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(-) Description

Title :  TRANSALDOLASE FROM THERMOPLASMA ACIDOPHILUM IN COMPLEX WITH D-FRUCTOSE 6-PHOSPHATE SCHIFF-BASE INTERMEDIATE
 
Authors :  A. Lehwess-Litzmann, P. Neumann, C. Parthier, K. Tittmann
Date :  16 May 11  (Deposition) - 24 Aug 11  (Release) - 05 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A,B,C,D,E  (2x)
Keywords :  Alpha-Beta Barrel, Conformational Selection, Domain Swapping, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Lehwess-Litzmann, P. Neumann, C. Parthier, S. Ludtke, R. Golbik, R. Ficner, K. Tittmann
Twisted Schiff Base Intermediates And Substrate Locale Revise Transaldolase Mechanism.
Nat. Chem. Biol. V. 7 678 2011
PubMed-ID: 21857661  |  Reference-DOI: 10.1038/NCHEMBIO.633

(-) Compounds

Molecule 1 - PROBABLE TRANSALDOLASE
    ChainsA, B, C, D, E
    EC Number2.2.1.2
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A(+)
    Expression System StrainBL21(DE3)STAR
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneTA0616, TAL
    Organism ScientificTHERMOPLASMA ACIDOPHILUM
    Organism Taxid273075
    StrainATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit ABCDE
Biological Unit 1 (2x)ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1F6R5Ligand/IonFRUCTOSE -6-PHOSPHATE
2GOL3Ligand/IonGLYCEROL
Biological Unit 1 (2, 16)
No.NameCountTypeFull Name
1F6R10Ligand/IonFRUCTOSE -6-PHOSPHATE
2GOL6Ligand/IonGLYCEROL

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:137 , ASN A:170 , ILE A:172 , HIS A:173 , ARG A:176 , HOH A:240 , ASN E:170 , ILE E:172 , HIS E:173 , ARG E:176 , HOH E:246BINDING SITE FOR RESIDUE GOL A 224
2AC2SOFTWAREASP B:137 , ASN B:170 , ILE B:172 , HIS B:173 , ARG B:176 , ASN D:170 , ILE D:172 , HIS D:173 , ARG D:176 , HOH D:253BINDING SITE FOR RESIDUE GOL B 224
3AC3SOFTWAREARG A:176 , VAL A:179 , ILE A:180 , HOH A:692BINDING SITE FOR RESIDUE GOL A 225
4AC4SOFTWAREASP C:6 , THR C:26 , THR C:27 , ASN C:28 , LYS C:86 , ASN C:108 , THR C:110 , SER C:130 , PHE C:132 , ARG C:135 , ALA C:166 , SER C:167 , HOH C:270 , HOH C:483 , HOH C:579 , HOH C:597BINDING SITE FOR RESIDUE F6R C 224
5AC5SOFTWAREASP A:6 , THR A:26 , THR A:27 , ASN A:28 , LYS A:86 , ASN A:108 , THR A:110 , SER A:130 , PHE A:132 , ARG A:135 , ALA A:166 , SER A:167 , ARG A:169 , HOH A:245 , HOH A:247BINDING SITE FOR RESIDUE F6R A 226
6AC6SOFTWAREASP B:6 , THR B:26 , THR B:27 , ASN B:28 , LYS B:86 , THR B:110 , SER B:130 , PHE B:132 , ARG B:135 , ALA B:166 , SER B:167 , ARG B:169 , HOH B:253 , HOH B:267 , HOH B:683BINDING SITE FOR RESIDUE F6R B 225
7AC7SOFTWAREASP D:6 , THR D:27 , ASN D:28 , LYS D:86 , ASN D:108 , THR D:110 , SER D:130 , PHE D:132 , ARG D:135 , ALA D:166 , SER D:167 , ARG D:169 , HOH D:258 , HOH D:264 , HOH D:277BINDING SITE FOR RESIDUE F6R D 224
8AC8SOFTWAREASP E:6 , THR E:27 , ASN E:28 , LYS E:86 , THR E:110 , SER E:130 , PHE E:132 , ARG E:135 , ALA E:166 , SER E:167 , ARG E:169 , HOH E:345 , HOH E:599 , HOH E:760BINDING SITE FOR RESIDUE F6R E 224

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3S1V)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3S1V)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3S1V)

(-) PROSITE Motifs  (2, 10)

Asymmetric Unit (2, 10)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRANSALDOLASE_1PS01054 Transaldolase signature 1.TAL_THEAC24-32
 
 
 
 
  5A:24-32
B:24-32
C:24-32
D:24-32
E:24-32
2TRANSALDOLASE_2PS00958 Transaldolase active site.TAL_THEAC83-100
 
 
 
 
  5A:83-100
B:83-100
C:83-100
D:83-100
E:83-100
Biological Unit 1 (2, 20)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRANSALDOLASE_1PS01054 Transaldolase signature 1.TAL_THEAC24-32
 
