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(-) Description

Title :  STUDIES OF ASYMMETRY IN THE THREE-DIMENSIONAL STRUCTURE OF LOBSTER D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
 
Authors :  D. Moras, K. W. Olsen, M. N. Sabesan, M. Buehner, G. C. Ford, M. G. Rossman
Date :  01 Jul 75  (Deposition) - 17 Feb 77  (Release) - 29 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  G,R
Keywords :  Oxido-Reductase(Aldehyde/Donr, Nad/Accpt), Oxido-Reductase(Aldehyde- Donr, Nad-Accpt) Complex, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Moras, K. W. Olsen, M. N. Sabesan, M. Buehner, G. C. Ford, M. G. Rossmann
Studies Of Asymmetry In The Three-Dimensional Structure Of Lobster D-Glyceraldehyde-3-Phosphate Dehydrogenase.
J. Biol. Chem. V. 250 9137 1975
PubMed-ID: 127793
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
    Chains: G, R
    EC Number: 1.2.1.12
    Engineered: YES
    Organism Common: AMERICAN LOBSTER
    Organism Scientific: HOMARUS AMERICANUS
    Organism Taxid: 6706

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : GR

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1ACE2Mod. Amino AcidACETYL GROUP
2NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
3PO44Ligand/IonPHOSPHATE ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01ABGAUTHORASN G:6 , ASN G:31 , ASP G:32 , PHE G:34 , THR G:96 , PHE G:99RESIDUES INTERACTING WITH THE ADENINE BASE OF THE COFACTOR
02ABRAUTHORASN R:6 , ASN R:31 , ASP R:32 , PHE R:34 , THR R:96 , PHE R:99RESIDUES INTERACTING WITH THE ADENINE BASE OF THE COFACTOR
03AC3SOFTWAREGLY G:7 , PHE G:8 , GLY G:9 , ARG G:10 , ILE G:11 , ASP G:32 , PHE G:34 , ILE G:35 , PHE G:99 , SER G:119 , GLU G:314BINDING SITE FOR RESIDUE NAD G 335
04AC4SOFTWAREPHE R:8 , ARG R:10 , ASP R:32 , THR R:96 , PHE R:99 , SER R:119 , ALA R:120 , CYS R:149 , ASN R:313 , TYR R:317BINDING SITE FOR RESIDUE NAD R 339
05AC7SOFTWARETHR R:179BINDING SITE FOR RESIDUE PO4 R 337
06AC8SOFTWARETHR R:150 , THR R:208 , GLY R:209BINDING SITE FOR RESIDUE PO4 R 338
07APGAUTHORARG G:10 , ALA G:180RESIDUES INTERACTING WITH THE PHOSPHATE OF THE ADENOSINE NUCLEOTIDE OF THE NAD COFACTOR
08APRAUTHORARG R:10 , ALA R:180RESIDUES INTERACTING WITH THE PHOSPHATE OF THE ADENOSINE NUCLEOTIDE OF THE NAD COFACTOR
09ARGAUTHORGLY G:7 , ASP G:32 , PRO R:188RESIDUES INTERACTING WITH THE ADENOSINE RIBOSE OF THE NAD COFACTOR
10ARRAUTHORGLY R:7 , PHE R:8 , ASP R:32 , PRO G:188RESIDUES INTERACTING WITH THE ADENOSINE RIBOSE OF THE NAD COFACTOR
11NBGAUTHORILE G:11 , CYS G:149 , ASN G:313 , TYR G:317RESIDUES INTERACTING WITH THE NICOTINAMIDE BASE OF THE NAD COFACTOR
12NBRAUTHORILE R:11 , CYS R:149 , ASN R:313 , TYR R:317RESIDUES INTERACTING WITH THE NICOTINAMIDE BASE OF THE NAD COFACTOR
13NPGAUTHORILE G:11RESIDUES INTERACTING WITH THE PHOSPHATE OF THE NICOTINAMIDE NUCLEOTIDE OF THE NAD COFACTOR
14NPRAUTHORILE R:11RESIDUES INTERACTING WITH THE PHOSPHATE OF THE NICOTINAMIDE NUCLEOTIDE OF THE NAD COFACTOR
15NRGAUTHORTHR G:96 , GLY G:97 , SER G:119 , ALA G:120RESIDUES INTERACTING WITH THE RIBOSE OF THE NICOTINAMIDE NUCLEOTIDE OF THE NAD COFACTOR
16NRRAUTHORTHR R:96 , GLY R:97 , SER R:119 , ALA R:120RESIDUES INTERACTING WITH THE RIBOSE OF THE NICOTINAMIDE NUCLEOTIDE OF THE NAD COFACTOR

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1GPD)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1GPD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1GPD)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GAPDHPS00071 Glyceraldehyde 3-phosphate dehydrogenase active site.G3P_HOMAM146-153
 		  2G:147-154
R:147-154

(-) Exons   (0, 0)

(no "Exon" information available for 1GPD)

(-) 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 G from PDB  Type:PROTEIN  Length:334
 aligned with G3P_HOMAM | P00357 from UniProtKB/Swiss-Prot  Length:333

