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(-) Description

Title :  CRYSTAL STRUCTURE OF GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE ISOFORM 1 FROM K. MARXIANUS
 
Authors :  F. Ferreira-Da-Silva, P. J. B. Pereira, L. Gales, P. Moradas- Ferreira, A. M. Damas
Date :  25 Aug 06  (Deposition) - 12 Sep 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  O,P
Keywords :  Rossmann Fold, Apo Form, Dimer, Gapdh, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Ferreira-Da-Silva, P. J. Pereira, L. Gales, M. Roessle, D. I. Svergun, P. Moradas-Ferreira, A. M. Damas
The Crystal And Solution Structures Of Glyceraldehyde-3-Phosphate Dehydrogenase Reveal Different Quaternary Structures.
J. Biol. Chem. V. 281 33433 2006
PubMed-ID: 16963457  |  Reference-DOI: 10.1074/JBC.M605267200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE 1
    Chains: O, P
    EC Number: 1.2.1.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE32
    Expression System Strain: M15
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: GAP1
    Organism Scientific: KLUYVEROMYCES MARXIANUS
    Organism Taxid: 4911
    Strain: ATCC10022
    Synonym: GAPDH 1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : OP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1BME2Ligand/IonBETA-MERCAPTOETHANOL
2GLC2Ligand/IonALPHA-D-GLUCOSE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP O:38 , TYR O:42 , VAL O:57 , SER O:58 , TYR P:539BINDING SITE FOR RESIDUE GLC O 1952
2AC2SOFTWAREASP P:538 , ALA P:541 , TYR P:542 , VAL P:557 , SER P:558BINDING SITE FOR RESIDUE GLC P 1953
3AC3SOFTWARETHR O:208BINDING SITE FOR RESIDUE BME O 1023
4AC4SOFTWARETHR P:708BINDING SITE FOR RESIDUE BME P 1024

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2I5P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2I5P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2I5P)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GAPDHPS00071 Glyceraldehyde 3-phosphate dehydrogenase active site.G3P1_KLULA147-154  1O:147-154
G3P1_KLUMA147-154
 		  2O:147-154
P:647-654

(-) Exons   (0, 0)

(no "Exon" information available for 2I5P)

(-) 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 O from PDB  Type:PROTEIN  Length:309
 aligned with G3P1_KLULA | P17819 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:329
                                    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         
          G3P1_KLULA      1 MVKVAINGFGRIGRLVLRIALQRKALEVVAVNDPFISVDYAAYMFKYDSTHGRYKGEVTTSGNDLVIDGHKIAVFQEKDPANLPWGKLGVDIVIDSTGVFKELDSAQKHLDAGAKKVVITAPSKTAPMFVVGVNEDKYNGETIVSNASCTTNCLAPIAKIINDEFGIDEALMTTVHSITATQKTVDGPSHKDWRGGRTASGNIIPSSTGAAKAVGKVLPELQGKLTGMAFRVPTVDVSVVDLTVKLAKEATYDEIKAAVKKASQGKLKNVVGYTEDSVVSSDFLGDTHSTIFDASAGIQLSPKFVKVVAWYDNEYGYSERVVDLVEHVA  329
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2i5pO01 O:0-148,O:314-329 NAD(P)-binding Rossmann-like Domain                                                                                       2i5pO02 O:149-313 Dihydrodipico                    linate Reductase; domain 2                                                                                        2i5pO01          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhhhhhhhhh....eeeeeee....hhhhhhhhhhee...ee....eee...eeee..eeeeee...hhhhh........eeee......hhhhhhhhhhh...eeee..............hhhhh....eee..hhhhhhhhhhhhhhhhhh.eeeeeeeeee...--------------------....eeee.....hhhhhhhhhh..eeeeeee.....eeeeeeeeee....hhhhhhhhhhhhhhh.....eeee....hhhhhh.....eeee....eeee..eeeeeeeee.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------GAPDH   ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2i5p O    0 MVSIAINGFGRIGRLVLRIALERKNIDVVAINDPFISVDYAAYMFKYDSTHGKYKGEVSHDGSNLIINGKKVAVFQEKDPATLPWGKLGVDIAVDSTGVFKELDSAQKHIDAGAKKVVITAPSKTAPMFVVGVNEDKYNGEKIVSNASCTTNCLAPIAKIINDEFGIEEGLMTTVHSIT--------------------SGNIIPSSTGAAKAVGKVLPELQGKLTGMAFRVPTTDVSVVDLTVKLVKAATYDEIKAAVKKVSEGKLKDVVGYTEDAVVSSDFLGDTHSTIFDAAAGIQLSPKFVKLVAWYDNEYGYSTRVVDLVEHVA  329
                                     9        19        29   | || 39        49        59        69        79        89        99       109       119   ||  129      138A|      150       160       170        |-         -       200       210       220       230       240       250       260       270       280       290       300       310       320         
                                                           32A ||                                                                                   122A|           138A|                                   179                  200                                                                                                                                 
                                                              34|                                                                                     124             141                                                                                                                                                                                            
                                                               36                                                                                                                                                                                                                                                                                                    


