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(-) Description

Title :  CRYSTAL STRUCTURE OF PHOSPHATE BOUND APO GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE 1 FROM MRSA252 AT 2.2 ANGSTROM RESOLUTION
 
Authors :  S. Mukherjee, D. Dutta, B. Saha, A. K. Das
Date :  23 Dec 09  (Deposition) - 18 Aug 10  (Release) - 11 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  O,P,Q,R
Keywords :  Glycolysis, Oxidoreductase, Nad (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Mukherjee, D. Dutta, B. Saha, A. K. Das
Crystal Structure Of Glyceraldehyde-3-Phosphate Dehydrogenase 1 From Methicillin-Resistant Staphylococcus Aureus Mrsa252 Provides Novel Insights Into Substrate Binding And Catalytic Mechanism.
J. Mol. Biol. V. 401 949 2010
PubMed-ID: 20620151  |  Reference-DOI: 10.1016/J.JMB.2010.07.002

(-) Compounds

Molecule 1 - GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE 1
    Chains: Q, P, R, O
    EC Number: 1.2.1.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE30
    Expression System Strain: M15
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: GAP, GAP1, GAPA, GAPA1, SAR0828
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 282458
    Strain: MRSA252
    Synonym: GAPDH 1

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : OPQR

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1PO44Ligand/IonPHOSPHATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER R:150 , CYS R:151 , THR R:152 , HIS R:178 , THR R:211 , GLY R:212BINDING SITE FOR RESIDUE PO4 R 337
2AC2SOFTWARESER P:150 , CYS P:151 , THR P:152 , HIS P:178 , THR P:211 , GLY P:212 , HOH P:369BINDING SITE FOR RESIDUE PO4 P 337
3AC3SOFTWARESER O:150 , CYS O:151 , THR O:152 , HIS O:178 , THR O:211 , GLY O:212 , HOH O:339BINDING SITE FOR RESIDUE PO4 O 337
4AC4SOFTWARESER Q:150 , CYS Q:151 , THR Q:152 , HIS Q:178 , THR Q:211 , GLY Q:212BINDING SITE FOR RESIDUE PO4 Q 337

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3L6O)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3L6O)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3L6O)

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GAPDHPS00071 Glyceraldehyde 3-phosphate dehydrogenase active site.G3P1_STAAR149-156
 
 
 		  4O:149-156
P:149-156
Q:149-156
R:149-156

(-) Exons   (0, 0)

(no "Exon" information available for 3L6O)

(-) 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:333
 aligned with G3P1_STAAR | Q6GIL8 from UniProtKB/Swiss-Prot  Length:336

    Alignment length:333
                                    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   
           G3P1_STAAR     1 MAVKVAINGFGRIGRLAFRRIQEVEGLEVVAVNDLTDDDMLAHLLKYDTMQGRFTGEVEVVDGGFRVNGKEVKSFSEPDASKLPWKDLNIDVVLECTGFYTDKDKAQAHIEAGAKKVLISAPATGDLKTIVFNTNHQELDGSETVVSGASCTTNSLAPVAKVLNDDFGLVEGLMTTIHAYTGDQNTQDAPHRKGDKRRARAAAENIIPNSTGAAKAIGKVIPEIDGKLDGGAQRVPVATGSLTELTVVLEKQDVTVEQVNEAMKNASNESFGYTEDEIVSSDVVGMTYGSLFDATQTRVMSVGDRQLVKVAAWYDNEMSYTAQLVRTLAYLAE 333
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhh..........eeee..eeee..eeeeee................eeee......hhhhhhhhhhhh..eeee...............hhhhh.....eee..hhhhhhhhhhhhhhhhhhheeeeeeeeeee.....................hhhhh.eee.hhhhhhh...hhhhh..eeeeeeee.....eeeeeeeee.....hhhhhhhhhhhh....eeee....hhhhhh.....eeee.hhheeeee..eeeeeeeeee..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------GAPDH   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l6o O   1 MAVKVAINGFGRIGRLAFRRIQEVEGLEVVAVNDLTDDDMLAHLLKYDTMQGRFTGEVEVVDGGFRVNGKEVKSFSEPDASKLPWKDLNIDVVLECTGFYTDKDKAQAHIEAGAKKVLISAPATGDLKTIVFNTNHQELDGSETVVSGASCTTNSLAPVAKVLNDDFGLVEGLMTTIHAYTGDQNTQDAPHRKGDKRRARAAAENIIPNSTGAAKAIGKVIPEIDGKLDGGAQRVPVATGSLTELTVVLEKQDVTVEQVNEAMKNASNESFGYTEDEIVSSDVVGMTYGSLFDATQTRVMSVGDRQLVKVAAWYDNEMSYTAQLVRTLAYLAE 333
                                    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   


