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(-) Description

Title :  CRYSTAL STRUCTURE OF ANCESTRAL APICOMPLEXAN MALATE DEHYDROGENASE WITH OXAMATE.
 
Authors :  J. I. Boucher, J. R. Jacobowitz, B. C. Beckett, S. Classen, D. L. Theobal
Date :  16 May 14  (Deposition) - 02 Jul 14  (Release) - 01 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Ancestral Sequence Reconstruction, Dehydrogenase, Apicomplexa, Specificity, Oxidoreductase (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: PLASID
    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  (3, 10)

Asymmetric/Biological Unit (3, 10)
No.NameCountTypeFull Name
1NA2Ligand/IonSODIUM ION
2NAI4Ligand/Ion1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
3OXM4Ligand/IonOXAMIC ACID

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:122 , ARG A:153 , HIS A:177 , GLY A:220 , NAI A:403 , HOH A:520 , HOH A:596 , HOH A:609binding site for residue OXM A 401
02AC2SOFTWAREGLY A:13 , ILE A:15 , GLY A:16 , THR A:79 , NAI A:403binding site for residue NA A 402
03AC3SOFTWAREGLY A:13 , ASN A:14 , ILE A:15 , PHE A:34 , ASP A:35 , ILE A:36 , VAL A:37 , MET A:40 , THR A:79 , ALA A:80 , GLY A:81 , ILE A:100 , VAL A:120 , ASN A:122 , MET A:145 , LEU A:149 , HIS A:177 , OXM A:401 , NA A:402 , HOH A:502 , HOH A:518 , HOH A:536 , HOH A:538 , HOH A:539 , HOH A:540 , HOH A:542 , HOH A:560 , HOH A:573 , GLY D:87binding site for residue NAI A 403
04AC4SOFTWAREASN B:122 , ARG B:153 , HIS B:177 , GLY B:220 , NAI B:402 , HOH B:528binding site for residue OXM B 401
05AC5SOFTWAREGLY B:13 , ASN B:14 , ILE B:15 , PHE B:34 , 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 , ASN B:122 , MET B:145 , LEU B:149 , HIS B:177 , ALA B:232 , OXM B:401 , HOH B:508 , HOH B:509 , HOH B:512 , HOH B:523 , HOH B:526 , HOH B:544 , HOH B:545 , HOH B:546 , HOH B:548 , HOH B:562binding site for residue NAI B 402
06AC6SOFTWAREASN C:122 , ARG C:153 , HIS C:177 , GLY C:220 , NAI C:402 , HOH C:587binding site for residue OXM C 401
07AC7SOFTWAREGLY C:13 , ASN C:14 , ILE C:15 , ASP C:35 , ILE C:36 , VAL C:37 , MET C:40 , THR C:79 , ALA C:80 , GLY C:81 , ILE C:100 , VAL C:120 , ASN C:122 , MET C:145 , LEU C:149 , HIS C:177 , OXM C:401 , HOH C:517 , HOH C:518 , HOH C:533 , HOH C:548 , HOH C:571binding site for residue NAI C 402
08AC8SOFTWAREASN D:122 , ARG D:153 , HIS D:177 , GLY D:220 , NAI D:403 , HOH D:529binding site for residue OXM D 401
09AC9SOFTWAREGLY D:13 , GLY D:16 , THR D:79 , NAI D:403binding site for residue NA D 402
10AD1SOFTWAREGLY 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 , MET D:145 , LEU D:149 , HIS D:177 , OXM D:401 , NA D:402 , HOH D:525 , HOH D:544 , HOH D:545 , HOH D:561 , HOH D:569 , HOH D:596 , HOH D:610 , HOH D:633binding site for residue NAI D 403

(-) SS Bonds  (0, 0)

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

(-) 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 4PLH)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4PLH)

(-) 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:313
                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh....eeee.hhhhhh...eeee.......hhhhhhhhhhhhhhhhhhhhhhh...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
                 4plh A   3 QRKKISLIGAGNIGGTLAHLIAQKELGDVVLFDIVEGMPQGKALDISHSSPIMGSNVKITGTNNYEDIKGSDVVIITAGIPRSRDDLLSVNAKIMKDVAENIKKYCPNAFVIVVTNPLDVMVYVLHKYSGLPHNKVCGMAGVLDSSRFRYFLAEKLNVSPNDVQAMVIGGHGDTMVPLTRYCTVGGIPLTEFIKQGWITQEEIDEIVERTRNAGGEIVNLLKTGSAYFAPAASAIEMAESYLKDKKRILPCSAYLEGQYGVKDLFVGVPVIIGKNGVEKIIELELTEEEQEMFDKSVESVRELVETVKKLNAL 319
                                    12        22        32        42        52        62        72        82 ||     96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316   
                                                                                                            84|                                                                                                                                                                                                                                      
                                                                                                             89                                                                                                                                                                                                                                      


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
                 4plh 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:305
                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh....eeee.hhhhhh...eeee.....hhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee.hhhhhhhhhhhhhhhhhh.hhh.ee..ee..hhhhhee.hhh.ee..eehhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...eeeeeeeeee.hhh.eeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4plh C   3 QRKKISLIGAGNIGGTLAHLIAQKELGDVVLFDIVEGMPQGKALDISHSSPIMGSNVKITGTNNYEDIKGSDVVIITAGIDLLSVNAKIMKDVAENIKKYCPNAFVIVVTNPLDVMVYVLHKYSGLPHNKVCGMAGVLDSSRFRYFLAEKLNVSPNDVQAMVIGGHGDTMVPLTRYCTVGGIPLTEFIKQGWITQEEIDEIVERTRNAGGEIVNLLKTGSAYFAPAASAIEMAESYLKDKKRILPCSAYLEGQYGVKDLFVGVPVIIGKNGVEKIIELELTEEEQEMFDKSVESVRELVETVKKL 316
                                    12        22        32        42        52        62        72        82|      101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311     
                                                                                                          82|                                                                                                                                                                                                                                
                                                                                                           92                                                                                                                                                                                                                                


Chain D 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...........hhhhhhhhhhhhhhhhhhhhhhh...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
                 4plh D   2 TQRKKISLIGAGNIGGTLAHLIAQKELGDVVLFDIVEGMPQGKALDISHSSPIMGSNVKITGTNNYEDIKGSDVVIITAGIPRKPGMSRDDLLSVNAKIMKDVAENIKKYCPNAFVIVVTNPLDVMVYVLHKYSGLPHNKVCGMAGVLDSSRFRYFLAEKLNVSPNDVQAMVIGGHGDTMVPLTRYCTVGGIPLTEFIKQGWITQEEIDEIVERTRNAGGEIVNLLKTGSAYFAPAASAIEMAESYLKDKKRILPCSAYLEGQYGVKDLFVGVPVIIGKNGVEKIIELELTEEEQEMFDKSVESVRELVETVKKLN 317
                                    11        21        31        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
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 4PLH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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        A0A075B5H2_9 | A0A075B5H2: 4plw

(-) Related Entries Specified in the PDB File

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