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(-) Description

Title :  CRYSTAL STRUCTURE OF ANCESTRAL APICOMPLEXAN MALATE DEHYDROGENASE WITH LACTATE.
 
Authors :  J. I. Boucher, J. R. Jacobowitz, B. C. Beckett, S. Classen, D. L. Theobal
Date :  19 May 14  (Deposition) - 02 Jul 14  (Release) - 25 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Ancestral Sequence Reconstruction, Dehydrogenase, Apicomplexa, Specificity (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. I. Boucher, J. R. Jacobowitz, B. C. Beckett, S. Classen, D. L. Theobald
An Atomic-Resolution View Of Neofunctionalization In The Evolution Of Apicomplexan Lactate Dehydrogenases.
Elife V. 3 02304 2014
PubMed-ID: 24966208  |  Reference-DOI: 10.7554/ELIFE.02304

(-) Compounds

Molecule 1 - MALATE DEHYDROGENASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 DE3 (PLYSS)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: APICOMPLEXA
    Organism Taxid: 5794

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1NAI4Ligand/Ion1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
2PO44Ligand/IonPHOSPHATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:13 , ASN A:14 , ILE A:15 , ASP A:35 , ILE A:36 , VAL A:37 , MET A:40 , THR A:79 , ALA A:80 , GLY A:81 , PRO A:83 , ILE A:100 , VAL A:120 , THR A:121 , ASN A:122 , MET A:145 , LEU A:149 , HIS A:177 , ALA A:232 , PRO A:236 , PO4 A:402 , HOH A:515 , HOH A:516 , HOH A:541 , HOH A:560 , HOH A:563 , HOH A:581 , HOH A:588 , HOH A:596 , HOH A:631 , HOH A:638 , HOH A:750 , GLY D:87binding site for residue NAI A 401
2AC2SOFTWAREARG A:84 , ARG A:90 , ASN A:122 , ARG A:153 , HIS A:177 , GLY A:220 , NAI A:401 , HOH A:543binding site for residue PO4 A 402
3AC3SOFTWAREGLY B:13 , ASN B:14 , ILE B:15 , ASP B:35 , ILE B:36 , VAL B:37 , MET B:40 , THR B:79 , ALA B:80 , GLY B:81 , ILE B:82 , PRO B:83 , ILE B:100 , VAL B:120 , THR B:121 , ASN B:122 , MET B:145 , LEU B:149 , HIS B:177 , ALA B:232 , PRO B:236 , PO4 B:402 , HOH B:527 , HOH B:528 , HOH B:531 , HOH B:542 , HOH B:545 , HOH B:558 , HOH B:559 , HOH B:560 , HOH B:574 , HOH B:625 , HOH B:700binding site for residue NAI B 401
4AC4SOFTWAREASN B:122 , ARG B:153 , HIS B:177 , GLY B:220 , NAI B:401 , HOH B:547 , HOH B:611binding site for residue PO4 B 402
5AC5SOFTWAREGLY C:13 , ASN C:14 , ILE C:15 , PHE C:34 , ASP C:35 , ILE C:36 , VAL C:37 , MET C:40 , TYR C:67 , THR C:79 , ALA C:80 , GLY C:81 , ILE C:82 , PRO C:83 , ASN C:97 , ILE C:100 , VAL C:120 , ASN C:122 , MET C:145 , LEU C:149 , HIS C:177 , ALA C:232 , PRO C:236 , PO4 C:402 , HOH C:560 , HOH C:561 , HOH C:577 , HOH C:593 , HOH C:617 , HOH C:663 , HOH C:677 , HOH C:680 , HOH C:689 , HOH C:702binding site for residue NAI C 401
6AC6SOFTWAREARG C:84 , ARG C:90 , ASN C:122 , ARG C:153 , HIS C:177 , GLY C:220 , NAI C:401 , HOH C:634binding site for residue PO4 C 402
7AC7SOFTWAREGLY D:13 , ASN D:14 , ILE D:15 , ASP D:35 , ILE D:36 , VAL D:37 , MET D:40 , THR D:79 , ALA D:80 , GLY D:81 , ILE D:100 , VAL D:120 , ASN D:122 , LEU D:124 , MET D:145 , LEU D:149 , HIS D:177 , ALA D:232 , PRO D:236 , PO4 D:402 , HOH D:542 , HOH D:560 , HOH D:561 , HOH D:576 , HOH D:585 , HOH D:606 , HOH D:615 , HOH D:617 , HOH D:629 , HOH D:631 , HOH D:636 , HOH D:648binding site for residue NAI D 401
8AC8SOFTWAREASN D:122 , ARG D:153 , HIS D:177 , GLY D:220 , NAI D:401 , HOH D:719 , HOH D:730binding site for residue PO4 D 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Asn A:122 -Pro A:123
2Asn B:122 -Pro B:123
3Asn C:122 -Pro C:123
4Asn D:122 -Pro D:123

