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(-) Description

Title :  DIHYDROXYACETONE PHOSPHATE SCHIFF BASE AND ENAMINE INTERMEDIATES IN D33N MUTANT FRUCTOSE-1,6-BISPHOSPHATE ALDOLASE FROM RABBIT MUSCLE
 
Authors :  M. St-Jean, J. Sygusch
Date :  12 Jun 08  (Deposition) - 28 Apr 09  (Release) - 04 Aug 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.94
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Aldolase, Mutant, Iminium, Schiff Base, Enamine, Intermediate, Covalent, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. St-Jean, C. Blonski, J. Sygusch
Charge Stabilization And Entropy Reduction Of Central Lysine Residues In Fructose-Bisphosphate Aldolase
Biochemistry V. 48 4528 2009
PubMed-ID: 19354220  |  Reference-DOI: 10.1021/BI8021558
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FRUCTOSE-BISPHOSPHATE ALDOLASE A
    Chains: A, B, C, D
    EC Number: 4.1.2.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PPB14
    Expression System Strain: BL-21 SI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ALDOA
    Mutation: YES
    Organism Common: RABBIT
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
    Synonym: MUSCLE-TYPE ALDOLASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
113P4Ligand/Ion1,3-DIHYDROXYACETONEPHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:31 , ASN A:33 , LYS A:146 , LYS A:229 , SER A:271 , GLY A:272 , SER A:300 , TYR A:301 , GLY A:302 , ARG A:303BINDING SITE FOR RESIDUE 13P A 3001
2AC2SOFTWAREALA B:31 , ASN B:33 , LYS B:146 , LYS B:229 , LEU B:270 , SER B:271 , GLY B:272 , SER B:300 , TYR B:301 , GLY B:302 , ARG B:303BINDING SITE FOR RESIDUE 13P B 3002
3AC3SOFTWAREALA C:31 , ASN C:33 , LYS C:146 , LYS C:229 , LEU C:270 , SER C:271 , GLY C:272 , SER C:300 , TYR C:301 , GLY C:302 , ARG C:303BINDING SITE FOR RESIDUE 13P C 3003
4AC4SOFTWAREASN D:33 , LYS D:146 , LYS D:229 , SER D:271 , GLY D:272 , SER D:300 , TYR D:301 , GLY D:302 , ARG D:303BINDING SITE FOR RESIDUE 13P D 3004

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Thr A:157 -Pro A:158
2Thr B:157 -Pro B:158
3Thr C:157 -Pro C:158
4Thr D:157 -Pro D:158

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ALDOLASE_CLASS_IPS00158 Fructose-bisphosphate aldolase class-I active site.ALDOA_RABIT222-232
 
 
 		  4A:221-231
B:221-231
C:221-231
D:221-231

(-) Exons   (0, 0)

(no "Exon" information available for 3DFO)

(-) 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:350
 aligned with ALDOA_RABIT | P00883 from UniProtKB/Swiss-Prot  Length:364

    Alignment length:363
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361   
          ALDOA_RABIT     2 PHSHPALTPEQKKELSDIAHRIVAPGKGILAADESTGSIAKRLQSIGTENTEENRRFYRQLLLTADDRVNPCIGGVILFHETLYQKADDGRPFPQVIKSKGGVVGIKVDKGVVPLAGTNGETTTQGLDGLSERCAQYKKDGADFAKWRCVLKIGEHTPSALAIMENANVLARYASICQQNGIVPIVEPEILPDGDHDLKRCQYVTEKVLAAVYKALSDHHIYLEGTLLKPNMVTPGHACTQKYSHEEIAMATVTALRRTVPPAVTGVTFLSGGQSEEEASINLNAINKCPLLKPWALTFSYGRALQASALKAWGGKKENLKAAQEEYVKRALANSLACQGKYTPSGQAGAAASESLFISNHAY 364
               SCOP domains d3dfoa_ A: Fructose-1,6-bisphosphate aldolase                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 3dfoA00 A:1-363 Aldolase class I                                                                                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhh....eeeee......hhhhhhhh....hhhhhhhhhhhhhh.hhhhh..eeeeeehhhhhh.......hhhhhhhhh..eeeee....eee.......eee....hhhhhhhhhhhh...eeeeeeee.......hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee......hhhhhhhhhhhhhhhhhhhhhhh..hhhh.ee...............hhhhhhhhhhhhhhh.......eeee.....hhhhhhhhhhhhhhh......eeeeeehhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.......-------------hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ALDOLASE_CL------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dfo A   1 PHSHPALTPEQKKELSDIAHRIVAPGKGILAANESTGSIAKRLQSIGTENTEENRRFYRQLLLTADDRVNPCIGGVILFHETLYQKADDGRPFPQVIKSKGGVVGIKVDKGVVPLAGTNGETTTQGLDGLSERCAQYKKDGADFAKWRCVLKIGEHTPSALAIMENANVLARYASICQQNGIVPIVEPEILPDGDHDLKRCQYVTEKVLAAVYKALSDHHIYLEGTLLKPNMVTPGHACTQKYSHEEIAMATVTALRRTVPPAVTGVTFLSGGQSEEEASINLNAINKCPLLKPWALTFSYGRALQASALKAWGGKKENLKAAQEEYVKRALANSLACQGKYTPS-------------SNHAY 363
                                    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    |    -       360   
                                                                                                                                                                                                                                                                                                                                                                                  345           359    


