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(-) Description

Title :  CRYSTAL STRUCTURE OF FRUCTOSE-1,6-BISPHOSPHATE ALDOLASE IN THERMUS CALDOPHILUS
 
Authors :  J. H. Lee, Y. J. Im, S. -H. Rho, M. -K. Kim, G. B. Kang, S. H. Eom
Date :  03 Jan 06  (Deposition) - 08 Aug 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Beta-Alpha-Barrels, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. H. Lee, J. Bae, D. Kim, Y. Choi, Y. J. Im, S. Koh, J. S. Kim, M. -K. Kim, G. B. Kang, S. -I. Hong, D. -S. Lee, S. H. Eom
Stereoselectivity Of Fructose-1, 6-Bisphosphate Aldolase In Thermus Caldophilus
Biochem. Biophys. Res. Commun. V. 347 616 2006
PubMed-ID: 16843441  |  Reference-DOI: 10.1016/J.BBRC.2006.06.139
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FRUCTOSE-BISPHOSPHATE ALDOLASE
    Chains: A, B, C, D
    EC Number: 4.1.2.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PKK223-3
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS CALDOPHILUS
    Organism Taxid: 272
    Synonym: FRUCTOSE-1,6-BISPHOSPHATE ALDOLASE, FBA

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 36)

Asymmetric/Biological Unit (2, 36)
No.NameCountTypeFull Name
113P4Ligand/Ion1,3-DIHYDROXYACETONEPHOSPHATE
2MSE32Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:80 , HIS A:81 , HIS A:178 , GLY A:179 , LYS A:182 , HIS A:208 , GLY A:209 , ALA A:210 , SER A:211 , ASN A:251 , ASP A:253 , THR A:254BINDING SITE FOR RESIDUE 13P A 1063
2AC2SOFTWAREASN B:23 , ASP B:80 , HIS B:81 , HIS B:178 , GLY B:179 , LYS B:182 , HIS B:208 , GLY B:209 , ALA B:210 , SER B:211 , ASN B:251 , ASP B:253 , THR B:254 , HOH B:1086BINDING SITE FOR RESIDUE 13P B 1073
3AC3SOFTWAREASP C:80 , HIS C:81 , HIS C:178 , GLY C:179 , LYS C:182 , HIS C:208 , GLY C:209 , ALA C:210 , SER C:211 , ASN C:251 , ASP C:253 , THR C:254 , HOH C:1130BINDING SITE FOR RESIDUE 13P C 1083
4AC4SOFTWAREASP D:80 , HIS D:81 , HIS D:178 , LYS D:182 , HIS D:208 , GLY D:209 , ALA D:210 , SER D:211 , ASN D:251 , THR D:252 , ASP D:253 , THR D:254BINDING SITE FOR RESIDUE 13P D 1093

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2FJK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2FJK)

(-) 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:305
 aligned with ALF_THECA | Q703I2 from UniProtKB/Swiss-Prot  Length:305

    Alignment length:305
                                    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     
            ALF_THECA     1 MLVTGLEILRKARAEGYGVGAFNTNNMEFTQAILEAAEEMKSPVILALSEGAMKYGGRALTRMVVALAQEARVPVAVHLDHGSSYESVLKALREGFTSVMIDKSHEDFETNVRETKRVVEAAHAVGVTVEAELGRLAGIEEHVAVDEKDALLTNPEEARIFMERTGADYLAVAIGTSHGAYKGKGRPFIDHPRLARIAKLVPAPLVLHGASAVPQELVERFRAAGGEIGEASGIHPEDIKKAISLGIAKINTDTDLRLAFTALVRETLGKNPKEFDPRKYLGPAREAVKEVVKSRMELFGSVGRA 305
               SCOP domains d2fjka_ A: automated matches                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains -2fjkA00 A:2-305 Aldolase class I                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.hhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhh.eeee.hhhhhhhhhhhhhhhhhhhhh.....eeee.....hhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhh..eeeeee....................hhhhhhhhhhhh.....ee.................hhhhhhhhhhhh...eee......hhhhhhhhhhh..........hhhhhhhhhhh.eeeeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fjk A   1 mLVTGLEILRKARAEGYGVGAFNTNNmEFTQAILEAAEEmKSPVILALSEGAmKYGGRALTRmVVALAQEARVPVAVHLDHGSSYESVLKALREGFTSVmIDKSHEDFETNVRETKRVVEAAHAVGVTVEAELGRLAGIEEHVAVDEKDALLTNPEEARIFmERTGADYLAVAIGTSHGAYKGKGRPFIDHPRLARIAKLVPAPLVLHGASAVPQELVERFRAAGGEIGEASGIHPEDIKKAISLGIAKINTDTDLRLAFTALVRETLGKNPKEFDPRKYLGPAREAVKEVVKSRmELFGSVGRA 305
                            |       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     
                            |                        27-MSE       40-MSE       53-MSE    63-MSE                              100-MSE                                                       162-MSE                                                                                                                               296-MSE     
                            1-MSE                                                                                                                                                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:298
 aligned with ALF_THECA | Q703I2 from UniProtKB/Swiss-Prot  Length:305

