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(-) Description

Title :  CRYSTAL STRUCTURE OF TRANSKETOLASE IN COMPLEX WITH THIAMINE DIPHOSPHATE, RIBOSE-5-PHOSPHATE AND CALCIUM ION
 
Authors :  B. Nocek, M. Makowska-Grzyska, N. Maltseva, A. Joachimiak, W. Anderso For Structural Genomics Of Infectious Diseases (Csgid)
Date :  15 Mar 10  (Deposition) - 28 Apr 10  (Release) - 01 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.59
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Transketolase, Thiamine Pyrophosphate, Calcium Binding, Ribose-5- Phosphate Bound, Niaid, Csgid, Transferase, Structural Genomics, Center For Structural Genomics Of Infectious Diseases (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Nocek, M. Makowska-Grzyska, N. Maltseva, S. Grimshaw, A. Joachimiak, W. Anderson
Crystal Structure Of Transketolase In Complex With Thiamine Diphosphate, Ribose-5-Phosphate And Calcium Ion
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TRANSKETOLASE
    Chains: A
    EC Number: 2.2.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: TKT, CJ1645
    Organism Scientific: CAMPYLOBACTER JEJUNI
    Organism Taxid: 192222
    Strain: NCTC 11168

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 15)

Asymmetric Unit (7, 15)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3GOL1Ligand/IonGLYCEROL
4MSE9Mod. Amino AcidSELENOMETHIONINE
5PO41Ligand/IonPHOSPHATE ION
6R5P1Ligand/IonRIBOSE-5-PHOSPHATE
7TPP1Ligand/IonTHIAMINE DIPHOSPHATE
Biological Unit 1 (6, 28)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3GOL2Ligand/IonGLYCEROL
4MSE18Mod. Amino AcidSELENOMETHIONINE
5PO42Ligand/IonPHOSPHATE ION
6R5P2Ligand/IonRIBOSE-5-PHOSPHATE
7TPP2Ligand/IonTHIAMINE DIPHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:9 , SER A:43 , ARG A:289 , PHE A:290 , SER A:292 , HOH A:766BINDING SITE FOR RESIDUE GOL A 2001
2AC2SOFTWAREALA A:31 , HIS A:67 , GLY A:114 , LEU A:116 , GLY A:151 , ASP A:152 , GLY A:153 , GLU A:157 , ASN A:182 , ILE A:184 , ILE A:186 , ILE A:242 , HIS A:256 , ASP A:364 , GLU A:391 , PHE A:417 , TYR A:420 , R5P A:701 , HOH A:756 , CA A:801 , HOH A:1086BINDING SITE FOR RESIDUE TPP A 5001
3AC3SOFTWAREASP A:152 , ASN A:182 , ILE A:184 , HOH A:794 , TPP A:5001BINDING SITE FOR RESIDUE CA A 801
4AC4SOFTWAREPHE A:595 , HOH A:872BINDING SITE FOR RESIDUE EDO A 1002
5AC5SOFTWAREHIS A:28 , HIS A:101 , ILE A:186 , HIS A:256 , ARG A:341 , SER A:368 , HIS A:441 , ASP A:449 , HIS A:453 , ARG A:499 , HOH A:1195 , HOH A:1196 , HOH A:1197 , TPP A:5001BINDING SITE FOR RESIDUE R5P A 701
6AC6SOFTWAREHIS A:281 , PRO A:283 , GLN A:284 , HOH A:811 , HOH A:822BINDING SITE FOR RESIDUE PO4 A 633

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3M6L)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Phe A:379 -Val A:380

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3M6L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3M6L)

(-) Exons   (0, 0)

(no "Exon" information available for 3M6L)

(-) 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:632
 aligned with Q0P7Y3_CAMJE | Q0P7Y3 from UniProtKB/TrEMBL  Length:632