Chain P from PDB  Type:PROTEIN  Length:334
 aligned with G3P1_STAAR | Q6GIL8 from UniProtKB/Swiss-Prot  Length:336

    Alignment length:334
                                    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    
           G3P1_STAAR     1 MAVKVAINGFGRIGRLAFRRIQEVEGLEVVAVNDLTDDDMLAHLLKYDTMQGRFTGEVEVVDGGFRVNGKEVKSFSEPDASKLPWKDLNIDVVLECTGFYTDKDKAQAHIEAGAKKVLISAPATGDLKTIVFNTNHQELDGSETVVSGASCTTNSLAPVAKVLNDDFGLVEGLMTTIHAYTGDQNTQDAPHRKGDKRRARAAAENIIPNSTGAAKAIGKVIPEIDGKLDGGAQRVPVATGSLTELTVVLEKQDVTVEQVNEAMKNASNESFGYTEDEIVSSDVVGMTYGSLFDATQTRVMSVGDRQLVKVAAWYDNEMSYTAQLVRTLAYLAEL 334
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhh....eeeeeee...hhhhhhhhhhh..........eeee..eeee..eeeeee...hhhhh........eeee......hhhhhhhhhhhh..eeee...............hhhhh.....eee..hhhhhhhhhhhhhhhhhh.eeeeeeeeeee.....................hhhhh.eee..hhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeee.....hhhhhhhhhhhh....eeee....hhhhhh.....eeee.hhheeeee..eeeeeeeeee..hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------GAPDH   ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l6o P   1 MAVKVAINGFGRIGRLAFRRIQEVEGLEVVAVNDLTDDDMLAHLLKYDTMQGRFTGEVEVVDGGFRVNGKEVKSFSEPDASKLPWKDLNIDVVLECTGFYTDKDKAQAHIEAGAKKVLISAPATGDLKTIVFNTNHQELDGSETVVSGASCTTNSLAPVAKVLNDDFGLVEGLMTTIHAYTGDQNTQDAPHRKGDKRRARAAAENIIPNSTGAAKAIGKVIPEIDGKLDGGAQRVPVATGSLTELTVVLEKQDVTVEQVNEAMKNASNESFGYTEDEIVSSDVVGMTYGSLFDATQTRVMSVGDRQLVKVAAWYDNEMSYTAQLVRTLAYLAEL 334
                                    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    


Chain Q from PDB  Type:PROTEIN  Length:334
 aligned with G3P1_STAAR | Q6GIL8 from UniProtKB/Swiss-Prot  Length:336

    Alignment length:334
                                    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    
           G3P1_STAAR     1 MAVKVAINGFGRIGRLAFRRIQEVEGLEVVAVNDLTDDDMLAHLLKYDTMQGRFTGEVEVVDGGFRVNGKEVKSFSEPDASKLPWKDLNIDVVLECTGFYTDKDKAQAHIEAGAKKVLISAPATGDLKTIVFNTNHQELDGSETVVSGASCTTNSLAPVAKVLNDDFGLVEGLMTTIHAYTGDQNTQDAPHRKGDKRRARAAAENIIPNSTGAAKAIGKVIPEIDGKLDGGAQRVPVATGSLTELTVVLEKQDVTVEQVNEAMKNASNESFGYTEDEIVSSDVVGMTYGSLFDATQTRVMSVGDRQLVKVAAWYDNEMSYTAQLVRTLAYLAEL 334
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhh....eeeeeee...hhhhhhhhhhh..........eee...eeee..eeeeee...hhhhh........eeee......hhhhhhhhhhhh..eeee...............hhhhh.....eee..hhhhhhhhhhhhhhhhhhheeeeeeeeeee...........................eee...........hhhhh..eeeeeeee.....eeeeeeeee.....hhhhhhhhhhhh....eeee....hhhhhh.....eeee.hhheeeee..eeeeeeeeee..hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------GAPDH   ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l6o Q   1 MAVKVAINGFGRIGRLAFRRIQEVEGLEVVAVNDLTDDDMLAHLLKYDTMQGRFTGEVEVVDGGFRVNGKEVKSFSEPDASKLPWKDLNIDVVLECTGFYTDKDKAQAHIEAGAKKVLISAPATGDLKTIVFNTNHQELDGSETVVSGASCTTNSLAPVAKVLNDDFGLVEGLMTTIHAYTGDQNTQDAPHRKGDKRRARAAAENIIPNSTGAAKAIGKVIPEIDGKLDGGAQRVPVATGSLTELTVVLEKQDVTVEQVNEAMKNASNESFGYTEDEIVSSDVVGMTYGSLFDATQTRVMSVGDRQLVKVAAWYDNEMSYTAQLVRTLAYLAEL 334
                                    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    


