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(-) Description

Title :  CRYSTAL STRUCTURE OF APO TRANSKETOLASE FROM FRANCISELLA TULARENSIS
 
Authors :  S. M. Anderson, Z. Wawrzak, T. Skarina, E. Gordon, K. Kwon, A. Savchenko W. F. Anderson, Center For Structural Genomics Of Infectious D (Csgid)
Date :  13 Nov 09  (Deposition) - 01 Dec 09  (Release) - 14 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rossmann Fold, Transketolase, Csgid, Transferase, Structural Genomics, Center For Structural Genomics Of Infectious Diseases (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. M. Anderson, Z. Wawrzak, T. Skarina, E. Gordon, K. Kwon, A. Savchenko, W. F. Anderson
Crystal Structure Of Apo Transketolase From Francisella Tularensis
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TRANSKETOLASE
    Chains: A, B
    EC Number: 2.2.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TKTA, FTT1369C, FTT_1369C
    Mutation: YES
    Organism Scientific: FRANCISELLA TULARENSIS SUBSP. TULARENSIS
    Organism Taxid: 177416
    Strain: SCHU S4

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 42)

Asymmetric/Biological Unit (2, 42)
No.NameCountTypeFull Name
1MSE40Mod. Amino AcidSELENOMETHIONINE
2OCS2Mod. Amino AcidCYSTEINESULFONIC ACID

(-) Sites  (0, 0)

(no "Site" information available for 3KOM)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3KOM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3KOM)

(-) 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:654
 aligned with Q5NF74_FRATT | Q5NF74 from UniProtKB/TrEMBL  Length:663

    Alignment length:661
                                    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       622       632       642       652       662 
         Q5NF74_FRATT     3 LSIPREFSNAIRFLSIDATLKAKSGHPGMPMGMADIATVLWTKFLKHNPNNPHWINRDRFVLSNGHGSMLLYSLLHLTGYDLSIEDIKNFRQLHSKTPGHPEYGYTPGVETTTGPLGQGVANAVGMALGEKLLSDRYNTPDLKVIDHHTYVFLGDGCLMEGVSHEACSLAGTLGLNKLVAFWDDNNISIDGDTKGWFSDNTPERFRAYGWHVIENVDGHDFVAIEKAINEAHSQQQKPTLICCKTVIGFGSPEKAGTASVHGSPLSDQERASAAKELNWDYQAFEIPQDVYKYWDAREKGQALEANWQGQWNLFKDSPKFDEFERVLSKELPVGLESAINDYIASQLSNPVKVATRKASQMVLEVLCKNMPEMFGGSADLTGSNNTNWSGSVWLNNTQEGANYLSYGVREFGMAAIMNGLSLYGGIKPYGGTFLVFSDYSRNAIRMSALMKQPVVHVMSHDSIGLGEDGPTHQPIEHVPSLRLIPNLSVWRPADTIETMIAWKEAVKSKDTPSVMVLTRQNLMPVVQTQHQVANIARGGYLVKDNPDAKLTIVATGSEVELAVKVANEFEKKGIKLNVASIPCVEVFATQAHEYKKTVIKDDIPAVFVEMAQPDMWYKYMPKAGGEVKGIYSFGESAPAEDLFKRFGFTVENISNIVAKYV 663
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3komA01 A:3-326  [code=3.40.50.970, no name defined]                                                                                                                                                                                                                                                                                3komA02 A:327-538  [code=3.40.50.970, no name defined]                                                                                                                                                              3komA03 A:539-663  [code=3.40.50.920, no name defined]                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..............eeee....hhhhhhhhhhhhh...hhhhhh............................hhhhhhhhhhhhhhhhhhhhhh..........eeeeehhhhhhhhhhhhhhhhhhhhh...eeeeeee..