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(-) Description

Title :  CRYSTAL STRUCTURE OF ANCESTRAL APICOMPLEXAN LACTATE 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 :  1.19
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, 12)

Asymmetric Unit (3, 12)
No.NameCountTypeFull Name
1NA8Ligand/IonSODIUM ION
2NAI2Ligand/Ion1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
3OXM2Ligand/IonOXAMIC ACID
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
2NAI4Ligand/Ion1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
3OXM4Ligand/IonOXAMIC ACID

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:99 , ASN A:131 , ARG A:162 , HIS A:186 , GLY A:229 , NA A:406 , NAI A:409binding site for residue OXM A 401
02AC2SOFTWAREGLY A:17 , ILE A:19 , GLY A:20 , THR A:83 , NAI A:409binding site for residue NA A 402
03AC3SOFTWARELEU A:13 , ILE A:14 , GLY A:15 , MET A:23 , ILE A:81 , THR A:83binding site for residue NA A 403
04AC4SOFTWAREMET A:154 , ALA A:155 , GLY A:156 , VAL A:157 , MET A:252 , VAL A:265 , CYS A:266binding site for residue NA A 404
05AC5SOFTWAREGLY A:156 , VAL A:182 , ILE A:183 , GLY A:184 , VAL A:265 , GLY A:282 , HOH A:639 , HOH A:668binding site for residue NA A 405
06AC6SOFTWAREGLY A:229 , SER A:240 , ALA A:241 , OXM A:401binding site for residue NA A 406
07AC7SOFTWAREASP A:159 , ARG A:162 , MET A:190 , THR A:225 , NA A:408binding site for residue NA A 407
08AC8SOFTWAREARG A:99 , THR A:225 , LYS A:226 , ALA A:228 , GLY A:229 , NA A:407binding site for residue NA A 408
09AC9SOFTWAREGLY 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 , OXM A:401 , NA A:402 , HOH A:636 , HOH A:637 , HOH A:643 , HOH A:656 , HOH A:698 , HOH A:699 , HOH A:710binding site for residue NAI A 409
10AD1SOFTWARETRP B:97 , ARG B:99 , ASN B:131 , ARG B:162 , HIS B:186 , GLY B:229 , NAI B:403 , HOH B:629binding site for residue OXM B 401
11AD2SOFTWAREPRO B:122 , ASN B:123 , ALA B:124 , LEU B:146 , LYS B:150binding site for residue NA B 402
12AD3SOFTWAREGLY 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 , ILE B:129 , ASN B:131 , MET B:154 , LEU B:158 , HIS B:186 , PRO B:245 , OXM B:401 , HOH B:608 , HOH B:639 , HOH B:690 , HOH B:698 , HOH B:727 , HOH B:743 , HOH B:791 , HOH B:803binding site for residue NAI B 403

(-) SS Bonds  (0, 0)

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

(-) 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 4PLG)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4PLG)

(-) 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: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
                 4plg 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:321
                                                                                                                                                                                                                                                                                                                                                                 
               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
                 4plg B   5 MTKRKKISLIGSGMIGGTMAYLCAQKELGDVVLFDVVKNMPQGKALDLSHSSSIADTNVKVTGTNSYEDIKGSDVVIITAGLTKAPGKSDKEWSRDDLLPFNAKIMREVGENIKKYCPNAFVIVITNPLDVMVKVLHEHSGLPKNKVCGMAGVLDSSRFRHFIAEKLNVSPRDVQAMVIGAHGDKMVPLTRYVTVNGIPLQEFIKKGRITQEEIDEIVERTKNAGGEIVNLLGQGSAYFAPAASAIEMAEAYLKDKKRVLVCSCYLEGQYGHKDMFVGVPAVIGGNGVEKVIELELTPEEKELFDKSVEEVRKLQKAIKAL 325
                                    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
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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 4PLG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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        A0A075B5G8_9 | A0A075B5G8: 4plc 4plf

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