Chain B from PDB  Type:PROTEIN  Length:350
 aligned with ALDOA_RABIT | P00883 from UniProtKB/Swiss-Prot  Length:364

    Alignment length:363
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361   
          ALDOA_RABIT     2 PHSHPALTPEQKKELSDIAHRIVAPGKGILAADESTGSIAKRLQSIGTENTEENRRFYRQLLLTADDRVNPCIGGVILFHETLYQKADDGRPFPQVIKSKGGVVGIKVDKGVVPLAGTNGETTTQGLDGLSERCAQYKKDGADFAKWRCVLKIGEHTPSALAIMENANVLARYASICQQNGIVPIVEPEILPDGDHDLKRCQYVTEKVLAAVYKALSDHHIYLEGTLLKPNMVTPGHACTQKYSHEEIAMATVTALRRTVPPAVTGVTFLSGGQSEEEASINLNAINKCPLLKPWALTFSYGRALQASALKAWGGKKENLKAAQEEYVKRALANSLACQGKYTPSGQAGAAASESLFISNHAY 364
               SCOP domains d3dfob_ B: Fructose-1,6-bisphosphate aldolase                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 3dfoB00 B:1-363 Aldolase class I                                                                                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhh....hhhhhhhhhhhhhh.hhhhh..eeeeeehhhhhh.......hhhhhhhh...eeeee....eee.......eee....hhhhhhhhhhhh...eeeeeeee.......hhhhhhhhhhhhhhhhhhhhh...eeeeeeee......hhhhhhhhhhhhhhhhhhhhhhh..hhhh.ee...............hhhhhhhhhhhhhhh.......eeee.....hhhhhhhhhhhhhhh......eeeeeehhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.......-------------hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ALDOLASE_CL------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dfo B   1 PHSHPALTPEQKKELSDIAHRIVAPGKGILAANESTGSIAKRLQSIGTENTEENRRFYRQLLLTADDRVNPCIGGVILFHETLYQKADDGRPFPQVIKSKGGVVGIKVDKGVVPLAGTNGETTTQGLDGLSERCAQYKKDGADFAKWRCVLKIGEHTPSALAIMENANVLARYASICQQNGIVPIVEPEILPDGDHDLKRCQYVTEKVLAAVYKALSDHHIYLEGTLLKPNMVTPGHACTQKYSHEEIAMATVTALRRTVPPAVTGVTFLSGGQSEEEASINLNAINKCPLLKPWALTFSYGRALQASALKAWGGKKENLKAAQEEYVKRALANSLACQGKYTPS-------------SNHAY 363
                                    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    |    -       360   
                                                                                                                                                                                                                                                                                                                                                                                  345           359    


Chain C from PDB  Type:PROTEIN  Length:351
 aligned with ALDOA_RABIT | P00883 from UniProtKB/Swiss-Prot  Length:364

    Alignment length:363
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361   
          ALDOA_RABIT     2 PHSHPALTPEQKKELSDIAHRIVAPGKGILAADESTGSIAKRLQSIGTENTEENRRFYRQLLLTADDRVNPCIGGVILFHETLYQKADDGRPFPQVIKSKGGVVGIKVDKGVVPLAGTNGETTTQGLDGLSERCAQYKKDGADFAKWRCVLKIGEHTPSALAIMENANVLARYASICQQNGIVPIVEPEILPDGDHDLKRCQYVTEKVLAAVYKALSDHHIYLEGTLLKPNMVTPGHACTQKYSHEEIAMATVTALRRTVPPAVTGVTFLSGGQSEEEASINLNAINKCPLLKPWALTFSYGRALQASALKAWGGKKENLKAAQEEYVKRALANSLACQGKYTPSGQAGAAASESLFISNHAY 364
               SCOP domains d3dfoc_ C: Fructose-1,6-bisphosphate aldolase                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 3dfoC00 C:1-363 Aldolase class I                                                                                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhh....eeeee..hhhhhhhhhhh.....hhhhhhhhhhhhhh........eeeeeehhhhhh.......hhhhhhhhh..eeeee....eee.......eee....hhhhhhhhhhhh...eeeeeeee.......hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee......hhhhhhhhhhhhhhhhhhhhhhh..hhhh.ee...............hhhhhhhhhhhhhhh.......eeee.....hhhhhhhhhhhhhhh......eeeeeehhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh........------------hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ALDOLASE_CL------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dfo C   1 PHSHPALTPEQKKELSDIAHRIVAPGKGILAANESTGSIAKRLQSIGTENTEENRRFYRQLLLTADDRVNPCIGGVILFHETLYQKADDGRPFPQVIKSKGGVVGIKVDKGVVPLAGTNGETTTQGLDGLSERCAQYKKDGADFAKWRCVLKIGEHTPSALAIMENANVLARYASICQQNGIVPIVEPEILPDGDHDLKRCQYVTEKVLAAVYKALSDHHIYLEGTLLKPNMVTPGHACTQKYSHEEIAMATVTALRRTVPPAVTGVTFLSGGQSEEEASINLNAINKCPLLKPWALTFSYGRALQASALKAWGGKKENLKAAQEEYVKRALANSLACQGKYTPSG------------SNHAY 363
                                    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     |   -       360   
                                                                                                                                                                                                                                                                                                                                                                                   346          359    