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4PLW)

(-) Sequences/Alignments

Asymmetric/Biological 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:317
                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh....eeee.hhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee.hhhhhhhhhhhhhhhhhh.hhh.ee..ee.......ee.hhh.ee..eehhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...eeeeeeeeee.hhh.eeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4plw A   3 QRKKISLIGAGNIGGTLAHLIAQKELGDVVLFDIVEGMPQGKALDISHSSPIMGSNVKITGTNNYEDIKGSDVVIITAGIPRKPGMSRDDLLSVNAKIMKDVAENIKKYCPNAFVIVVTNPLDVMVYVLHKYSGLPHNKVCGMAGVLDSSRFRYFLAEKLNVSPNDVQAMVIGGHGDTMVPLTRYCTVGGIPLTEFIKQGWITQEEIDEIVERTRNAGGEIVNLLKTGSAYFAPAASAIEMAESYLKDKKRILPCSAYLEGQYGVKDLFVGVPVIIGKNGVEKIIELELTEEEQEMFDKSVESVRELVETVKKLNAL 319
                                    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       


Chain B from PDB  Type:PROTEIN  Length:313
                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh....eeee.hhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee.hhhhhhhhhhhhhhhhhh.hhh.ee..ee.......ee.hhh.ee..eehhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...eeeeeeeeee.hhh.eeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4plw B   3 QRKKISLIGAGNIGGTLAHLIAQKELGDVVLFDIVEGMPQGKALDISHSSPIMGSNVKITGTNNYEDIKGSDVVIITAGIPRKPGMSRDDLLSVNAKIMKDVAENIKKYCPNAFVIVVTNPLDVMVYVLHKYSGLPHNKVCGMAGVLDSSRFRYFLAEKLNVSPNDVQAMVIGGHGDTMVPLTRYCTVGGIPLTEFIKQGWITQEEIDEIVERTRNAGGEIVNLLKTGSAYFAPAASAIEMAESYLKDKKRILPCSAYLEGQYGVKDLFVGVPVIIGKNGVEKIIELELTEEEQEMFDKSVESVRELVETVKK 315
                                    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   


Chain C from PDB  Type:PROTEIN  Length:316
                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh....eeee.hhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee.hhhhhhhhhhhhhhhhhh.hhh.ee..ee.......ee.hhh.ee..eehhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...eeeeeeeeee.hhh.eeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4plw C   3 QRKKISLIGAGNIGGTLAHLIAQKELGDVVLFDIVEGMPQGKALDISHSSPIMGSNVKITGTNNYEDIKGSDVVIITAGIPRKPGMSRDDLLSVNAKIMKDVAENIKKYCPNAFVIVVTNPLDVMVYVLHKYSGLPHNKVCGMAGVLDSSRFRYFLAEKLNVSPNDVQAMVIGGHGDTMVPLTRYCTVGGIPLTEFIKQGWITQEEIDEIVERTRNAGGEIVNLLKTGSAYFAPAASAIEMAESYLKDKKRILPCSAYLEGQYGVKDLFVGVPVIIGKNGVEKIIELELTEEEQEMFDKSVESVRELVETVKKLNA 318
                                    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      


Chain D from PDB  Type:PROTEIN  Length:315
                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh....eeee.hhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee.hhhhhhhhhhhhhhhhhh.hhh.ee..ee.......ee.hhh.ee..eehhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...eeeeeeeeee.hhh.eeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4plw D   3 QRKKISLIGAGNIGGTLAHLIAQKELGDVVLFDIVEGMPQGKALDISHSSPIMGSNVKITGTNNYEDIKGSDVVIITAGIPRKPGMSRDDLLSVNAKIMKDVAENIKKYCPNAFVIVVTNPLDVMVYVLHKYSGLPHNKVCGMAGVLDSSRFRYFLAEKLNVSPNDVQAMVIGGHGDTMVPLTRYCTVGGIPLTEFIKQGWITQEEIDEIVERTRNAGGEIVNLLKTGSAYFAPAASAIEMAESYLKDKKRILPCSAYLEGQYGVKDLFVGVPVIIGKNGVEKIIELELTEEEQEMFDKSVESVRELVETVKKLN 317
                                    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
   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 4PLW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4PLW)

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        A0A075B5H2_9 | A0A075B5H2: 4plh

(-) Related Entries Specified in the PDB File

4plc 4plf 4plg 4plh 4plt 4plv 4ply 4plz