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(-) Description

Title :  CRYSTAL STRUCTURE OF CRYPTOSPORIDIUM PARVUM PYRUVATE KINASE
 
Authors :  W. J. Cook, D. Chattopadhyay
Date :  17 Feb 12  (Deposition) - 17 Oct 12  (Release) - 23 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Pyruvate, Kinase, Glycolysis, Cryptosporidium, Allosteric Enzyme, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. J. Cook, O. Senkovich, K. Aleem, D. Chattopadhyay
Crystal Structure Of Cryptosporidium Parvum Pyruvate Kinase
Plos One V. 7 46875 2012
PubMed-ID: 23056503  |  Reference-DOI: 10.1371/JOURNAL.PONE.0046875

(-) Compounds

Molecule 1 - PYRUVATE KINASE
    Chains: A, B
    EC Number: 2.7.1.40
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CGD1_2040
    Organism Scientific: CRYPTOSPORIDIUM PARVUM
    Organism Taxid: 353152
    Strain: IOWA II

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric Unit (3, 14)
No.NameCountTypeFull Name
1ACT6Ligand/IonACETATE ION
2GOL4Ligand/IonGLYCEROL
3SO44Ligand/IonSULFATE ION
Biological Unit 1 (3, 28)
No.NameCountTypeFull Name
1ACT12Ligand/IonACETATE ION
2GOL8Ligand/IonGLYCEROL
3SO48Ligand/IonSULFATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:432 , GLU A:433 , THR A:434 , THR A:437BINDING SITE FOR RESIDUE SO4 A 601
02AC2SOFTWAREHIS A:101 , SER A:102 , THR A:103 , LYS A:464 , LYS A:470 , THR A:471BINDING SITE FOR RESIDUE SO4 A 602
03AC3SOFTWAREARG A:74 , ASN A:76 , LYS A:270 , GLU A:272 , SER A:362 , ACT A:605 , HOH A:761BINDING SITE FOR RESIDUE GOL A 603
04AC4SOFTWAREASN A:229 , GLU A:458 , ARG A:461BINDING SITE FOR RESIDUE GOL A 604
05AC5SOFTWAREARG A:74 , ASN A:76 , SER A:362 , GLY A:363 , GOL A:603BINDING SITE FOR RESIDUE ACT A 605
06AC6SOFTWAREHIS A:79 , GLY A:80 , ARG A:198BINDING SITE FOR RESIDUE ACT A 606
07AC7SOFTWAREARG A:93BINDING SITE FOR RESIDUE ACT A 607
08AC8SOFTWARETHR B:432 , THR B:434 , ASN B:436 , THR B:437BINDING SITE FOR RESIDUE SO4 B 601
09AC9SOFTWAREHIS B:101 , SER B:102 , THR B:103 , LYS B:464 , LYS B:470 , THR B:471BINDING SITE FOR RESIDUE SO4 B 602
10BC1SOFTWAREARG B:74 , ASN B:76 , LYS B:270 , GLU B:272 , ACT B:605BINDING SITE FOR RESIDUE GOL B 603
11BC2SOFTWAREASN B:229 , PRO B:457 , GLU B:458 , ARG B:461BINDING SITE FOR RESIDUE GOL B 604
12BC3SOFTWAREARG B:74 , ASN B:76 , SER B:362 , GLY B:363 , GOL B:603BINDING SITE FOR RESIDUE ACT B 605
13BC4SOFTWAREHIS B:79 , GLY B:80 , ARG B:198BINDING SITE FOR RESIDUE ACT B 606
14BC5SOFTWAREHIS A:396 , HIS B:399 , SER B:400 , LYS B:404 , HOH B:741BINDING SITE FOR RESIDUE ACT B 607

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:26 -B:312
2A:312 -B:26

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Lys A:404 -Pro A:405
2Lys B:404 -Pro B:405

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4DRS)

(-) 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:485
 aligned with Q5CSM7_CRYPI | Q5CSM7 from UniProtKB/TrEMBL  Length:532