 
 
 
  10A:24-32
B:24-32
C:24-32
D:24-32
E:24-32
2TRANSALDOLASE_2PS00958 Transaldolase active site.TAL_THEAC83-100
 
 
 
 
  10A:83-100
B:83-100
C:83-100
D:83-100
E:83-100

(-) Exons   (0, 0)

(no "Exon" information available for 3S1V)

(-) 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:223
 aligned with TAL_THEAC | Q9HKI3 from UniProtKB/Swiss-Prot  Length:223

    Alignment length:223
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220   
            TAL_THEAC     1 MKIFLDTANIDEIRTGVNWGIVDGVTTNPTLISKEAVNGKKYGDIIREILKIVDGPVSVEVVSTKYEGMVEEARKIHGLGDNAVVKIPMTEDGLRAIKTLSSEHINTNCTLVFNPIQALLAAKAGATYVSPFVGRLDDIGEDGMQIIDMIRTIFNNYIIKTQILVASIRNPIHVLRSAVIGADVVTVPFNVLKSLMKHPKTDEGLAKFLEDWKKVSPDGKLIL 223
               SCOP domains d3s1va_ A: automated matches                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhh....eee.hhhhhhhhh....hhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhh...eeeehhhhhhhh...hhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhh..eeeehhhhhhhh..hhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------TRANSALDO--------------------------------------------------TRANSALDOLASE_2   --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s1v A   1 MKIFLDTANIDEIRTGVNWGIVDGVTTNPTLISKEAVNGKKYGDIIREILKIVDGPVSVEVVSTKYEGMVEEARKIHGLGDNAVVKIPMTEDGLRAIKTLSSEHINTNCTLVFNPIQALLAAKAGVTYVSPFVGRLDDIGEDGMQIIDMIRTIFNNYIIKTQILVASIRNPIHVLRSAVIGADVVTVPFNVLKSLMKHPKTDEGLAKFLEDWKKVSPDGKLIL 223
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220   

Chain B from PDB  Type:PROTEIN  Length:223
 aligned with TAL_THEAC | Q9HKI3 from UniProtKB/Swiss-Prot  Length:223

    Alignment length:223
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220   
            TAL_THEAC     1 MKIFLDTANIDEIRTGVNWGIVDGVTTNPTLISKEAVNGKKYGDIIREILKIVDGPVSVEVVSTKYEGMVEEARKIHGLGDNAVVKIPMTEDGLRAIKTLSSEHINTNCTLVFNPIQALLAAKAGATYVSPFVGRLDDIGEDGMQIIDMIRTIFNNYIIKTQILVASIRNPIHVLRSAVIGADVVTVPFNVLKSLMKHPKTDEGLAKFLEDWKKVSPDGKLIL 223
               SCOP domains d3s1vb_ B: automated matches                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhh....ee.hhhhhhhhh....hhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhh...eeeehhhhhhhh...hhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhh..eeeehhhhhhhh..hhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------TRANSALDO--------------------------------------------------TRANSALDOLASE_2   --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s1v B   1 MKIFLDTANIDEIRTGVNWGIVDGVTTNPTLISKEAVNGKKYGDIIREILKIVDGPVSVEVVSTKYEGMVEEARKIHGLGDNAVVKIPMTEDGLRAIKTLSSEHINTNCTLVFNPIQALLAAKAGVTYVSPFVGRLDDIGEDGMQIIDMIRTIFNNYIIKTQILVASIRNPIHVLRSAVIGADVVTVPFNVLKSLMKHPKTDEGLAKFLEDWKKVSPDGKLIL 223
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220   

Chain C from PDB  Type:PROTEIN  Length:223
 aligned with TAL_THEAC | Q9HKI3 from UniProtKB/Swiss-Prot  Length:223

    Alignment length:223
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220   
            TAL_THEAC     1 MKIFLDTANIDEIRTGVNWGIVDGVTTNPTLISKEAVNGKKYGDIIREILKIVDGPVSVEVVSTKYEGMVEEARKIHGLGDNAVVKIPMTEDGLRAIKTLSSEHINTNCTLVFNPIQALLAAKAGATYVSPFVGRLDDIGEDGMQIIDMIRTIFNNYIIKTQILVASIRNPIHVLRSAVIGADVVTVPFNVLKSLMKHPKTDEGLAKFLEDWKKVSPDGKLIL 223
               SCOP domains d3s1vc_ C: automated matches                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhh.....eee.hhhhhhhhh....hhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhh...eeeehhhhhhhh...hhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhh..eeeehhhhhhhhh.hhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------TRANSALDO--------------------------------------------------TRANSALDOLASE_2   --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s1v C   1 MKIFLDTANIDEIRTGVNWGIVDGVTTNPTLISKEAVNGKKYGDIIREILKIVDGPVSVEVVSTKYEGMVEEARKIHGLGDNAVVKIPMTEDGLRAIKTLSSEHINTNCTLVFNPIQALLAAKAGVTYVSPFVGRLDDIGEDGMQIIDMIRTIFNNYIIKTQILVASIRNPIHVLRSAVIGADVVTVPFNVLKSLMKHPKTDEGLAKFLEDWKKVSPDGKLIL 223
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220   

