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(-) Description

Title :  CRYSTAL STRUCTURE OF CGD1_2040, A PYRUVATE KINASE FROM CRYPTOSPORIDIUM PARVUM
 
Authors :  A. K. Wernimont, A. Hutchinson, A. Hassanali, I. Kozieradzki, D. Cossa A. Bochkarev, C. H. Arrowsmith, A. M. Edwards, C. Bountra, J. Weigelt, T. Hills, J. C. Pizarro, Structural Genomics Consortium (Sgc)
Date :  23 Mar 10  (Deposition) - 21 Jul 10  (Release) - 21 Jul 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.64
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Cryptosporidium Parvum, Parasitology, Pyruvate Kiase, Glycolysis, Kinase, Magnesium, Pyruvate, Transferase, Structural Genomics, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. K. Wernimont, A. Hutchinson, A. Hassanali, I. Kozieradzki, D. Cossar, A. Bochkarev, C. H. Arrowsmith, A. M. Edwards, C. Bountra, J. Weigelt, R. Hui, T. Hills, J. C. Pizarro
Crystal Structure Of Cgd1_2040, A Pyruvate Kinase From Cryptosporidium Parvum
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PYRUVATE KINASE
    Chains: A, B
    EC Number: 2.7.1.40
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15MLH
    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  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1CIT2Ligand/IonCITRIC ACID
2SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1CIT4Ligand/IonCITRIC ACID
2SO44Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:82 , LYS A:278 , GLU A:280 , ALA A:301 , ARG A:302 , GLY A:303 , ASP A:304 , THR A:336BINDING SITE FOR RESIDUE CIT A 535
2AC2SOFTWARETHR A:440 , GLU A:441 , THR A:442 , ASN A:444 , THR A:445BINDING SITE FOR RESIDUE SO4 A 536
3AC3SOFTWAREARG B:82 , LYS B:278 , GLU B:280 , ALA B:301 , ARG B:302 , GLY B:303 , ASP B:304 , THR B:336 , HOH B:573BINDING SITE FOR RESIDUE CIT B 535
4AC4SOFTWARETHR B:440 , GLU B:441 , THR B:442 , ASN B:444 , THR B:445 , HOH B:567BINDING SITE FOR RESIDUE SO4 B 536

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3MA8)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Glu A:129 -Gly A:130
2Ile A:203 -Gly A:204
3Lys A:412 -Pro A:413
4Gly B:131 -Lys B:132
5Lys B:412 -Pro B:413

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3MA8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3MA8)

(-) Exons   (0, 0)

(no "Exon" information available for 3MA8)

(-) 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:490
 aligned with Q5CSM7_CRYPI | Q5CSM7 from UniProtKB/TrEMBL  Length:532

    Alignment length:499
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523         
         Q5CSM7_CRYPI    34 GMDKICSPLADNDVTQRKTQIICTIGPSCNNVESLIGLIDKGMSVARLNFSHGDHESHFKTLQNIREAAKARPHSTVGIMLDTKGPEIRTGMLEGGKPIELKAGQTLKITTDYSMLGNSECISCSYSLLPKSVQIGSTVLIADGSLSTQVLEIGDDFIVCKVLNSVTIGERKNMNLPGCKVHLPIIGDKDRHDIVDFALKYNLDFIALSFVQNGADVQLCRQIISENTQYSNGIPSSIKIISKIENLEGVINFDSICSESDGIMVARGDLGMEIPPEKIFVAQKCMISKCNVAGKPVVTATQMLESMIKSNRPTRAEMTDVANAVLDGSDCVMLSGETANGAFPFDAVNVMSRVCAQAETCIDYPVLYHAIHSSVPKPVAVPEAIACSAVESAHDVNAKLIITITETGNTARLISKYRPSQTIIACTAKPEVARGLKIARGVKTYVLNSIHHSEVVISNALALAKEESLIESGDFAIAVHGVKESCPGSCNLMKIVRCP 532
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh..hhhhhhh...eeeee.hhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhhh.....eeeee.......................--.ee...........ee....hhhhhh....eeee....eeeeeeee...eeeeee...........ee...........hhhhhhhhhh........eeee....hhhhhhhhhhhhhhh...........eeeeee.hhhhhhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhh....hhhhhhhhhhhhhhh..eeeehhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhh....eeeeee.hhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhh.......eeeeee..-------..eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ma8 A  36 GMDKICSPLADNDVTQRKTQIICTIGPSCNNVESLIGLIDKGMSVARLNFSHGDHESHFKTLQNIREAAKARPHSTVGIMLDTKGPEIRTGMLEGGKPIELKAGQ--KITTDYSMLGNSECISCSYSLLPKSVQIGSTVLIADGSLSTQVLEIGDDFIVCKVLNSVTIGERKNMNLPGCKVHLPIIGDKDRHDIVDFALKYNLDFIALSFVQNGADVQLCRQIISENTQYSNGIPSSIKIISKIENLEGVINFDSICSESDGIMVARGDLGMEIPPEKIFVAQKCMISKCNVAGKPVVTATQMLESMIKSNRPTRAEMTDVANAVLDGSDCVMLSGETANGAFPFDAVNVMSRVCAQAETCIDYPVLYHAIHSSVPKPVAVPEAIACSAVESAHDVNAKLIITITETGNTARLISKYRPSQTIIACTAKPEVARGLKIARGVKTYVLNSIHHSEVVISNALALAKEESLIESGDFAIAVHGV-------CNLMKIVRCP 534
                                    45        55        65        75        85        95       105       115       125       135    |  145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515 |     525         
                                                                                                                                  140  |                                                                                                                                                                                                                                                                                                                                                                                   517     525         
                                                                                                                                     143                                                                                                                                                                                                                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:495
 aligned with Q5CSM7_CRYPI | Q5CSM7 from UniProtKB/TrEMBL  Length:532