Chain O from PDB  Type:PROTEIN  Length:309
 aligned with G3P1_KLUMA | P84998 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:329
                                    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         
          G3P1_KLUMA      1 MVSIAINGFGRIGRLVLRIALERKNIDVVAINDPFISVDYAAYMFKYDSTHGKYKGEVSHDGSNLIINGKKVAVFQEKDPATLPWGKLGVDIAVDSTGVFKELDSAQKHIDAGAKKVVITAPSKTAPMFVVGVNEDKYNGEKIVSNASCTTNCLAPIAKIINDEFGIEEGLMTTVHSITATQKTVDGPSHKDWRGGRTASGNIIPSSTGAAKAVGKVLPELQGKLTGMAFRVPTTDVSVVDLTVKLVKAATYDEIKAAVKKVSEGKLKDVVGYTEDAVVSSDFLGDTHSTIFDAAAGIQLSPKFVKLVAWYDNEYGYSTRVVDLVEHVA  329
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2i5pO01 O:0-148,O:314-329 NAD(P)-binding Rossmann-like Domain                                                                                       2i5pO02 O:149-313 Dihydrodipico                    linate Reductase; domain 2                                                                                        2i5pO01          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhhhhhhhhh....eeeeeee....hhhhhhhhhhee...ee....eee...eeee..eeeeee...hhhhh........eeee......hhhhhhhhhhh...eeee..............hhhhh....eee..hhhhhhhhhhhhhhhhhh.eeeeeeeeee...--------------------....eeee.....hhhhhhhhhh..eeeeeee.....eeeeeeeeee....hhhhhhhhhhhhhhh.....eeee....hhhhhh.....eeee....eeee..eeeeeeeee.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------GAPDH   ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2i5p O    0 MVSIAINGFGRIGRLVLRIALERKNIDVVAINDPFISVDYAAYMFKYDSTHGKYKGEVSHDGSNLIINGKKVAVFQEKDPATLPWGKLGVDIAVDSTGVFKELDSAQKHIDAGAKKVVITAPSKTAPMFVVGVNEDKYNGEKIVSNASCTTNCLAPIAKIINDEFGIEEGLMTTVHSIT--------------------SGNIIPSSTGAAKAVGKVLPELQGKLTGMAFRVPTTDVSVVDLTVKLVKAATYDEIKAAVKKVSEGKLKDVVGYTEDAVVSSDFLGDTHSTIFDAAAGIQLSPKFVKLVAWYDNEYGYSTRVVDLVEHVA  329
                                     9        19        29   | || 39        49        59        69        79        89        99       109       119   ||  129      138A|      150       160       170        |-         -       200       210       220       230       240       250       260       270       280       290       300       310       320         
                                                           32A ||                                                                                   122A|           138A|                                   179                  200                                                                                                                                 
                                                              34|                                                                                     124             141                                                                                                                                                                                            
                                                               36                                                                                                                                                                                                                                                                                                    