Chain R from PDB  Type:PROTEIN  Length:334
 aligned with G3P1_STAAR | Q6GIL8 from UniProtKB/Swiss-Prot  Length:336

    Alignment length:334
                                    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    
           G3P1_STAAR     1 MAVKVAINGFGRIGRLAFRRIQEVEGLEVVAVNDLTDDDMLAHLLKYDTMQGRFTGEVEVVDGGFRVNGKEVKSFSEPDASKLPWKDLNIDVVLECTGFYTDKDKAQAHIEAGAKKVLISAPATGDLKTIVFNTNHQELDGSETVVSGASCTTNSLAPVAKVLNDDFGLVEGLMTTIHAYTGDQNTQDAPHRKGDKRRARAAAENIIPNSTGAAKAIGKVIPEIDGKLDGGAQRVPVATGSLTELTVVLEKQDVTVEQVNEAMKNASNESFGYTEDEIVSSDVVGMTYGSLFDATQTRVMSVGDRQLVKVAAWYDNEMSYTAQLVRTLAYLAEL 334
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --Gp_dh_N-3l6oR05 R:3-151                                                                                                                              ----Gp_dh_C-3l6oR01 R:156-314                                                                                                                                      -------------------- Pfam domains (1)
           Pfam domains (2) --Gp_dh_N-3l6oR06 R:3-151                                                                                                                              ----Gp_dh_C-3l6oR02 R:156-314                                                                                                                                      -------------------- Pfam domains (2)
           Pfam domains (3) --Gp_dh_N-3l6oR07 R:3-151                                                                                                                              ----Gp_dh_C-3l6oR03 R:156-314                                                                                                                                      -------------------- Pfam domains (3)
           Pfam domains (4) --Gp_dh_N-3l6oR08 R:3-151                                                                                                                              ----Gp_dh_C-3l6oR04 R:156-314                                                                                                                                      -------------------- Pfam domains (4)
         Sec.struct. author ..eeeeee..hhhhhhhhhhh.....eeeeeee...hhhhhhhhhhh..........eeee..eeee..eeeeee...hhhhhhhhhhh..eeee......hhhhhhhhhhhh..eeee...............hhhhh.....eee..hhhhhhhhhhhhhhhhhhheeeeeeeeeee...........................eee..hhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeee.....hhhhhhhhhhhhh...eeee....hhhhhh.....eeee.hhheeeee..eeeeeeeeee..hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------GAPDH   ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l6o R   1 MAVKVAINGFGRIGRLAFRRIQEVEGLEVVAVNDLTDDDMLAHLLKYDTMQGRFTGEVEVVDGGFRVNGKEVKSFSEPDASKLPWKDLNIDVVLECTGFYTDKDKAQAHIEAGAKKVLISAPATGDLKTIVFNTNHQELDGSETVVSGASCTTNSLAPVAKVLNDDFGLVEGLMTTIHAYTGDQNTQDAPHRKGDKRRARAAAENIIPNSTGAAKAIGKVIPEIDGKLDGGAQRVPVATGSLTELTVVLEKQDVTVEQVNEAMKNASNESFGYTEDEIVSSDVVGMTYGSLFDATQTRVMSVGDRQLVKVAAWYDNEMSYTAQLVRTLAYLAEL 334
                                    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
   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 3L6O)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3L6O)

(-) Pfam Domains  (2, 8)

Asymmetric/Biological Unit
(-)
Clan: GADPH_aa-bio_dh (59)
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain O,P,Q,R   (G3P1_STAAR | Q6GIL8)
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:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        G3P1_STAAR | Q6GIL8: 3hq4 3k73 3k9q 3ksd 3ksz 3kv3 3l4s 3lc1 3lc2 3lc7 3lvf 3vaz 5t73

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3L6O)