-----hhhhh...hhhhhhhhh..eeeeeee..hhhhhhhhhhhhhhh....eeeeee.....................hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh....hhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhh..eeeee...--....................eee...hhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhhh....eeeee..hhhhh.........hhhhhhhh....eee...hhhhhhhhhhhhhhh....eeee....ee.....hhhhhhhhh...eeee.......eeee..hhhhhhhhhhhhhhhh....eeee..hhhhhhh.hhhhhhhhh.....eeee....hhhhhhhh....eeee.........hhhhhhhhhh.hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kom A   3 LSIPREFSNAIRFLSIDATLKAKSGHPGmPmGmADIATVLWTKFLKHNPNNPHWINRDRFVLSNGHGSmLLYSLLHLTGYDLSIEDIKNFRQLHSKTPGHPEYGYTPGVETTTGPLGQGVANAVGmALGEKLLSDRYNTPDLKVIDHHTYVFLGDGcLmEGVSHEACSLAGTLGLNKLVAFWDDNN-----DTKGWFSDNTPERFRAYGWHVIENVDGHDFVAIEKAINEAHSQQQKPTLICCKTVIGFGSPEKAGTASVHGSPLSDQERASAAKELNWDYQAFEIPQDVYKYWDAREKGQALEANWQGQRNLFKDSPKFDEFERVLSKELPVGLESAINDYIASQLSNPVKVATRKASQmVLEVLCKNmPEmFGGSADL--SNNTNWSGSVWLNNTQEGANYLSYGVREFGmAAImNGLSLYGGIKPYGGTFLVFSDYSRNAIRmSALmKQPVVHVmSHDSIGLGEDGPTHQPIEHVPSLRLIPNLSVWRPADTIETmIAWKEAVKSKDTPSVmVLTRQNLmPVVQTQHQVANIARGGYLVKDNPDAKLTIVATGSEVELAVKVANEFEKKGIKLNVASIPCVEVFATQAHEYKKTVIKDDIPAVFVEmAQPDmWYKYmPKAGGEVKGIYSFGESAPAEDLFKRFGFTVENISNIVAKYV 663
                                    12        22        32| |     42        52        62        72        82        92       102       112       122     | 132       142       152      |162       172       182     |   - |     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    |  622       632       642       652       662 
                                                       31-MSE                                  71-MSE                                                  128-MSE                        159-OCS                      188   194                                                                                                                                                                      363-MSE  372-MSE   382  |                           415-MSE                          448-MSE     460-MSE                                  501-MSE         517-MSE 525-MSE                                                                                612-MSE|    |                                         
                                                         33-MSE                                                                                                                         161-MSE                                                                                                                                                                                                               375-MSE   385                               419-MSE                          452-MSE                                                                                                                                                              617-MSE|                                         
                                                           35-MSE                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    622-MSE                                     