    Alignment length:305
                                    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     
            ALF_THECA     1 MLVTGLEILRKARAEGYGVGAFNTNNMEFTQAILEAAEEMKSPVILALSEGAMKYGGRALTRMVVALAQEARVPVAVHLDHGSSYESVLKALREGFTSVMIDKSHEDFETNVRETKRVVEAAHAVGVTVEAELGRLAGIEEHVAVDEKDALLTNPEEARIFMERTGADYLAVAIGTSHGAYKGKGRPFIDHPRLARIAKLVPAPLVLHGASAVPQELVERFRAAGGEIGEASGIHPEDIKKAISLGIAKINTDTDLRLAFTALVRETLGKNPKEFDPRKYLGPAREAVKEVVKSRMELFGSVGRA 305
               SCOP domains d2fjkb_ B: automated matches                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains -2fjkB00 B:2-305 Aldolase class I                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhh...ee.......hhhhhhhhhhhhhhhhhhh..eeeeee......-------.......hhhhhhhhhhhh...eeee.................hhhhhhhhhhhh...eee......hhhhhhhhhhh..........hhhhhhhhhhh.eeeeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fjk B   1 mLVTGLEILRKARAEGYGVGAFNTNNmEFTQAILEAAEEmKSPVILALSEGAmKYGGRALTRmVVALAQEARVPVAVHLDHGSSYESVLKALREGFTSVmIDKSHEDFETNVRETKRVVEAAHAVGVTVEAELGRLAGI-------EKDALLTNPEEARIFmERTGADYLAVAIGTSHGAYKGKGRPFIDHPRLARIAKLVPAPLVLHGASAVPQELVERFRAAGGEIGEASGIHPEDIKKAISLGIAKINTDTDLRLAFTALVRETLGKNPKEFDPRKYLGPAREAVKEVVKSRmELFGSVGRA 305
                            |       10        20      | 30        40        50  |     60  |     70        80        90       100       110       120       130        |-      |150       160 |     170       180       190       200       210       220       230       240       250       260       270       280       290     | 300     
                            1-MSE                    27-MSE       40-MSE       53-MSE    63-MSE                              100-MSE                                139     147            162-MSE                                                                                                                               296-MSE     


Chain C from PDB  Type:PROTEIN  Length:299
 aligned with ALF_THECA | Q703I2 from UniProtKB/Swiss-Prot  Length:305

