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(-) Description

Title :  CRYSTAL STRUCTURE OF ANCESTRAL APICOMPLEXAN LACTATE DEHYDROGENASE WITH LACTATE.
 
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 :  1.35
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
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
    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

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2NAI1Ligand/Ion1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
3PYR2Ligand/IonPYRUVIC ACID
Biological Unit 1 (3, 8)
No.NameCountTypeFull Name
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
2NAI2Ligand/Ion1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
3PYR4Ligand/IonPYRUVIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:17 , MET A:18 , ILE A:19 , PHE A:38 , ASP A:39 , VAL A:40 , VAL A:41 , MET A:44 , THR A:83 , ALA A:84 , GLY A:85 , LEU A:86 , THR A:87 , ASN A:106 , ILE A:109 , ILE A:129 , ASN A:131 , MET A:154 , LEU A:158 , HIS A:186 , ALA A:241 , PRO A:245 , PYR A:402 , HOH A:531 , HOH A:536 , HOH A:675 , HOH A:682 , HOH A:690 , HOH A:694 , HOH A:755 , HOH A:766 , HOH A:818 , HOH A:836 , HOH A:917 , HOH A:1054binding site for residue NAI A 401
2AC2SOFTWAREARG A:99 , ASN A:131 , ARG A:162 , HIS A:186 , GLY A:229 , NAI A:401 , HOH A:680binding site for residue PYR A 402
3AC3SOFTWAREGLY B:17 , MET B:18 , ILE B:19 , PHE B:38 , ASP B:39 , VAL B:40 , VAL B:41 , 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 , ILE B:129 , THR B:130 , ASN B:131 , MET B:154 , LEU B:158 , HIS B:186 , PYR B:402 , HOH B:633 , HOH B:672 , HOH B:707 , HOH B:721 , HOH B:737 , HOH B:744 , HOH B:751 , HOH B:775 , HOH B:798 , HOH B:828 , HOH B:931binding site for residue NAD B 401
4AC4SOFTWARETRP B:97 , ARG B:99 , ASN B:131 , ARG B:162 , HIS B:186 , GLY B:229 , NAD B:401 , HOH B:653binding site for residue PYR B 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asn A:131 -Pro A:132
2Asn B:131 -Pro B:132

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4PLF)

(-) 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:325
                                                                                                                                                                                                                                                                                                                                                                     
               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
                 4plf A   5 MTKRKKISLIGSGMIGGTMAYLCAQKELGDVVLFDVVKNMPQGKALDLSHSSSIADTNVKVTGTNSYEDIKGSDVVIITAGLTKAPGKSDKEWSRDDLLPFNAKIMREVGENIKKYCPNAFVIVITNPLDVMVKVLHEHSGLPKNKVCGMAGVLDSSRFRHFIAEKLNVSPRDVQAMVIGAHGDKMVPLTRYVTVNGIPLQEFIKKGRITQEEIDEIVERTKNAGGEIVNLLGQGSAYFAPAASAIEMAEAYLKDKKRVLVCSCYLEGQYGHKDMFVGVPAVIGGNGVEKVIELELTPEEKELFDKSVEEVRKLQKAIKALGLEH 329
                                    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:330
                                                                                                                                                                                                                                                                                                                                                                          
               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.....hhhhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4plf B   5 MTKRKKISLIGSGMIGGTMAYLCAQKELGDVVLFDVVKNMPQGKALDLSHSSSIADTNVKVTGTNSYEDIKGSDVVIITAGLTKAPGKSDKEWSRDDLLPFNAKIMREVGENIKKYCPNAFVIVITNPLDVMVKVLHEHSGLPKNKVCGMAGVLDSSRFRHFIAEKLNVSPRDVQAMVIGAHGDKMVPLTRYVTVNGIPLQEFIKKGRITQEEIDEIVERTKNAGGEIVNLLGQGSAYFAPAASAIEMAEAYLKDKKRVLVCSCYLEGQYGHKDMFVGVPAVIGGNGVEKVIELELTPEEKELFDKSVEEVRKLQKAIKALGLEHHHHHH 334
                                    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       334
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  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 4PLF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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    (no "Gene Ontology" information available for 4PLF)

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        A0A075B5G8_9 | A0A075B5G8: 4plc 4plg

(-) Related Entries Specified in the PDB File

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