    Alignment length:501
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531 
         Q5CSM7_CRYPI    32 CLGMDKICSPLADNDVTQRKTQIICTIGPSCNNVESLIGLIDKGMSVARLNFSHGDHESHFKTLQNIREAAKARPHSTVGIMLDTKGPEIRTGMLEGGKPIELKAGQTLKITTDYSMLGNSECISCSYSLLPKSVQIGSTVLIADGSLSTQVLEIGDDFIVCKVLNSVTIGERKNMNLPGCKVHLPIIGDKDRHDIVDFALKYNLDFIALSFVQNGADVQLCRQIISENTQYSNGIPSSIKIISKIENLEGVINFDSICSESDGIMVARGDLGMEIPPEKIFVAQKCMISKCNVAGKPVVTATQMLESMIKSNRPTRAEMTDVANAVLDGSDCVMLSGETANGAFPFDAVNVMSRVCAQAETCIDYPVLYHAIHSSVPKPVAVPEAIACSAVESAHDVNAKLIITITETGNTARLISKYRPSQTIIACTAKPEVARGLKIARGVKTYVLNSIHHSEVVISNALALAKEESLIESGDFAIAVHGVKESCPGSCNLMKIVRCP 532
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh..hhhhhhh...eeeee.hhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh......eeeee.....ee.........eee....eeeee..........eee....hhhhhh....eeee....eeeeeeee...eeeeee...eee....eee...........hhhhhhhhhhh.......eeee....hhhhhhhhhhhhhhh...........eeeeee.hhhhhhhhhhhhhhh.eeeeehhhhhhhh...hhhhhhhhhhhhhhhhh..eeee...hhhhhh....hhhhhhhhhhhhhhh..eeeehhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhh....eeeeee.hhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhh.......eeeeee...------..eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ma8 B  34 CLGMDKICSPLADNDVTQRKTQIICTIGPSCNNVESLIGLIDKGMSVARLNFSHGDHESHFKTLQNIREAAKARPHSTVGIMLDTKGPEIRTGMLEGGKPIELKAGQTLKITTDYSMLGNSECISCSYSLLPKSVQIGSTVLIADGSLSTQVLEIGDDFIVCKVLNSVTIGERKNMNLPGCKVHLPIIGDKDRHDIVDFALKYNLDFIALSFVQNGADVQLCRQIISENTQYSNGIPSSIKIISKIENLEGVINFDSICSESDGIMVARGDLGMEIPPEKIFVAQKCMISKCNVAGKPVVTATQMLESMIKSNRPTRAEMTDVANAVLDGSDCVMLSGETANGAFPFDAVNVMSRVCAQAETCIDYPVLYHAIHSSVPKPVAVPEAIACSAVESAHDVNAKLIITITETGNTARLISKYRPSQTIIACTAKPEVARGLKIARGVKTYVLNSIHHSEVVISNALALAKEESLIESGDFAIAVHGVK------CNLMKIVRCP 534
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513    |    - |     533 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              518    525
   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 3MA8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MA8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3MA8)

(-) 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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