    Alignment length:334
                             1                                                                                                                                                                                                                                                                                                                                            
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329    
            G3P_HOMAM     - -SKIGINGFGRIGRLVLRAALSCGAQVVAVNDPFIALEYMVYMFKYDSTHGVFKGEVKMEDGALVVDGKKITVFNEMKPENIPWSKAGAEYIVESTGVFTTIEKASAHFKGGAKKVVISAPSADAPMFVCGVNLEKYSKDMTVVSNASCTTNCLAPVAKVLHENFEIVEGLMTTVHAVTATQKTVDGPSAKDWRGGRGAAQNIIPSSTGAAKAVGKVIPELDGKLTGMAFRVPTPDVSVVDLTVRLGKECSYDDIKAAMKTASEGPLQGFLGYTEDDVVSSDFIGDNRSSIFDAKAGIQLSKTFVKVVSWYDNEFGYSQRVIDLLKHMQKVDSA 333
               SCOP domains -d1gpdg1 G:1-148,G:313-334 Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)                                                                         d1gpdg2 G:149-312 Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)                                                                                                  d1gpdg1                SCOP domains
               CATH domains -1gpdG01 G:1-147,G:314-333 NAD(P)-binding Rossmann-like Domain                                                                                     1gpdG02 G:148-313 Dihydrodipicolinate Reductase; domain 2                                                                                                             1gpdG01             - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.hhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhh.........eeeee..eeeee....eee...............eeeeee.....hhhhhhhhhhhh..eeeeee.....eee.............eeeeeehhhhhhhhhhhhhhhhhhh.eeeeeeeeeeee.....eeeeeeeeee.........eeeeehhhhhhhhhh.....eeeeeeeeee..eeeeeeeeeee....hhhhhhhhhhhhhhh.....eee................eeee.....eee.eeeeeeeeeehhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------GAPDH   ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gpd G   0 xSKIGINGFGRIGRLVLRAALSCGAQVVAVNDPFIALEYMVYMFKYDSTHGVFKGEVKMEDGALVVDGKKITVFNEMKPENIPWSKAGAEYIVESTGVFTTIEKASAHFKGGAKKVVISAPSADAPMFVCGVNLEKYSKDMTVVSNASCTTNCLAPVAKVLHENFEIVEGLMTTVHAVTATQKTVDGPSAKDWRGGRGAAQNIIPSSTGAAKAVGKVIPELDGKLTGMAFRVPTPDVSVVDLTVRLGKECSYDDIKAAMKTASEGPLQGFLGYTEDDVVSSDFIGDNRSSIFDAKAGIQLSKTFVKVVSWYDNEFGYSQRVIDLLKHMQKVDSA 334
                            |        9        19   ||   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    
                            |                     23|                                                                                                                                                                                                                                                                                                                     
                            0-ACE                  25                                                                                                                                                                                                                                                                                                                     


Chain R from PDB  Type:PROTEIN  Length:334
 aligned with G3P_HOMAM | P00357 from UniProtKB/Swiss-Prot  Length:333

    Alignment length:334
                             1                                                                                                                                                                                                                                                                                                                                            
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329    
            G3P_HOMAM     - -SKIGINGFGRIGRLVLRAALSCGAQVVAVNDPFIALEYMVYMFKYDSTHGVFKGEVKMEDGALVVDGKKITVFNEMKPENIPWSKAGAEYIVESTGVFTTIEKASAHFKGGAKKVVISAPSADAPMFVCGVNLEKYSKDMTVVSNASCTTNCLAPVAKVLHENFEIVEGLMTTVHAVTATQKTVDGPSAKDWRGGRGAAQNIIPSSTGAAKAVGKVIPELDGKLTGMAFRVPTPDVSVVDLTVRLGKECSYDDIKAAMKTASEGPLQGFLGYTEDDVVSSDFIGDNRSSIFDAKAGIQLSKTFVKVVSWYDNEFGYSQRVIDLLKHMQKVDSA 333
               SCOP domains -d1gpdr1 R:1-148,R:313-334 Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)                                                                         d1gpdr2 R:149-312 Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)                                                                                                  d1gpdr1                SCOP domains
               CATH domains -1gpdR01 R:1-147,R:314-333 NAD(P)-binding Rossmann-like Domain                                                                                     1gpdR02 R:148-313 Dihydrodipicolinate Reductase; domain 2                                                                                                             1gpdR01             - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.hhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhh.........eeeee..eeeee....eee...............eeeeee.....hhhhhhhhhhhh..eeeeee.....eee.............eeeeeehhhhhhhhhhhhhhhhhhh.eeeeeeeeeeee.....eeeeeeeeee.........eeeeehhhhhhhhhh.....eeeeeeeeee..eeeeeeeeeee....hhhhhhhhhhhhhhh.....eee................eeee.....eee.eeeeeeeeeehhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------GAPDH   ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gpd R   0 xSKIGINGFGRIGRLVLRAALSCGAQVVAVNDPFIALEYMVYMFKYDSTHGVFKGEVKMEDGALVVDGKKITVFNEMKPENIPWSKAGAEYIVESTGVFTTIEKASAHFKGGAKKVVISAPSADAPMFVCGVNLEKYSKDMTVVSNASCTTNCLAPVAKVLHENFEIVEGLMTTVHAVTATQKTVDGPSAKDWRGGRGAAQNIIPSSTGAAKAVGKVIPELDGKLTGMAFRVPTPDVSVVDLTVRLGKECSYDDIKAAMKTASEGPLQGFLGYTEDDVVSSDFIGDNRSSIFDAKAGIQLSKTFVKVVSWYDNEFGYSQRVIDLLKHMQKVDSA 334
                            |        9        19   ||   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    
                            0-ACE                 23|                                                                                                                                                                                                                                                                                                                     
                                                   25
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1GPD)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain G,R   (G3P_HOMAM | P00357)
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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  1gpd
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        G3P_HOMAM | P00357: 4gpd

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