Chain B from PDB  Type:PROTEIN  Length:648
 aligned with Q5NF74_FRATT | Q5NF74 from UniProtKB/TrEMBL  Length:663

    Alignment length:660
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663
         Q5NF74_FRATT     4 SIPREFSNAIRFLSIDATLKAKSGHPGMPMGMADIATVLWTKFLKHNPNNPHWINRDRFVLSNGHGSMLLYSLLHLTGYDLSIEDIKNFRQLHSKTPGHPEYGYTPGVETTTGPLGQGVANAVGMALGEKLLSDRYNTPDLKVIDHHTYVFLGDGCLMEGVSHEACSLAGTLGLNKLVAFWDDNNISIDGDTKGWFSDNTPERFRAYGWHVIENVDGHDFVAIEKAINEAHSQQQKPTLICCKTVIGFGSPEKAGTASVHGSPLSDQERASAAKELNWDYQAFEIPQDVYKYWDAREKGQALEANWQGQWNLFKDSPKFDEFERVLSKELPVGLESAINDYIASQLSNPVKVATRKASQMVLEVLCKNMPEMFGGSADLTGSNNTNWSGSVWLNNTQEGANYLSYGVREFGMAAIMNGLSLYGGIKPYGGTFLVFSDYSRNAIRMSALMKQPVVHVMSHDSIGLGEDGPTHQPIEHVPSLRLIPNLSVWRPADTIETMIAWKEAVKSKDTPSVMVLTRQNLMPVVQTQHQVANIARGGYLVKDNPDAKLTIVATGSEVELAVKVANEFEKKGIKLNVASIPCVEVFATQAHEYKKTVIKDDIPAVFVEMAQPDMWYKYMPKAGGEVKGIYSFGESAPAEDLFKRFGFTVENISNIVAKYV 663
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3komB01 B:4-326  [code=3.40.50.970, no name defined]                                                                                                                                                                                                                                                                               3komB02 B:327-538  [code=3.40.50.970, no name defined]                                                                                                                                                              3komB03 B:539-663  [code=3.40.50.920, no name defined]                                                                        CATH domains
           Pfam domains (1) -Transketolase_N-3komB03 B:5-334                                                                                                                                                                                                                                                                                                           ------------------Transket_pyr-3komB01 B:353-526                                                                                                                                                --------------Transketolase_C-3komB05 B:541-655                                                                                  -------- Pfam domains (1)
           Pfam domains (2) -Transketolase_N-3komB04 B:5-334                                                                                                                                                                                                                                                                                                           ------------------Transket_pyr-3komB02 B:353-526                                                                                                                                                --------------Transketolase_C-3komB06 B:541-655                                                                                  -------- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..............eeee....hhhhhhhhhhhhh...hhhhhh............................hhhhhhhhhhhhhhhhhhhhhh..........eeeeehhhhhhhhhhhhhhhhhhhh....eeeeeeee.------.......hhhhhhhhh..eeeeeee..hhhhhhhhhhhhhh.....eeeeeee...........-----....hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh....hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh..eeeee....-....................eee...hhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhhh....eeeee..hhhhh.........hhhhhhhh....eee...hhhhhhhhhhhhhhh....eeee...........hhhhhhhhh...eeee.......eeee..hhhhhhhhhhhhhhhh....eeee..hhhhhhh.hhhhhhhhh.....eeee....hhhhhhhh....eeee.........hhhhhhhhhh.hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3kom B   4 SIPREFSNAIRFLSIDATLKAKSGHPGmPmGmADIATVLWTKFLKHNPNNPHWINRDRFVLSNGHGSmLLYSLLHLTGYDLSIEDIKNFRQLHSKTPGHPEYGYTPGVETTTGPLGQGVANAVGmALGEKLLSDRYNTPDLKVIDHHTYVFLGDGcLmEGVSHEACSLAGTLGLNKLVAFWDDNN------TKGWFSDNTPERFRAYGWHVIENVDGHDFVAIEKAINEAHSQQQKPTLICCKTVIGFGSPEKAG-----GSPLSDQERASAAKELNWDYQAFEIPQDVYKYWDAREKGQALEANWQGQRNLFKDSPKFDEFERVLSKELPVGLESAINDYIASQLSNPVKVATRKASQmVLEVLCKNmPEmFGGSADLT-SNNTNWSGSVWLNNTQEGANYLSYGVREFGmAAImNGLSLYGGIKPYGGTFLVFSDYSRNAIRmSALmKQPVVHVmSHDSIGLGEDGPTHQPIEHVPSLRLIPNLSVWRPADTIETmIAWKEAVKSKDTPSVmVLTRQNLmPVVQTQHQVANIARGGYLVKDNPDAKLTIVATGSEVELAVKVANEFEKKGIKLNVASIPCVEVFATQAHEYKKTVIKDDIPAVFVEmAQPDmWYKYmPKAGGEVKGIYSFGESAPAEDLFKRFGFTVENISNIVAKYV 663
                                    13        23       |33 |      43        53        63       |73        83        93       103       113       123    |  133       143       153     | 163       173       183    |    - |     203       213       223       233       243       253    |    -|      273       283       293       303       313       323       333       343       353       363       373 |     383 |     393       403       413 |   | 423       433       443    |  453      |463       473       483       493       503       513   |   523 |     533       543       553       563       573       583       593       603       613   |   623       633       643       653       663
                                                      31-MSE                                  71-MSE                                                  128-MSE                        159-OCS                      188    195                                                            258   264                                                                                                363-MSE  372-MSE    383 |                           415-MSE                          448-MSE     460-MSE                                  501-MSE         517-MSE 525-MSE                                                                                612-MSE|    |                                         
                                                        33-MSE                                                                                                                         161-MSE                                                                                                                                                                                                               375-MSE   385                               419-MSE                          452-MSE                                                                                                                                                              617-MSE|                                         
                                                          35-MSE                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    622-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 3KOM)

(-) CATH Domains  (2, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (3, 6)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q5NF74_FRATT | Q5NF74)
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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