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(-) Description

Title :  CRYSTAL STRUCTURE OF ANCESTRAL APICOMPLEXAN LACTATE DEHYDROGENASE WITH MALATE.
 
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 :  1.50
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 - LACTATE 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  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2NAI2Ligand/Ion1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
3PYR4Ligand/IonPYRUVIC ACID

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:97 , ARG A:99 , ASN A:131 , ARG A:162 , HIS A:186 , GLY A:229 , NAI A:402 , HOH A:578binding site for residue PYR A 401
2AC2SOFTWAREGLY A:17 , MET A:18 , ILE A:19 , PHE A:38 , ASP A:39 , VAL A:40 , VAL A:41 , TYR A:71 , THR A:83 , ALA A:84 , GLY A:85 , LEU A:86 , THR A:87 , LEU A:102 , ASN A:106 , ILE A:109 , GLU A:112 , ILE A:129 , THR A:130 , ASN A:131 , MET A:154 , LEU A:158 , HIS A:186 , ALA A:241 , PRO A:245 , PYR A:401 , HOH A:546 , HOH A:549 , HOH A:558 , HOH A:592 , HOH A:643 , HOH A:664 , HOH A:676 , HOH A:681 , HOH A:751 , HOH A:826binding site for residue NAI A 402
3AC3SOFTWARETRP B:97 , ARG B:99 , ASN B:131 , ARG B:162 , HIS B:186 , NAD B:402 , HOH B:651binding site for residue PYR B 401
4AC4SOFTWAREGLY B:17 , MET B:18 , ILE B:19 , PHE B:38 , ASP B:39 , VAL B:40 , VAL B:41 , MET B:44 , TYR B:71 , THR B:83 , ALA B:84 , GLY B:85 , LEU B:86 , THR B:87 , LEU B:102 , ASN B:106 , ILE B:109 , GLU B:112 , ILE B:129 , THR B:130 , ASN B:131 , MET B:154 , LEU B:158 , HIS B:186 , ALA B:241 , PYR B:401 , HOH B:527 , HOH B:590 , HOH B:593 , HOH B:603 , HOH B:669 , HOH B:701 , HOH B:706 , HOH B:767binding site for residue NAD B 402
5AC5SOFTWARETRP C:97 , ARG C:99 , ASN C:131 , ARG C:162 , HIS C:186 , GLY C:229 , NAI C:402 , HOH C:545binding site for residue PYR C 401
6AC6SOFTWAREGLY C:17 , MET C:18 , ILE C:19 , PHE C:38 , ASP C:39 , VAL C:40 , VAL C:41 , THR C:83 , ALA C:84 , GLY C:85 , LEU C:86 , THR C:87 , LEU C:102 , ASN C:106 , ILE C:109 , GLU C:112 , ILE C:129 , THR C:130 , ASN C:131 , MET C:154 , LEU C:158 , HIS C:186 , ALA C:241 , PRO C:245 , PYR C:401 , HOH C:551 , HOH C:556 , HOH C:559 , HOH C:635 , HOH C:636 , HOH C:640 , HOH C:741 , HOH C:764 , HOH C:767 , HOH C:840binding site for residue NAI C 402
7AC7SOFTWARETRP D:97 , ARG D:99 , ASN D:131 , ARG D:162 , HIS D:186 , GLY D:229 , NAD D:402 , HOH D:624binding site for residue PYR D 401
8AC8SOFTWAREGLY D:17 , MET D:18 , ILE D:19 , PHE D:38 , ASP D:39 , VAL D:40 , VAL D:41 , MET D:44 , TYR D:71 , THR D:83 , ALA D:84 , GLY D:85 , LEU D:86 , THR D:87 , ILE D:129 , ASN D:131 , MET D:154 , LEU D:158 , HIS D:186 , PYR D:401 , HOH D:531 , HOH D:576 , HOH D:646 , HOH D:680 , HOH D:689 , HOH D:735binding site for residue NAD D 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Asn A:131 -Pro A:132
2Asn B:131 -Pro B:132
3Asn C:131 -Pro C:132
4Asn D:131 -Pro D:132

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4PLC)

