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(-) Description

Title :  CRYSTAL STRUCTURE OF GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE COMPLEXED WITH CP12 IN THE PRESENCE OF COPPER FROM SYNECHOCOCCUS ELONGATUS
 
Authors :  H. Matsumura, A. Kai, T. Inoue
Date :  04 Jul 11  (Deposition) - 11 Jan 12  (Release) - 12 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (2x)
Keywords :  Alpha/Beta Fold, Oxidoreductase-Protein Binding Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Matsumura, A. Kai, T. Maeda, M. Tamoi, A. Satoh, H. Tamura, M. Hirose T. Ogawa, N. Kizu, A. Wadano, T. Inoue, S. Shigeoka
Structure Basis For The Regulation Of Glyceraldehyde-3-Phosphate Dehydrogenase Activity Via The Intrinsically Disordered Protein Cp12.
Structure V. 19 1846 2011
PubMed-ID: 22153507  |  Reference-DOI: 10.1016/J.STR.2011.08.016

(-) Compounds

Molecule 1 - GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE (NADP+)
    Chains: A, B
    EC Number: 1.2.1.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: GAP2, SYNPCC7942_1742
    Organism Scientific: SYNECHOCOCCUS ELONGATUS
    Organism Taxid: 1140
    Strain: PCC 7942
    Synonym: GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE (NADP+) (PHOSPHORYLATING)
 
Molecule 2 - CP12
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 51-75
    Gene: CP12, SYNPCC7942_0361
    Organism Scientific: SYNECHOCOCCUS ELONGATUS
    Organism Taxid: 1140
    Strain: PCC 7942

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (2x): ABCD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1CU2Ligand/IonCOPPER (II) ION
2NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1CU-1Ligand/IonCOPPER (II) ION
2NAD4Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:9 , PHE A:10 , GLY A:11 , ARG A:12 , ILE A:13 , ASN A:35 , ASN A:36 , THR A:37 , ARG A:80 , SER A:98 , THR A:99 , GLY A:100 , THR A:122 , ALA A:123 , CYS A:155 , LEU A:186 , ASN A:318 , TYR A:322 , HOH A:343 , HOH A:345 , HOH A:353 , HOH A:358 , HOH A:365 , HOH A:372 , HOH A:389 , HOH A:412 , HOH A:421 , TYR C:73 , HOH C:108BINDING SITE FOR RESIDUE NAD A 340
2AC2SOFTWARECYS A:155 , THR A:156 , ASP C:75BINDING SITE FOR RESIDUE CU A 341
3AC3SOFTWAREGLY B:9 , PHE B:10 , GLY B:11 , ARG B:12 , ILE B:13 , ASN B:35 , ASN B:36 , THR B:37 , ARG B:80 , SER B:98 , THR B:99 , GLY B:100 , THR B:122 , ALA B:123 , CYS B:155 , LEU B:186 , ASN B:318 , TYR B:322 , HOH B:343 , HOH B:354 , HOH B:358 , HOH B:402 , HOH B:403 , HOH B:409 , HOH B:410 , HOH B:437 , ASP D:66 , TYR D:73 , ASP D:74BINDING SITE FOR RESIDUE NAD B 340
4AC4SOFTWARECYS B:155 , THR B:156 , HIS B:182 , ASP D:75BINDING SITE FOR RESIDUE CU B 341

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1C:61 -C:70
2D:61 -D:70

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3B1J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3B1J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3B1J)

(-) Exons   (0, 0)

(no "Exon" information available for 3B1J)

(-) 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 A from PDB  Type:PROTEIN  Length:338
 aligned with Q9R6W2_SYNE7 | Q9R6W2 from UniProtKB/TrEMBL  Length:339

    Alignment length:338
                                    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        
         Q9R6W2_SYNE7     1 MTIRVAINGFGRIGRNFLRCWFGRQNTDLEVVAINNTSDARTAAHLLEYDSVLGRFNADISYDENSITVNGKTMKIVCDRNPLNLPWKEWDIDLVIESTGVFVTAEGASKHIQAGAKKVLITAPGKGEGVGTYVIGVNDSEYRHEDFAVISNASCTTNCLAPVAKVLHDNFGIIKGTMTTTHSYTLDQRILDASHRDLRRARAAAVNIVPTTTGAAKAVALVIPELKGKLNGIALRVPTPNVSVVDLVVQVEKPTITEQVNEVLQKASQTTMKGIIKYSDLPLVSSDFRGTDESSIVDSSLTLVMDGDLVKVIAWYDNEWGYSQRVVDLAELAARKWA 338
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhhhh....eeeeeee...hhhhhhhhhhh..........eeee..eeee..eeeeee...hhhhh........eeee......hhhhhhhhhhh...eeee.........ee.....hhhhh......eee..hhhhhhhhhhhhhhhhhh.eeeeeeeeeee.........................eeee.hhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeee....hhhhhhhhhhhhhhh.....eeee....hhhhhh.....eeee.hhheee...eeeeeeee..hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b1j A   1 MTIRVAINGFGRIGRNFLRCWFGRQNTDLEVVAINNTSDARTAAHLLEYDSVLGRFNADISYDENSITVNGKTMKIVCDRNPLNLPWKEWDIDLVIESTGVFVTAEGASKHIQAGAKKVLITAPGKGEGVGTYVIGVNDSEYRHEDFAVISNASCTTNCLAPVAKVLHDNFGIIKGTMTTTHSYTLDQRILDASHRDLRRARAAAVNIVPTTTGAAKAVALVIPELKGKLNGIALRVPTPNVSVVDLVVQVEKPTITEQVNEVLQKASQTTMKGIIKYSDLPLVSSDFRGTDESSIVDSSLTLVMDGDLVKVIAWYDNEWGYSQRVVDLAELAARKWA 338
                                    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 B from PDB  Type:PROTEIN  Length:338
 aligned with Q9R6W2_SYNE7 | Q9R6W2 from UniProtKB/TrEMBL  Length:339