    Alignment length:504
                                    38        48        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       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528    
         Q5CSM7_CRYPI    29 KATCLGMDKICSPLADNDVTQRKTQIICTIGPSCNNVESLIGLIDKGMSVARLNFSHGDHESHFKTLQNIREAAKARPHSTVGIMLDTKGPEIRTGMLEGGKPIELKAGQTLKITTDYSMLGNSECISCSYSLLPKSVQIGSTVLIADGSLSTQVLEIGDDFIVCKVLNSVTIGERKNMNLPGCKVHLPIIGDKDRHDIVDFALKYNLDFIALSFVQNGADVQLCRQIISENTQYSNGIPSSIKIISKIENLEGVINFDSICSESDGIMVARGDLGMEIPPEKIFVAQKCMISKCNVAGKPVVTATQMLESMIKSNRPTRAEMTDVANAVLDGSDCVMLSGETANGAFPFDAVNVMSRVCAQAETCIDYPVLYHAIHSSVPKPVAVPEAIACSAVESAHDVNAKLIITITETGNTARLISKYRPSQTIIACTAKPEVARGLKIARGVKTYVLNSIHHSEVVISNALALAKEESLIESGDFAIAVHGVKESCPGSCNLMKIVRCP 532
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhh---------.....eeeee.hhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh......eeeee................ee.....eeeee..........eee..............eeee....eeeeeeee...eeeee.....ee.....ee...........hhhhhhhhhhh.......eeee....hhhhhhhhhhhhhh............eeeeee.hhhhhhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhh....hhhhhhhhhhhhhhh..eeeehhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhh....eeeeee.hhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhh.......eeeee.----------..eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4drs A  23 KATCLGMDKI---------TQRKTQIICTIGPSCNNVESLIGLIDKGMSVARLNFSHGDHESHFKTLQNIREAAKARPHSTVGIMLDTKGPEIRTGMLEGGKPIELKAGQTLKITTDYSMLGNSECISCSYSLLPKSVQIGSTVLIADGSLSTQVLEIGDDFIVCKVLNSVTIGERKNMNLPGCKVHLPIIGDKDRHDIVDFALKYNLDFIALSFVQNGADVQLCRQIISENTQYSNGIPSSIKIISKIENLEGVINFDSICSESDGIMVARGDLGMEIPPEKIFVAQKCMISKCNVAGKPVVTATQMLESMIKSNRPTRAEMTDVANAVLDGSDCVMLSGETANGAFPFDAVNVMSRVCAQAETCIDYPVLYHAIHSSVPKPVAVPEAIACSAVESAHDVNAKLIITITETGNTARLISKYRPSQTIIACTAKPEVARGLKIARGVKTYVLNSIHHSEVVISNALALAKEESLIESGDFAIAVH----------NLMKIVRCP 526
                                    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       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502    |    -     | 522    
                                    32        42                                                                                                                                                                                                                                                                                                                                                                                                                                                                              507        518        


Chain B from PDB  Type:PROTEIN  Length:485
 aligned with Q5CSM7_CRYPI | Q5CSM7 from UniProtKB/TrEMBL  Length:532

    Alignment length:504
                                    38        48        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       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528    
         Q5CSM7_CRYPI    29 KATCLGMDKICSPLADNDVTQRKTQIICTIGPSCNNVESLIGLIDKGMSVARLNFSHGDHESHFKTLQNIREAAKARPHSTVGIMLDTKGPEIRTGMLEGGKPIELKAGQTLKITTDYSMLGNSECISCSYSLLPKSVQIGSTVLIADGSLSTQVLEIGDDFIVCKVLNSVTIGERKNMNLPGCKVHLPIIGDKDRHDIVDFALKYNLDFIALSFVQNGADVQLCRQIISENTQYSNGIPSSIKIISKIENLEGVINFDSICSESDGIMVARGDLGMEIPPEKIFVAQKCMISKCNVAGKPVVTATQMLESMIKSNRPTRAEMTDVANAVLDGSDCVMLSGETANGAFPFDAVNVMSRVCAQAETCIDYPVLYHAIHSSVPKPVAVPEAIACSAVESAHDVNAKLIITITETGNTARLISKYRPSQTIIACTAKPEVARGLKIARGVKTYVLNSIHHSEVVISNALALAKEESLIESGDFAIAVHGVKESCPGSCNLMKIVRCP 532
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhh---------.....eeeee.hhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh......eeeee.........ee.....ee.....eeeee.....ee...eee..............eeee....eeeeeeee...eeeeee....ee.....ee...........hhhhhhhhhh........eeee....hhhhhhhhhhhhhhh...........eeeeee.hhhhhhhhhhhhhhh.eeee...hhhhhhhhhhhhhhhhhhhhhhhhhh..eee....hhhhhh....hhhhhhhhhhhhhhh..eeeehhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhh....eeeeee.hhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhh.......eeeee.----------..eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4drs B  23 KATCLGMDKI---------TQRKTQIICTIGPSCNNVESLIGLIDKGMSVARLNFSHGDHESHFKTLQNIREAAKARPHSTVGIMLDTKGPEIRTGMLEGGKPIELKAGQTLKITTDYSMLGNSECISCSYSLLPKSVQIGSTVLIADGSLSTQVLEIGDDFIVCKVLNSVTIGERKNMNLPGCKVHLPIIGDKDRHDIVDFALKYNLDFIALSFVQNGADVQLCRQIISENTQYSNGIPSSIKIISKIENLEGVINFDSICSESDGIMVARGDLGMEIPPEKIFVAQKCMISKCNVAGKPVVTATQMLESMIKSNRPTRAEMTDVANAVLDGSDCVMLSGETANGAFPFDAVNVMSRVCAQAETCIDYPVLYHAIHSSVPKPVAVPEAIACSAVESAHDVNAKLIITITETGNTARLISKYRPSQTIIACTAKPEVARGLKIARGVKTYVLNSIHHSEVVISNALALAKEESLIESGDFAIAVH----------NLMKIVRCP 526
                                    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       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502    |    -     | 522    
                                    32        42                                                                                                                                                                                                                                                                                                                                                                                                                                                                              507        518
   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 4DRS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q5CSM7_CRYPI | Q5CSM7)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0030955    potassium ion binding    Interacting selectively and non-covalently with potassium (K+) ions.
    GO:0004743    pyruvate kinase activity    Catalysis of the reaction: ATP + pyruvate = ADP + phosphoenolpyruvate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    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:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.

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