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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 :  19 May 14  (Deposition) - 02 Jul 14  (Release) - 25 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
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: B, A, 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
2OXM4Ligand/IonOXAMIC ACID

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY B:13 , ASN B:14 , ILE B:15 , PHE B:34 , ASP B:35 , ILE B:36 , VAL B:37 , MET B:40 , TYR B:67 , THR B:79 , ALA B:80 , GLY B:81 , ILE B:82 , PRO B:83 , ASN B:102 , ILE B:105 , VAL B:125 , ASN B:127 , LEU B:129 , MET B:150 , LEU B:154 , HIS B:182 , ALA B:237 , PRO B:241 , OXM B:402 , HOH B:519 , HOH B:522 , HOH B:525 , HOH B:549 , HOH B:564 , HOH B:612 , HOH B:619 , HOH B:632 , HOH B:733binding site for residue NAI B 401
2AC2SOFTWARETRP B:93 , ARG B:95 , ASN B:127 , ARG B:158 , HIS B:182 , GLY B:225 , ALA B:237 , NAI B:401 , HOH B:550 , HOH B:612binding site for residue OXM B 402
3AC3SOFTWAREGLY A:13 , ASN A:14 , ILE A:15 , PHE A:34 , ASP A:35 , ILE A:36 , VAL A:37 , MET A:40 , TYR A:67 , THR A:79 , ALA A:80 , GLY A:81 , ILE A:82 , PRO A:83 , ILE A:105 , VAL A:125 , THR A:126 , ASN A:127 , MET A:150 , LEU A:154 , HIS A:182 , ALA A:237 , OXM A:402 , HOH A:522 , HOH A:527 , HOH A:537 , HOH A:554 , HOH A:561 , HOH A:599 , HOH A:625 , HOH A:642 , HOH A:661 , HOH A:725binding site for residue NAI A 401
4AC4SOFTWARETRP A:93 , ARG A:95 , ASN A:127 , ARG A:158 , HIS A:182 , ALA A:237 , NAI A:401 , HOH A:537 , HOH A:544binding site for residue OXM A 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:102 , ILE C:105 , VAL C:125 , THR C:126 , ASN C:127 , LEU C:129 , MET C:150 , LEU C:154 , HIS C:182 , ALA C:237 , PRO C:241 , OXM C:402 , HOH C:527 , HOH C:545 , HOH C:563 , HOH C:572 , HOH C:573 , HOH C:583 , HOH C:589 , HOH C:604 , HOH C:673binding site for residue NAI C 401
6AC6SOFTWARETRP C:93 , ARG C:95 , ASN C:127 , ARG C:158 , HIS C:182 , GLY C:225 , NAI C:401 , HOH C:544 , HOH C:572binding site for residue OXM C 402
7AC7SOFTWAREGLY D:13 , ASN D:14 , ILE D:15 , PHE D:34 , ASP D:35 , ILE D:36 , VAL D:37 , MET D:40 , THR D:79 , ALA D:80 , GLY D:81 , ILE D:82 , PRO D:83 , LEU D:98 , ASN D:102 , ILE D:105 , VAL D:125 , ASN D:127 , MET D:150 , LEU D:154 , HIS D:182 , ALA D:237 , PRO D:241 , OXM D:402 , HOH D:520 , HOH D:548 , HOH D:549 , HOH D:556 , HOH D:566 , HOH D:574 , HOH D:609 , HOH D:619 , HOH D:629 , HOH D:652binding site for residue NAI D 401
8AC8SOFTWARETRP D:93 , ARG D:95 , ASN D:127 , ARG D:158 , HIS D:182 , NAI D:401 , HOH D:524 , HOH D:566binding site for residue OXM D 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Asn B:127 -Pro B:128
2Asn A:127 -Pro A:128
3Asn C:127 -Pro C:128
4Asn D:127 -Pro D:128

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4PLT)

