulting in the formation of pyridoxine, 2-methyl-3-hydroxy-4,5-bis(hydroxymethyl)pyridine, one of the vitamin B6 compounds.
    GO:0016114    terpenoid biosynthetic process    The chemical reactions and pathways resulting in the formation of terpenoids, any member of a class of compounds characterized by an isoprenoid chemical structure.
    GO:0009228    thiamine biosynthetic process    The chemical reactions and pathways resulting in the formation of thiamine (vitamin B1), a water soluble vitamin present in fresh vegetables and meats, especially liver.
    GO:0006744    ubiquinone biosynthetic process    The chemical reactions and pathways resulting in the formation of ubiquinone, a lipid-soluble electron-transporting coenzyme.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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2o1x