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(-) Description

Title :  STRUCTURE, FUNCTION, STABILITY AND KNOCKOUT PHENOTYPE OF DIHYDRODIPICOLINATE SYNTHASE FROM STREPTOCOCCUS PNEUMONIAE
 
Authors :  M. A. Gorman
Date :  10 Jan 12  (Deposition) - 12 Jun 13  (Release) - 12 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.91
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Lyase, Dihydrodipicolinate Synthase, Lysine Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Dogovski, M. A. Gorman, N. E. Ketaren, J. Praszkier, G. Bryant, J. Yang, M. D. W. Griffin, F. G. Pearce, S. K. Bhargava, R. C. J. Dobson, C. A. Hutton, J. A. Gerrard, R. M. Robins-Browne, G. B. Jameson, M. W. Parker, M. A. Perugini
Structure, Function, Stability And Knockout Phenotype Of Dihydrodipicolinate Synthase From Streptococcus Pneumoniae
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DIHYDRODIPICOLINATE SYNTHASE
    Chains: A, B
    EC Number: 4.2.1.52
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET101/D-TOPO
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CGSSP3BS71_00085, DAPA
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 406556
    Strain: A5LD17

 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, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2K4Ligand/IonPOTASSIUM ION
3MES2Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1GOL8Ligand/IonGLYCEROL
2K-1Ligand/IonPOTASSIUM ION
3MES4Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:159 , HIS A:161 , ILE A:164BINDING SITE FOR RESIDUE K A 401
02AC2SOFTWARESER A:54 , LEU A:57 , GLU A:62BINDING SITE FOR RESIDUE K A 402
03AC3SOFTWAREALA A:14 , LEU A:46 , GLY A:49 , THR A:50 , THR A:51 , TYR A:140 , LYS A:168 , ILE A:209 , GOL A:404 , MES A:406 , HOH A:619 , TYR B:114BINDING SITE FOR RESIDUE GOL A 403
04AC4SOFTWAREALA A:48 , GLY A:49 , THR A:50 , SER A:54 , GLY A:84 , LEU A:108 , ALA A:109 , ILE A:110 , GOL A:403 , TYR B:114BINDING SITE FOR RESIDUE GOL A 404
05AC5SOFTWARETHR A:56 , ARG A:273 , LEU A:274 , LEU A:307 , ARG A:308 , ASP B:87 , THR B:88 , ARG B:89BINDING SITE FOR RESIDUE GOL A 405
06AC6SOFTWARETYR A:140 , ILE A:142 , ARG A:145 , GLY A:192 , GLU A:193 , PHE A:250 , GOL A:403 , HOH A:606 , HOH A:619BINDING SITE FOR RESIDUE MES A 406
07AC7SOFTWAREALA B:159 , HIS B:161 , ILE B:164BINDING SITE FOR RESIDUE K B 401
08AC8SOFTWARESER B:54 , LEU B:57 , GLU B:62 , HOH B:572BINDING SITE FOR RESIDUE K B 402
09AC9SOFTWARETYR A:114 , ALA B:14 , LEU B:46 , GLY B:49 , THR B:50 , THR B:51 , LEU B:108 , TYR B:140 , LYS B:168 , MES B:404 , HOH B:528 , HOH B:542BINDING SITE FOR RESIDUE GOL B 403
10BC1SOFTWARETHR B:51 , TYR B:140 , ARG B:145 , GLU B:193 , PHE B:250 , GOL B:403 , HOH B:566 , HOH B:604BINDING SITE FOR RESIDUE MES B 404

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3VFL)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ser A:254 -Pro A:255
2Leu A:274 -Pro A:275
3Ser B:254 -Pro B:255
4Leu B:274 -Pro B:275

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3VFL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3VFL)

(-) Exons   (0, 0)

(no "Exon" information available for 3VFL)

(-) 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:308
                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d3vfla_ A: automated matches                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh...eeee..............hhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhh....eeeeehhhhhh...hhhhhhhhhh...eeeeee..hhhhhhhhhhhh....eeee.hhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh..............hhhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vfl A   2 SYQDLKECKIITAFITPFHEDGSINFDAIPALIEHLLAHHTDGILLAGTTAESPTLTHDEELELFAAVQKVVNGRVPLIAGVGTNDTRDSIEFVKEVAEFGGFAAGLAIVPYYNKPSQEGMYQHFKAIADASDLPIIIYNIPGRVVVELTPETMLRLADHPNIIGVKECTSLANMAYLIEHKPEEFLIYTGEDGDAFHAMNLGADGVISVASHTNGDEMHEMFTAIAESDMKKAAAIQRKFIPKVNALFSYPSPAPVKAILNYMGFEAGPTRLPLVPAPEEDVKRIIKVVVDGDYEATTVTGVLRPDY 311
                                    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       303        
                                                                                                                                                                                                                                                                                                                                   299|         
                                                                                                                                                                                                                                                                                                                                    302         


Chain B from PDB  Type:PROTEIN  Length:306
                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d3vflb_ B: automated matches                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhh...eeee...........hhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhh....eeeeehhhhhh...hhhhhhhhhh...eeeeee..hhhhhhhhhhhh....eeee.hhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh..............hhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3vfl B   2 SYQDLKECKIITAFITPFHEDGSINFDAIPALIEHLLAHHTDGILLAGTTAESPTLTHDEELELFAAVQKVVNGRVPLIAGVGTNDTRDSIEFVKEVAEFGGFAAGLAIVPYYNKPSQEGMYQHFKAIADASDLPIIIYNIPGRVVVELTPETMLRLADHPNIIGVKECTSLANMAYLIEHKPEEFLIYTGEDGDAFHAMNLGADGVISVASHTNGDEMHEMFTAIAESDMKKAAAIQRKFIPKVNALFSYPSPAPVKAILNYMGFEAGPTRLPLVPAPEEDVKRIIKVVVDGDYETVTGVLRPDY 311
                                    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     ||305      
                                                                                                                                                                                                                                                                                                                                 297|         
                                                                                                                                                                                                                                                                                                                                  302
   Legend:   → Mismatch (orange background)
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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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VFL)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VFL)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3VFL)

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  Cis Peptide Bonds
    Leu A:274 - Pro A:275   [ RasMol ]  
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  4.2.1.52
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(-) Related Entries Specified in the PDB File

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3hij CRYSTAL STRUCTURE OF DIHYDRODIPICOLINATE SYNTHASE FROM BACILLUS ANTHRACIS IN COMPLEX WITH ITS SUBSTRATE, PYRUVATE