Chain P from PDB  Type:PROTEIN  Length:309
 aligned with G3P1_KLUMA | P84998 from UniProtKB/Swiss-Prot  Length:329

    Alignment length:329
                                    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         
          G3P1_KLUMA      1 MVSIAINGFGRIGRLVLRIALERKNIDVVAINDPFISVDYAAYMFKYDSTHGKYKGEVSHDGSNLIINGKKVAVFQEKDPATLPWGKLGVDIAVDSTGVFKELDSAQKHIDAGAKKVVITAPSKTAPMFVVGVNEDKYNGEKIVSNASCTTNCLAPIAKIINDEFGIEEGLMTTVHSITATQKTVDGPSHKDWRGGRTASGNIIPSSTGAAKAVGKVLPELQGKLTGMAFRVPTTDVSVVDLTVKLVKAATYDEIKAAVKKVSEGKLKDVVGYTEDAVVSSDFLGDTHSTIFDAAAGIQLSPKFVKLVAWYDNEYGYSTRVVDLVEHVA  329
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2i5pP01 P:500-648,P:814-829 NAD(P)-binding Rossmann-like Domain                                                                                     2i5pP02 P:649-813 Dihydrodipico                    linate Reductase; domain 2                                                                                        2i5pP01          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhhhhhhhhh....eeeeeee....hhhhhhhhhhee...ee....eee...eeee..eeeeee...hhhhhhhhhhh..eeee......hhhhhhhhhhh...eeee..............hhhhh....eee..hhhhhhhhhhhhhhhhhh.eeeeeeeeee...--------------------....eeee.hhhhhhhhhhhhhh..eeeeeee.....eeeeeeeeee....hhhhhhhhhhhhhhhhhhh.eeee....hhhhhh.....eeeeeeeeeeee..eeeeeeeee.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------GAPDH   ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2i5p P  500 MVSIAINGFGRIGRLVLRIALERKNIDVVAINDPFISVDYAAYMFKYDSTHGKYKGEVSHDGSNLIINGKKVAVFQEKDPATLPWGKLGVDIAVDSTGVFKELDSAQKHIDAGAKKVVITAPSKTAPMFVVGVNEDKYNGEKIVSNASCTTNCLAPIAKIINDEFGIEEGLMTTVHSIT--------------------SGNIIPSSTGAAKAVGKVLPELQGKLTGMAFRVPTTDVSVVDLTVKLVKAATYDEIKAAVKKVSEGKLKDVVGYTEDAVVSSDFLGDTHSTIFDAAAGIQLSPKFVKLVAWYDNEYGYSTRVVDLVEHVA  829
                                   509       519       529   | ||539       549       559       569       579       589       599       609       619   ||  629      638A|      650       660       670        |-         -       700       710       720       730       740       750       760       770       780       790       800       810       820         
                                                          532A ||                                                                                   622A|           638A|                                   679                  700                                                                                                                                 
                                                             534|                                                                                     624             641                                                                                                                                                                                            
                                                              536
   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 2I5P)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2I5P)

(-) Gene Ontology  (9, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain O   (G3P1_KLULA | P17819)
molecular function
    GO:0051287    NAD binding    Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
    GO:0050661    NADP binding    Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
    GO:0004365    glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity    Catalysis of the reaction: D-glyceraldehyde 3-phosphate + phosphate + NAD+ = 3-phospho-D-glyceroyl phosphate + NADH + H+.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016620    oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP.
biological process
    GO:0006006    glucose metabolic process    The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides.
    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:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain O,P   (G3P1_KLUMA | P84998)
molecular function
    GO:0051287    NAD binding    Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
    GO:0050661    NADP binding    Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
    GO:0004365    glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity    Catalysis of the reaction: D-glyceraldehyde 3-phosphate + phosphate + NAD+ = 3-phospho-D-glyceroyl phosphate + NADH + H+.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016620    oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP.
biological process
    GO:0006006    glucose metabolic process    The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides.
    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:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
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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