    Alignment length:338
                                    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        
         Q9R6W2_SYNE7     1 MTIRVAINGFGRIGRNFLRCWFGRQNTDLEVVAINNTSDARTAAHLLEYDSVLGRFNADISYDENSITVNGKTMKIVCDRNPLNLPWKEWDIDLVIESTGVFVTAEGASKHIQAGAKKVLITAPGKGEGVGTYVIGVNDSEYRHEDFAVISNASCTTNCLAPVAKVLHDNFGIIKGTMTTTHSYTLDQRILDASHRDLRRARAAAVNIVPTTTGAAKAVALVIPELKGKLNGIALRVPTPNVSVVDLVVQVEKPTITEQVNEVLQKASQTTMKGIIKYSDLPLVSSDFRGTDESSIVDSSLTLVMDGDLVKVIAWYDNEWGYSQRVVDLAELAARKWA 338
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhhhhhhhhh......eeeeeee...hhhhhhhhhhh..........eeee..eeee..eeeeee...hhhhh.hhhhh..eeee......hhhhhhhhhhh...eeee........eee.....hhhhh......eee..hhhhhhhhhhhhhhhhhhheeeeeeeeeee...................hhhhh.eeee.hhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeee....hhhhhhhhhhhhhhh.....eeee....hhhhhh.....eeee.hhheee...eeeeeeee..hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b1j B   1 MTIRVAINGFGRIGRNFLRCWFGRQNTDLEVVAINNTSDARTAAHLLEYDSVLGRFNADISYDENSITVNGKTMKIVCDRNPLNLPWKEWDIDLVIESTGVFVTAEGASKHIQAGAKKVLITAPGKGEGVGTYVIGVNDSEYRHEDFAVISNASCTTNCLAPVAKVLHDNFGIIKGTMTTTHSYTLDQRILDASHRDLRRARAAAVNIVPTTTGAAKAVALVIPELKGKLNGIALRVPTPNVSVVDLVVQVEKPTITEQVNEVLQKASQTTMKGIIKYSDLPLVSSDFRGTDESSIVDSSLTLVMDGDLVKVIAWYDNEWGYSQRVVDLAELAARKWA 338
                                    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 C from PDB  Type:PROTEIN  Length:22
 aligned with Q6BBK3_SYNE7 | Q6BBK3 from UniProtKB/TrEMBL  Length:75

    Alignment length:22
                                    63        73  
         Q6BBK3_SYNE7    54 EPFFGDYCSENPDAAECLIYDD  75
               SCOP domains ---------------------- SCOP domains
               CATH domains ---------------------- CATH domains
               Pfam domains ---------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ---------------------- SAPs(SNPs)
                    PROSITE ---------------------- PROSITE
                 Transcript ---------------------- Transcript
                 3b1j C  54 EPFFGDYCSENPDAAECLIYDD  75
                                    63        73  


Chain D from PDB  Type:PROTEIN  Length:23
 aligned with Q6BBK3_SYNE7 | Q6BBK3 from UniProtKB/TrEMBL  Length:75

    Alignment length:23
                                    62        72   
         Q6BBK3_SYNE7    53 TEPFFGDYCSENPDAAECLIYDD  75
               SCOP domains ----------------------- SCOP domains
               CATH domains ----------------------- CATH domains
               Pfam domains ----------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------- SAPs(SNPs)
                    PROSITE ----------------------- PROSITE
                 Transcript ----------------------- Transcript
                 3b1j D  53 TEPFFGDYCSENPDAAECLIYDD  75
                                    62        72
   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 3B1J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3B1J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3B1J)

(-) Gene Ontology  (8, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9R6W2_SYNE7 | Q9R6W2)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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.

Chain C,D   (Q6BBK3_SYNE7 | Q6BBK3)
molecular function
    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.

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 Related Entries

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(-) Related Entries Specified in the PDB File

3b1k