    Alignment length:305
                                    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     
            ALF_THECA     1 MLVTGLEILRKARAEGYGVGAFNTNNMEFTQAILEAAEEMKSPVILALSEGAMKYGGRALTRMVVALAQEARVPVAVHLDHGSSYESVLKALREGFTSVMIDKSHEDFETNVRETKRVVEAAHAVGVTVEAELGRLAGIEEHVAVDEKDALLTNPEEARIFMERTGADYLAVAIGTSHGAYKGKGRPFIDHPRLARIAKLVPAPLVLHGASAVPQELVERFRAAGGEIGEASGIHPEDIKKAISLGIAKINTDTDLRLAFTALVRETLGKNPKEFDPRKYLGPAREAVKEVVKSRMELFGSVGRA 305
               SCOP domains d2fjkc_ C: automated matches                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains -2fjkC00 C:2-305 Aldolase class I                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhh...eee......hhhhhhhhhhhhhhhhhhh..eeeee........------.......hhhhhhhhhhhh...eee..................hhhhhhhhhhhh...eee......hhhhhhhhhh...........hhhhhhhhhhh.eeeeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fjk C   1 mLVTGLEILRKARAEGYGVGAFNTNNmEFTQAILEAAEEmKSPVILALSEGAmKYGGRALTRmVVALAQEARVPVAVHLDHGSSYESVLKALREGFTSVmIDKSHEDFETNVRETKRVVEAAHAVGVTVEAELGRLAGIE------EKDALLTNPEEARIFmERTGADYLAVAIGTSHGAYKGKGRPFIDHPRLARIAKLVPAPLVLHGASAVPQELVERFRAAGGEIGEASGIHPEDIKKAISLGIAKINTDTDLRLAFTALVRETLGKNPKEFDPRKYLGPAREAVKEVVKSRmELFGSVGRA 305
                            |       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     
                            1-MSE                    27-MSE       40-MSE       53-MSE    63-MSE                              100-MSE                                 140    147            162-MSE                                                                                                                               296-MSE     


Chain D from PDB  Type:PROTEIN  Length:290
 aligned with ALF_THECA | Q703I2 from UniProtKB/Swiss-Prot  Length:305

    Alignment length:305
                                    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     
            ALF_THECA     1 MLVTGLEILRKARAEGYGVGAFNTNNMEFTQAILEAAEEMKSPVILALSEGAMKYGGRALTRMVVALAQEARVPVAVHLDHGSSYESVLKALREGFTSVMIDKSHEDFETNVRETKRVVEAAHAVGVTVEAELGRLAGIEEHVAVDEKDALLTNPEEARIFMERTGADYLAVAIGTSHGAYKGKGRPFIDHPRLARIAKLVPAPLVLHGASAVPQELVERFRAAGGEIGEASGIHPEDIKKAISLGIAKINTDTDLRLAFTALVRETLGKNPKEFDPRKYLGPAREAVKEVVKSRMELFGSVGRA 305
               SCOP domains d2fjkd_ D: automated matches                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains -2fjkD00 D:2-305 Aldolase class I                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhh...eeeeee...---------------..hhhhhhhhhhhh...eeee.................hhhhhhhhhhhh...eee......hhhhhhhhhhh..........hhhhhhhhhhh.eeeeeehhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fjk D   1 mLVTGLEILRKARAEGYGVGAFNTNNmEFTQAILEAAEEmKSPVILALSEGAmKYGGRALTRmVVALAQEARVPVAVHLDHGSSYESVLKALREGFTSVmIDKSHEDFETNVRETKRVVEAAHAVGVTVEAELGRL---------------LTNPEEARIFmERTGADYLAVAIGTSHGAYKGKGRPFIDHPRLARIAKLVPAPLVLHGASAVPQELVERFRAAGGEIGEASGIHPEDIKKAISLGIAKINTDTDLRLAFTALVRETLGKNPKEFDPRKYLGPAREAVKEVVKSRmELFGSVGRA 305
                            |       10        20      | 30        40        50  |     60  |     70        80        90       100       110       120       130     |   -         - |     160 |     170       180       190       200       210       220       230       240       250       260       270       280       290     | 300     
                            1-MSE                    27-MSE       40-MSE       53-MSE    63-MSE                              100-MSE                             136             152       162-MSE                                                                                                                               296-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  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (ALF_THECA | Q703I2)
molecular function
    GO:0016832    aldehyde-lyase activity    Catalysis of the cleavage of a C-C bond in a molecule containing a hydroxyl group and a carbonyl group to form two smaller molecules, each being an aldehyde or a ketone.
    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:0004332    fructose-bisphosphate aldolase activity    Catalysis of the reaction: D-fructose 1,6-bisphosphate = glycerone phosphate + D-glyceraldehyde-3-phosphate.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
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:0030388    fructose 1,6-bisphosphate metabolic process    The chemical reactions and pathways involving fructose 1,6-bisphosphate, also known as FBP. The D enantiomer is a metabolic intermediate in glycolysis and gluconeogenesis.
    GO:0006096    glycolytic process    The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.

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