Chain D from PDB  Type:PROTEIN  Length:223
 aligned with TAL_THEAC | Q9HKI3 from UniProtKB/Swiss-Prot  Length:223

    Alignment length:223
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220   
            TAL_THEAC     1 MKIFLDTANIDEIRTGVNWGIVDGVTTNPTLISKEAVNGKKYGDIIREILKIVDGPVSVEVVSTKYEGMVEEARKIHGLGDNAVVKIPMTEDGLRAIKTLSSEHINTNCTLVFNPIQALLAAKAGATYVSPFVGRLDDIGEDGMQIIDMIRTIFNNYIIKTQILVASIRNPIHVLRSAVIGADVVTVPFNVLKSLMKHPKTDEGLAKFLEDWKKVSPDGKLIL 223
               SCOP domains d3s1vd_ D: automated matches                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhh.....ee.hhhhhhhhh....hhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhh...eeeehhhhhhhh..hhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhh..eeeehhhhhhhh..hhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------TRANSALDO--------------------------------------------------TRANSALDOLASE_2   --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s1v D   1 MKIFLDTANIDEIRTGVNWGIVDGVTTNPTLISKEAVNGKKYGDIIREILKIVDGPVSVEVVSTKYEGMVEEARKIHGLGDNAVVKIPMTEDGLRAIKTLSSEHINTNCTLVFNPIQALLAAKAGVTYVSPFVGRLDDIGEDGMQIIDMIRTIFNNYIIKTQILVASIRNPIHVLRSAVIGADVVTVPFNVLKSLMKHPKTDEGLAKFLEDWKKVSPDGKLIL 223
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220   

Chain E from PDB  Type:PROTEIN  Length:223
 aligned with TAL_THEAC | Q9HKI3 from UniProtKB/Swiss-Prot  Length:223

    Alignment length:223
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220   
            TAL_THEAC     1 MKIFLDTANIDEIRTGVNWGIVDGVTTNPTLISKEAVNGKKYGDIIREILKIVDGPVSVEVVSTKYEGMVEEARKIHGLGDNAVVKIPMTEDGLRAIKTLSSEHINTNCTLVFNPIQALLAAKAGATYVSPFVGRLDDIGEDGMQIIDMIRTIFNNYIIKTQILVASIRNPIHVLRSAVIGADVVTVPFNVLKSLMKHPKTDEGLAKFLEDWKKVSPDGKLIL 223
               SCOP domains d3s1ve_ E: automated matches                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhh.....ee.hhhhhhhhh....hhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhh...eeeehhhhhhhh...hhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhh..eeeehhhhhhhh..hhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------TRANSALDO--------------------------------------------------TRANSALDOLASE_2   --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s1v E   1 MKIFLDTANIDEIRTGVNWGIVDGVTTNPTLISKEAVNGKKYGDIIREILKIVDGPVSVEVVSTKYEGMVEEARKIHGLGDNAVVKIPMTEDGLRAIKTLSSEHINTNCTLVFNPIQALLAAKAGVTYVSPFVGRLDDIGEDGMQIIDMIRTIFNNYIIKTQILVASIRNPIHVLRSAVIGADVVTVPFNVLKSLMKHPKTDEGLAKFLEDWKKVSPDGKLIL 223
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220   

   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  (1, 5)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3S1V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3S1V)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E   (TAL_THEAC | Q9HKI3)
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:0004801    sedoheptulose-7-phosphate:D-glyceraldehyde-3-phosphate glyceronetransferase activity    Catalysis of the reaction: sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate = D-erythrose 4-phosphate + D-fructose 6-phosphate.
    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:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0006098    pentose-phosphate shunt    The glucose-6-phosphate catabolic process in which, coupled to NADPH synthesis, glucose-6-P is oxidized with the formation of carbon dioxide (CO2) and ribulose 5-phosphate; ribulose 5-P then enters a series of reactions interconverting sugar phosphates. The pentose phosphate pathway is a major source of reducing equivalents for biosynthesis reactions and is also important for the conversion of hexoses to pentoses.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TAL_THEAC | Q9HKI33s0c 3s1u 3s1w 3s1x 4xz9

(-) Related Entries Specified in the PDB File

3s0c TRANSALDOLASE FROM THERMOPLASMA ACIDOPHILUM IN THE RESTING STATE
3s1u TRANSALDOLASE FROM THERMOPLASMA ACIDOPHILUM IN COMPLEX WITH D-ERYTHROSE 4-PHOSPHATE
3s1w
3s1x