(-) 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:319
                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..hhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh....eeee.hhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee.hhhhhhhhhhhhhhhhhh.hhh.ee..ee.......ee.hhh.ee..eehhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...eeeeeeeeee.hhh.eeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4plt A   2 TQRKKISLIGAGNIGGTLAHLIAQKELGDVVLFDIVEGMPQGKALDISHSSPIMGSNVKITGTNNYEDIKGSDVVIITAGIPRKPGKSDKEWSRDDLLSVNAKIMKDVAENIKKYCPNAFVIVVTNPLDVMVYVLHKYSGLPHNKVCGMAGVLDSSRFRYFLAEKLNVSPNDVQAMVIGGHGDTMVPLTRYCTVGGIPLTEFIKQGWITQEEIDEIVERTRNAGGEIVNLLKTGSAYFAPAASAIEMAESYLKDKKRILPCSAYLEGQYGVKDLFVGVPVIIGKNGVEKIIELELTEEEQEMFDKSVESVRELVETVKK 320
                                    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         


Chain B from PDB  Type:PROTEIN  Length:319
                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..hhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhh....eeee.hhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...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
                 4plt B   2 TQRKKISLIGAGNIGGTLAHLIAQKELGDVVLFDIVEGMPQGKALDISHSSPIMGSNVKITGTNNYEDIKGSDVVIITAGIPRKPGKSDKEWSRDDLLSVNAKIMKDVAENIKKYCPNAFVIVVTNPLDVMVYVLHKYSGLPHNKVCGMAGVLDSSRFRYFLAEKLNVSPNDVQAMVIGGHGDTMVPLTRYCTVGGIPLTEFIKQGWITQEEIDEIVERTRNAGGEIVNLLKTGSAYFAPAASAIEMAESYLKDKKRILPCSAYLEGQYGVKDLFVGVPVIIGKNGVEKIIELELTEEEQEMFDKSVESVRELVETVKK 320
                                    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         


Chain C from PDB  Type:PROTEIN  Length:318
                                                                                                                                                                                                                                                                                                                                                              
               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
                 4plt C   3 QRKKISLIGAGNIGGTLAHLIAQKELGDVVLFDIVEGMPQGKALDISHSSPIMGSNVKITGTNNYEDIKGSDVVIITAGIPRKPGKSDKEWSRDDLLSVNAKIMKDVAENIKKYCPNAFVIVVTNPLDVMVYVLHKYSGLPHNKVCGMAGVLDSSRFRYFLAEKLNVSPNDVQAMVIGGHGDTMVPLTRYCTVGGIPLTEFIKQGWITQEEIDEIVERTRNAGGEIVNLLKTGSAYFAPAASAIEMAESYLKDKKRILPCSAYLEGQYGVKDLFVGVPVIIGKNGVEKIIELELTEEEQEMFDKSVESVRELVETVKK 320
                                    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:318
                                                                                                                                                                                                                                                                                                                                                              
               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
                 4plt D   3 QRKKISLIGAGNIGGTLAHLIAQKELGDVVLFDIVEGMPQGKALDISHSSPIMGSNVKITGTNNYEDIKGSDVVIITAGIPRKPGKSDKEWSRDDLLSVNAKIMKDVAENIKKYCPNAFVIVVTNPLDVMVYVLHKYSGLPHNKVCGMAGVLDSSRFRYFLAEKLNVSPNDVQAMVIGGHGDTMVPLTRYCTVGGIPLTEFIKQGWITQEEIDEIVERTRNAGGEIVNLLKTGSAYFAPAASAIEMAESYLKDKKRILPCSAYLEGQYGVKDLFVGVPVIIGKNGVEKIIELELTEEEQEMFDKSVESVRELVETVKK 320
                                    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 4PLT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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    Asn A:127 - Pro A:128   [ RasMol ]  
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        A0A075B5H0_9 | A0A075B5H0: 4plv 4ply

(-) Related Entries Specified in the PDB File

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