    Alignment length:632
                                    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       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630  
         Q0P7Y3_CAMJE     1 MNIQILQEQANTLRFLSADMVQKANSGHPGAPLGLADILSVLSYHLKHNPKNPTWLNRDRLVFSGGHASALLYSFLHLSGYDLSLEDLKNFRQLHSKTPGHPEISTLGVEIATGPLGQGVANAVGFAMAAKKAQNLLGSDLIDHKIYCLCGDGDLQEGISYEACSLAGLHKLDNFILIYDSNNISIEGDVGLAFNENVKMRFEAQGFEVLSINGHDYEEINKALEQAKKSTKPCLIIAKTTIAKGAGELEGSHKSHGAPLGEEVIKKAKEQAGFDPNISFHIPQASKIRFESAVELGDLEEAKWKDKLEKSAKKELLERLLNPDFNKIAYPDFKGKDLATRDSNGEILNVLAKNLEGFLGGSADLGPSNKTELHSMGDFVEGKNIHFGIREHAMAAINNAFARYGIFLPFSATFFIFSEYLKPAARIAALMKIKHFFIFTHDSIGVGEDGPTHQPIEQLSTFRAMPNFLTFRPADGVENVKAWQIALNADIPSAFVLSRQKLKALNEPVFGDVKNGAYLLKESKEAKFTLLASGSEVWLCLESANELEKQGFACNVVSMPCFELFEKQDKAYQERLLKGEVIGVEAAHSNELYKFCHKVYGIESFGESGKDKDVFERFGFSVSKLVNFILSK 632
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----Transketolase_N-3m6lA02 A:5-325                                                                                                                                                                                                                                                                                                  ----------Transket_pyr-3m6lA01 A:336-504                                                                                                                                           ------------Transketolase_C-3m6lA03 A:517-625                                                                            ------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.............eeee.hhhhhhhhhhhhhhhh...hhhhhhh..........................hhhhhhhhhhhhhhhhhhhhhh.......eeeeeehhhhhhhhhhhhhhhhhhh....eeeeeee..ee..ee.hhh...hhhhhhhhh..eeeeee..hhhhhhhhhhhhhh....eeeeee......hhhhh.hhhhh....hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh................hhhhhhhhhhhhhhhhh..eeeee..hhhhhh.............eee...hhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhhhh...eeeee..hhhhh..hhhhh..hhhhhhhhh...eee...hhhhhhhhhhhhhhh...eeee...............hhhhh.eeee......eeeee...hhhhhhhhhhhhhhh...eeeee..hhhhhhh.hhhhhhhhh..eeeee....hhhhhhh..eee.........hhhhhhhhh..hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m6l A   1 mNIQILQEQANTLRFLSADmVQKANSGHPGAPLGLADILSVLSYHLKHNPKNPTWLNRDRLVFSGGHASALLYSFLHLSGYDLSLEDLKNFRQLHSKTPGHPEISTLGVEIATGPLGQGVANAVGFAmAAKKAQNLLGSDLIDHKIYCLCGDGDLQEGISYEACSLAGLHKLDNFILIYDSNNISIEGDVGLAFNENVKmRFEAQGFEVLSINGHDYEEINKALEQAKKSTKPCLIIAKTTIAKGAGELEGSHKSHGAPLGEEVIKKAKEQAGFDPNISFHIPQASKIRFESAVELGDLEEAKWKDKLEKSAKKELLERLLNPDFNKIAYPDFKGKDLATRDSNGEILNVLAKNLEGFLGGSADLGPSNKTELHSmGDFVEGKNIHFGIREHAmAAINNAFARYGIFLPFSATFFIFSEYLKPAARIAALmKIKHFFIFTHDSIGVGEDGPTHQPIEQLSTFRAmPNFLTFRPADGVENVKAWQIALNADIPSAFVLSRQKLKALNEPVFGDVKNGAYLLKESKEAKFTLLASGSEVWLCLESANELEKQGFACNVVSmPCFELFEKQDKAYQERLLKGEVIGVEAAHSNELYKFCHKVYGIESFGESGKDKDVFERFGFSVSKLVNFILSK 632
                            |       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       300       310       320       330       340       350       360       370     | 380       390   |   400       410       420       430|      440       450       460    |  470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630  
                            |                 20-MSE                                                                                                     128-MSE                                                                 200-MSE                                                                                                                                                                         376-MSE           394-MSE                              431-MSE                           465-MSE                                                                                       559-MSE                                                                     
                            1-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 3M6L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3M6L)

(-) Pfam Domains  (3, 3)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q0P7Y3_CAMJE | Q0P7Y3)
molecular function
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
    GO:0004802    transketolase activity    Catalysis of the reversible transfer of a 2-carbon ketol group (CH2OH-CO-) from a ketose phosphate donor to an aldose phosphate acceptor.
biological process
    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.

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 Related Entries

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

UniProtKB/TrEMBL
        Q0P7Y3_CAMJE | Q0P7Y3: 3l84 3m34 3m7i

(-) Related Entries Specified in the PDB File

3l84 RELATED ID: IDP90564 RELATED DB: TARGETDB
3m34