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(-) Description

Title :  X-RAY STRUCTURE OF CYTOPLASMIC GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE (GAPC1) COMPLEXED WITH NAD
 
Authors :  S. Fermani, M. Zaffagnini, R. Orru, G. Falini, P. Trost
Date :  26 Mar 15  (Deposition) - 13 Apr 16  (Release) - 12 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  O,R
Biol. Unit 1:  O,R  (2x)
Keywords :  Cytoplasm, Glycolysis, Rossmann Fold, Nad Complex, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Zaffagnini, S. Fermani, M. Calvaresi, R. Orru, L. Iommarini, F. Sparla, G. Falini, A. Bottoni, P. Trost
Tuning Cysteine Reactivity And Sulfenic Acid Stability By Protein Microenvironment In Glyceraldehyde-3-Phosphate Dehydrogenases Of Arabidopsis Thaliana.
Antioxid. Redox Signal. V. 24 502 2016
PubMed-ID: 26650776  |  Reference-DOI: 10.1089/ARS.2015.6417

(-) Compounds

Molecule 1 - GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE GAPC1, CYTOSOLIC
    Chains: O, R
    EC Number: 1.2.1.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28A(+)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: GAPC1, GAPC, GAPDH, AT3G04120, T6K12.26
    Organism Common: MOUSE-EAR CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: NAD-DEPENDENT GLYCERALDEHYDEPHOSPHATE DEHYDROGENASE C SUBUNIT 1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : OR
Biological Unit 1 (2x): OR

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric Unit (2, 9)
No.NameCountTypeFull Name
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2SO47Ligand/IonSULFATE ION
Biological Unit 1 (2, 18)
No.NameCountTypeFull Name
1NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2SO414Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN O:6 , GLY O:7 , PHE O:8 , GLY O:9 , ARG O:10 , ILE O:11 , ASN O:31 , ASP O:32 , PRO O:33 , PHE O:34 , ILE O:35 , ILE O:76 , ARG O:77 , SER O:95 , THR O:96 , GLY O:97 , PHE O:99 , SER O:119 , ALA O:120 , CYS O:149 , ALA O:180 , ASN O:313 , TYR O:317 , SO4 O:402 , HOH O:520binding site for residue NAD O 401
2AC2SOFTWARETHR O:179 , THR O:181 , ARG O:231 , NAD O:401binding site for residue SO4 O 402
3AC3SOFTWARESER O:148 , THR O:150 , THR O:208 , GLY O:209 , HOH O:503binding site for residue SO4 O 403
4AC4SOFTWARESER O:200 , PRO O:233 , SER R:200 , PHE R:201binding site for residue SO4 O 404
5AC5SOFTWAREASN R:6 , PHE R:8 , GLY R:9 , ARG R:10 , ILE R:11 , ASP R:32 , PRO R:33 , PHE R:34 , ARG R:77 , SER R:95 , THR R:96 , GLY R:97 , SER R:119 , ALA R:120 , ALA R:180 , ASN R:313 , TYR R:317 , SO4 R:402 , HOH R:514 , HOH R:529binding site for residue NAD R 401
6AC6SOFTWARETHR R:179 , THR R:181 , ARG R:231 , NAD R:401 , HOH R:531binding site for residue SO4 R 402
7AC7SOFTWARESER R:148 , THR R:150 , THR R:208 , GLY R:209 , ALA R:210binding site for residue SO4 R 403
8AC8SOFTWAREASN R:287 , TRP R:315binding site for residue SO4 R 404
9AC9SOFTWARELYS R:268 , ARG R:288 , HOH R:511 , HOH R:535binding site for residue SO4 R 405

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Z0H)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asn R:54 -Glu R:55

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Z0H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Z0H)

(-) Exons   (0, 0)

(no "Exon" information available for 4Z0H)

(-) Sequences/Alignments

Asymmetric 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
                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhh...........eeee...eeee..eeeeee...hhhhhhhhhhh..eeee......hhhhhhhhhhh...eeee..............hhhhh.....eee..hhhhhhhhhhhhhhhhhh.eeeeeeeeee...............hhhhhhhhhhh.eeee.hhhhhhhhhhhhhh..eeeeeee......eeeeeeeee....hhhhhhhhhhhhhhh.....eeee....hhhhhh.....eeee....eeee..eeeeeeee..hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z0h O   1 IRIGINGFGRIGRLVARVVLQRDDVELVAVNDPFITTEYMTYMFKYDSVHGQWKHNELKIKDEKTLLFGEKPVTVFGIRNPEDIPWAEAGADYVVESTGVFTDKDKAAAHLKGGAKKVVISAPSKDAPMFVVGVNEHEYKSDLDIVSNASCTTNCLAPLAKVINDRFGIVEGLMTTVHSITATQKTVDGPSMKDWRGGRAASFNIIPSSTGAAKAVGKVLPALNGKLTGMSFRVPTVDVSVVDLTVRLEKAATYDEIKKAIKEESEGKLKGILGYTEDDVVSTDFVGDNRSSIFDAKAGIALSDKFVKLVSWYDNEWGYSSRVVDLIVHMSKA 331
                                    10        20        30        40        50||      58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328   
                                                                            50A|                                                                                                                                                                                                                                                                                         
                                                                             50B                                                                                                                                                                                                                                                                                         


Chain R from PDB  Type:PROTEIN  Length:334
                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhhh.....eeeeee....hhhhhhhhhhh...........eeee...eeee..eeeeee...hhhhh.hhhhh..eeee......hhhhhhhhhhh...eeee..............hhhhh.....eee..hhhhhhhhhhhhhhhhhhheeeeeeeeee...............hhhhhhhhhhh.eee..hhhhhhhhhh......eeeeeee......eeeeeeeee....hhhhhhhhhhhhhhh.....eeee....hhhhhh.....eeee....ee....eeeeeeee..hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z0h R   0 KIRIGINGFGRIGRLVARVVLQRDDVELVAVNDPFITTEYMTYMFKYDSVHGQWKHNELKIKDEKTLLFGEKPVTVFGIRNPEDIPWAEAGADYVVESTGVFTDKDKAAAHLKGGAKKVVISAPSKDAPMFVVGVNEHEYKSDLDIVSNASCTTNCLAPLAKVINDRFGIVEGLMTTVHSITATQKTVDGPSMKDWRGGRAASFNIIPSSTGAAKAVGKVLPALNGKLTGMSFRVPTVDVSVVDLTVRLEKAATYDEIKKAIKEESEGKLKGILGYTEDDVVSTDFVGDNRSSIFDAKAGIALSDKFVKLVSWYDNEWGYSSRVVDLIVHMSKA 331
                                     9        19        29        39        49 ||     57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327    
                                                                             50A|                                                                                                                                                                                                                                                                                         
                                                                              50B
   Legend:   → Mismatch (orange background)
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  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 4Z0H)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Z0H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Z0H)

(-) Gene Ontology  (32, 32)

Asymmetric Unit(hide GO term definitions)

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    Asn R:54 - Glu R:55   [ RasMol ]  
 
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3k2b 3K2B IS THE X-RAY STRUCTURE OF THE CORRESPONDING CHLOROPLAST ISOFORM (GAPA) FROM THE SAME ORGANISM