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(-) Description

Title :  CRYSTAL STRUCTURE OF CRYPTOSPORIDIUM PARVUM GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
 
Authors :  A. K. Wernimont, J. Lew, I. Kozieradzki, D. Cossar, M. Schapiro, A. Boch C. H. Arrowsmith, C. Bountra, J. Weigelt, A. M. Edwards, R. Hui, J. Piza T. Hills, Structural Genomics Consortium (Sgc)
Date :  01 Apr 08  (Deposition) - 15 Apr 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A (2x),B (2x)
Keywords :  Gapdh, Glycolysis, Malaria, Structural Genomics, Oxidoreductase, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. K. Wernimont, J. Lew, I. Kozieradzki, D. Cossar, M. Schapiro, A. Bochkarev, C. Bountra, J. Weigelt, A. M. Edwards, R. Hui, J. Pizarro T. Hills
Crystal Structure Of Cryptosporidium Parvum Glyceraldehyde-3-Phosphate Dehydrogenase.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P15-MHL
    Expression System Strain: DH5A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CGD6_3790
    Organism Scientific: CRYPTOSPORIDIUM PARVUM IOWA II
    Organism Taxid: 353152
    Strain: IOWA TYPE II

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (2x): A (2x)B (2x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN B:23 , GLY B:24 , PHE B:25 , GLY B:26 , ARG B:27 , ILE B:28 , ASN B:48 , ASP B:49 , PRO B:50 , PHE B:51 , MET B:52 , ALA B:93 , LYS B:94 , SER B:112 , THR B:113 , GLY B:114 , PHE B:116 , SER B:136 , ALA B:137 , CYS B:168 , ALA B:199 , ASN B:334 , TYR B:338BINDING SITE FOR RESIDUE NAD B 401
2AC2SOFTWAREASN A:23 , GLY A:24 , PHE A:25 , GLY A:26 , ARG A:27 , ILE A:28 , ASN A:48 , ASP A:49 , PRO A:50 , PHE A:51 , MET A:52 , LYS A:94 , SER A:112 , THR A:113 , GLY A:114 , PHE A:116 , SER A:136 , ALA A:137 , CYS A:168 , ALA A:199 , ASN A:334 , TYR A:338BINDING SITE FOR RESIDUE NAD A 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Lys A:209 -Gly A:210

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3CPS)

(-) 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:334
 aligned with Q5CWT6_CRYPI | Q5CWT6 from UniProtKB/TrEMBL  Length:339

    Alignment length:337
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       
         Q5CWT6_CRYPI     3 ATLGINGFGRIGRLVLRACMERNDITVVAINDPFMDVEYMAYLLKYDSVHGNFNGTVEVSGKDLCINGKVVKVFQAKDPAEIPWGASGAQIVCESTGVFTTEEKASLHLKGGAKKVIISAPPKDNVPMYVMGVNNTEYDPSKFNVISNASCTTNCLAPLAKIINDKFGIVEGLMTTVHSLTANQLTVDGPSKGGKDWRAGRCAGNNIIPASTGAAKAVGKVIPALNGKLTGMAIRVPTPDVSVVDLTCKLAKPASIEEIYQAVKEASNGPMKGIMGYTSDDVVSTDFIGCKYSSIFDKNACIALNDSFVKLISWYDNESGYSNRLVDLAVYVASRGL 339
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3cpsA01 A:18-165,A:335-354 NAD(P)-binding Rossmann-like Domai n                                                                                     3cpsA02 A:166-334 Dihydrodipicolinate Reducta  se; domain 2                                                                                                              3cpsA01              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhh....eeeeee....hhhhhhhhhhh..........eee..-.eee..eeeeee...hhhhhhhhhhh..eeee......hhhhhhhhhh....eeee...............hhhhh......eee..hhhhhhhhhhhhhhhhhh.eeeeeeeeeee..............--.hhhhh......eeee.hhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeee....hhhhhhhhhhhhhhh.....eeee....hhhhhh.....eeee.hhheeee..eeeeeeee..hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cps A  18 GTLGINGFGRIGRLVLRACMERNDITVVAINDPFMDVEYMAYLLKYDSVHGNFNGTVEVSG-DLCINGKVVKVFQAKDPAEIPWGASGAQIVCESTGVFTTEEKASLHLKGGAKKVIISAPPKDNVPMYVMGVNNTEYDPSKFNVISNASCTTNCLAPLAKIINDKFGIVEGLMTTVHSLTANQLTVDGPSKG--DWRAGRCAGNNIIPASTGAAKAVGKVIPALNGKLTGMAIRVPTPDVSVVDLTCKLAKPASIEEIYQAVKEASNGPMKGIMGYTSDDVVSTDFIGCKYSSIFDKNACIALNDSFVKLISWYDNESGYSNRLVDLAVYVASRGL 354
                                    27        37        47        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       337       347       
                                                                                       78 |                                                                                                                               210  |                                                                                                                                             
                                                                                         80                                                                                                                                  213                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:333
 aligned with Q5CWT6_CRYPI | Q5CWT6 from UniProtKB/TrEMBL  Length:339

    Alignment length:337
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       
         Q5CWT6_CRYPI     3 ATLGINGFGRIGRLVLRACMERNDITVVAINDPFMDVEYMAYLLKYDSVHGNFNGTVEVSGKDLCINGKVVKVFQAKDPAEIPWGASGAQIVCESTGVFTTEEKASLHLKGGAKKVIISAPPKDNVPMYVMGVNNTEYDPSKFNVISNASCTTNCLAPLAKIINDKFGIVEGLMTTVHSLTANQLTVDGPSKGGKDWRAGRCAGNNIIPASTGAAKAVGKVIPALNGKLTGMAIRVPTPDVSVVDLTCKLAKPASIEEIYQAVKEASNGPMKGIMGYTSDDVVSTDFIGCKYSSIFDKNACIALNDSFVKLISWYDNESGYSNRLVDLAVYVASRGL 339
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3cpsB01 B:18-165,B:335-354 NAD(P)-binding Rossmann-like Doma in                                                                                     3cpsB02 B:166-334 Dihydrodipicolinate Reduct   ase; domain 2                                                                                                             3cpsB01              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhh....eeeeee....hhhhhhhhhhh..........eee.-..eee..eeeeee...hhhhhhhhhhh..eeee......hhhhhhhhhhhh..eeee...............hhhhh......eee..hhhhhhhhhhhhhhhhhh.eeeeeeeeeee.............---.hhhhh......eeee.hhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeee....hhhhhhhhhhhhhh......eeee....hhhhhh.....eeee....eeee..eeeeeeee..hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cps B  18 GTLGINGFGRIGRLVLRACMERNDITVVAINDPFMDVEYMAYLLKYDSVHGNFNGTVEVS-KDLCINGKVVKVFQAKDPAEIPWGASGAQIVCESTGVFTTEEKASLHLKGGAKKVIISAPPKDNVPMYVMGVNNTEYDPSKFNVISNASCTTNCLAPLAKIINDKFGIVEGLMTTVHSLTANQLTVDGPSK---DWRAGRCAGNNIIPASTGAAKAVGKVIPALNGKLTGMAIRVPTPDVSVVDLTCKLAKPASIEEIYQAVKEASNGPMKGIMGYTSDDVVSTDFIGCKYSSIFDKNACIALNDSFVKLISWYDNESGYSNRLVDLAVYVASRGL 354
                                    27        37        47        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       337       347       
                                                                                      77 |                                                                                                                               209 213                                                                                                                                             
                                                                                        79
   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 3CPS)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q5CWT6_CRYPI | Q5CWT6)
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.

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