Chain D from PDB  Type:PROTEIN  Length:360
 aligned with ALDOA_RABIT | P00883 from UniProtKB/Swiss-Prot  Length:364

    Alignment length:360
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361
          ALDOA_RABIT     2 PHSHPALTPEQKKELSDIAHRIVAPGKGILAADESTGSIAKRLQSIGTENTEENRRFYRQLLLTADDRVNPCIGGVILFHETLYQKADDGRPFPQVIKSKGGVVGIKVDKGVVPLAGTNGETTTQGLDGLSERCAQYKKDGADFAKWRCVLKIGEHTPSALAIMENANVLARYASICQQNGIVPIVEPEILPDGDHDLKRCQYVTEKVLAAVYKALSDHHIYLEGTLLKPNMVTPGHACTQKYSHEEIAMATVTALRRTVPPAVTGVTFLSGGQSEEEASINLNAINKCPLLKPWALTFSYGRALQASALKAWGGKKENLKAAQEEYVKRALANSLACQGKYTPSGQAGAAASESLFISN 361
               SCOP domains d3dfod_ D: Fructose-1,6-bisphosphate aldolase                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 3dfoD00 D:1-360 Aldolase class I                                                                                                                                                                                                                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhh....hhhhhhhhhhhhhh.hhhhh..eeeeeehhhhhh.......hhhhhhhhh..eeeee....eee.......eee....hhhhhhhhhhhh.eeeeeeeeee.......hhhhhhhhhhhhhhhhhhhhh...eeeeeeee......hhhhhhhhhhhhhhhhhhhhhhh..hhhh.ee...............hhhhhhhhhhhhhhh.......eeee.....hhhhhhhhhhhhhhh......eeeeeehhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..........hhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ALDOLASE_CL--------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3dfo D   1 PHSHPALTPEQKKELSDIAHRIVAPGKGILAANESTGSIAKRLQSIGTENTEENRRFYRQLLLTADDRVNPCIGGVILFHETLYQKADDGRPFPQVIKSKGGVVGIKVDKGVVPLAGTNGETTTQGLDGLSERCAQYKKDGADFAKWRCVLKIGEHTPSALAIMENANVLARYASICQQNGIVPIVEPEILPDGDHDLKRCQYVTEKVLAAVYKALSDHHIYLEGTLLKPNMVTPGHACTQKYSHEEIAMATVTALRRTVPPAVTGVTFLSGGQSEEEASINLNAINKCPLLKPWALTFSYGRALQASALKAWGGKKENLKAAQEEYVKRALANSLACQGKYTPSGQAGAAASESLFISN 360
                                    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
   Legend:   → Mismatch (orange background)
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  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 3DFO)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (ALDOA_RABIT | P00883)
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: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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    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.
    GO:0051289    protein homotetramerization    The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
cellular component
    GO:0031674    I band    A region of a sarcomere that appears as a light band on each side of the Z disc, comprising a region of the sarcomere where thin (actin) filaments are not overlapped by thick (myosin) filaments; contains actin, troponin, and tropomyosin; each sarcomere includes half of an I band at each end.
    GO:0031430    M band    The midline of aligned thick filaments in a sarcomere; location of specific proteins that link thick filaments. Depending on muscle type the M band consists of different numbers of M lines.
    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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  3dfo
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  ALDOA_RABIT | P00883
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 Related Entries

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

UniProtKB/Swiss-Prot
        ALDOA_RABIT | P00883: 1ado 1ewd 1ewe 1ex5 1j4e 1zah 1zai 1zaj 1zal 2ot0 2ot1 2qut 2quu 2quv 3b8d 3bv4 3dfn 3dfp 3dfq 3dfs 3dft 3lge 3tu9 5f4x 5vy5 6ald

(-) Related Entries Specified in the PDB File

3dfn 3dfp 3dfq 3dfs 3dft