(-) 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:324
                                                                                                                                                                                                                                                                                                                                                                    
               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.....hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4plc A   5 MTKRKKISLIGSGMIGGTMAYLCAQKELGDVVLFDVVKNMPQGKALDLSHSSSIADTNVKVTGTNSYEDIKGSDVVIITAGLTKAPGKSDKEWSRDDLLPFNAKIMREVGENIKKYCPNAFVIVITNPLDVMVKVLHEHSGLPKNKVCGMAGVLDSSRFRHFIAEKLNVSPRDVQAMVIGAHGDKMVPLTRYVTVNGIPLQEFIKKGRITQEEIDEIVERTKNAGGEIVNLLGQGSAYFAPAASAIEMAEAYLKDKKRVLVCSCYLEGQYGHKDMFVGVPAVIGGNGVEKVIELELTPEEKELFDKSVEEVRKLQKAIKALGLE 328
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324    


Chain B from PDB  Type:PROTEIN  Length:324
                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeee..hhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhh.....eeee.hhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee.hhhhhhhhhhhhhhhhhh.hhh.ee..ee.......ee.hhh.ee..eehhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...eeeeeeeeee.hhh.eeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4plc B   5 MTKRKKISLIGSGMIGGTMAYLCAQKELGDVVLFDVVKNMPQGKALDLSHSSSIADTNVKVTGTNSYEDIKGSDVVIITAGLTKAPGKSDKEWSRDDLLPFNAKIMREVGENIKKYCPNAFVIVITNPLDVMVKVLHEHSGLPKNKVCGMAGVLDSSRFRHFIAEKLNVSPRDVQAMVIGAHGDKMVPLTRYVTVNGIPLQEFIKKGRITQEEIDEIVERTKNAGGEIVNLLGQGSAYFAPAASAIEMAEAYLKDKKRVLVCSCYLEGQYGHKDMFVGVPAVIGGNGVEKVIELELTPEEKELFDKSVEEVRKLQKAIKALGLE 328
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324    


Chain C from PDB  Type:PROTEIN  Length:324
                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeee..hhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhh.....eeee.hhhhhh...eeee...............hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee.hhhhhhhhhhhhhhhhhh.hhh.ee..ee.......ee.hhh.ee..eehhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...eeeeeeeeee.hhh.eeeeeeeeeeee..eeeee.....hhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4plc C   5 MTKRKKISLIGSGMIGGTMAYLCAQKELGDVVLFDVVKNMPQGKALDLSHSSSIADTNVKVTGTNSYEDIKGSDVVIITAGLTKAPGKSDKEWSRDDLLPFNAKIMREVGENIKKYCPNAFVIVITNPLDVMVKVLHEHSGLPKNKVCGMAGVLDSSRFRHFIAEKLNVSPRDVQAMVIGAHGDKMVPLTRYVTVNGIPLQEFIKKGRITQEEIDEIVERTKNAGGEIVNLLGQGSAYFAPAASAIEMAEAYLKDKKRVLVCSCYLEGQYGHKDMFVGVPAVIGGNGVEKVIELELTPEEKELFDKSVEEVRKLQKAIKALGLE 328
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324    


Chain D from PDB  Type:PROTEIN  Length:324
                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeee..hhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhh.....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
                 4plc D   5 MTKRKKISLIGSGMIGGTMAYLCAQKELGDVVLFDVVKNMPQGKALDLSHSSSIADTNVKVTGTNSYEDIKGSDVVIITAGLTKAPGKSDKEWSRDDLLPFNAKIMREVGENIKKYCPNAFVIVITNPLDVMVKVLHEHSGLPKNKVCGMAGVLDSSRFRHFIAEKLNVSPRDVQAMVIGAHGDKMVPLTRYVTVNGIPLQEFIKKGRITQEEIDEIVERTKNAGGEIVNLLGQGSAYFAPAASAIEMAEAYLKDKKRVLVCSCYLEGQYGHKDMFVGVPAVIGGNGVEKVIELELTPEEKELFDKSVEEVRKLQKAIKALGLE 328
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324
   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 4PLC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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    Asn A:131 - Pro A:132   [ RasMol ]  
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(-) Related Entries Specified in the PDB File

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