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(-) Description

Title :  STRUCTURE OF DIHYDRODIPICOLINATE SYNTHASE FROM STREPTOCOCCUS PNEUMONIAE,BOUND TO PYRUVATE AND LYSINE
 
Authors :  M. A. Perugini, C. Dogovski, M. W. Parker, M. A. Gorman
Date :  06 Jun 12  (Deposition) - 18 Sep 13  (Release) - 18 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.88
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  8-Fold Alpha-/Beta-Barrel, Lyase, L-Aspartate-4-Semialdehyde Hydro- Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Perugini, C. Dogovski, M. W. Parker, M. A. Gorman, R. C. J. Dobson, G. B. Jameson, N. E. Ketaren, J. Praszkier, M. F. Bailey, G. Bryant, J. Yang, M. D. W. Griffin, F. G. Pearce, V. Mitsakos
Structure, Function, Stability And Knockout Phenotype Of Dihydrodipicolinate Synthase From Streptococcus Pneumoniae
To Be Published
PubMed: search

(-) 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
    Organism Scientific: STREPTOCOCCUS PNEUMONIAE
    Organism Taxid: 406556
    Strain: SP3-BS71

 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, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1KPI2Mod. Amino Acid(2S)-2-AMINO-6-[(1-HYDROXY-1-OXO-PROPAN-2-YLIDENE)AMINO]HEXANOIC ACID
2LYS2Mod. Amino AcidLYSINE
3NA2Ligand/IonSODIUM ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1KPI4Mod. Amino Acid(2S)-2-AMINO-6-[(1-HYDROXY-1-OXO-PROPAN-2-YLIDENE)AMINO]HEXANOIC ACID
2LYS4Mod. Amino AcidLYSINE
3NA-1Ligand/IonSODIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:54 , PRO A:55 , LEU A:57 , HIS A:59 , GLU A:62 , ASN A:86 , TYR A:113 , HOH A:538 , HOH A:615 , HOH A:630 , ASN B:86 , LYS B:401BINDING SITE FOR RESIDUE LYS A 401
2AC2SOFTWAREALA A:159 , HIS A:161 , ILE A:164 , HOH A:655BINDING SITE FOR RESIDUE NA A 402
3AC3SOFTWAREASN A:86 , LYS A:401 , SER B:54 , PRO B:55 , LEU B:57 , HIS B:59 , GLU B:62 , TYR B:113 , HOH B:533 , HOH B:615 , HOH B:616 , HOH B:633BINDING SITE FOR RESIDUE LYS B 401
4AC4SOFTWAREALA B:159 , HIS B:161 , ILE B:164 , HOH B:638 , HOH B:666BINDING SITE FOR RESIDUE NA B 402

(-) SS Bonds  (0, 0)

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

(-) 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 4FHA)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4FHA)

(-) 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 d4fhaa_ A: automated matches                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh...eeee..............hhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhh...eeeeehhhhhh...hhhhhhhhhh...eeeeee..hhhhhhhhhhhh....eeee.hhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh..............hhhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fha A   2 SYQDLKECKIITAFITPFHEDGSINFDAIPALIEHLLAHHTDGILLAGTTAESPTLTHDEELELFAAVQKVVNGRVPLIAGVGTNDTRDSIEFVKEVAEFGGFAAGLAIVPYYNKPSQEGMYQHFKAIADASDLPIIIYNIPGRVVVELTPETMLRLADHPNIIGVkECTSLANMAYLIEHKPEEFLIYTGEDGDAFHAMNLGADGVISVASHTNGDEMHEMFTAIAESDMKKAAAIQRKFIPKVNALFSYPSPAPVKAILNYMGFEAGPTRLPLVPAPEEDVKRIIKVVVDGDYEATVTGVLRPDYK 401
                                    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      |304      ||
                                                                                                                                                                                                168-KPI                                                                                                                           298|      311|
                                                                                                                                                                                                                                                                                                                                   302       401


Chain B from PDB  Type:PROTEIN  Length:308
                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d4fhab_ B: automated matches                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh...eeee...........hhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhh...eeeeehhhhhh...hhhhhhhhhh...eeeeee..hhhhhhhhhhhh....eeee....hhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh..............hhhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fha B   2 SYQDLKECKIITAFITPFHEDGSINFDAIPALIEHLLAHHTDGILLAGTTAESPTLTHDEELELFAAVQKVVNGRVPLIAGVGTNDTRDSIEFVKEVAEFGGFAAGLAIVPYYNKPSQEGMYQHFKAIADASDLPIIIYNIPGRVVVELTPETMLRLADHPNIIGVkECTSLANMAYLIEHKPEEFLIYTGEDGDAFHAMNLGADGVISVASHTNGDEMHEMFTAIAESDMKKAAAIQRKFIPKVNALFSYPSPAPVKAILNYMGFEAGPTRLPLVPAPEEDVKRIIKVVVDGDYEATVTGVLRPDYK 401
                                    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      |304      ||
                                                                                                                                                                                                168-KPI                                                                                                                           298|      311|
                                                                                                                                                                                                                                                                                                                                   302       401
   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 4FHA)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

(no "Entries Sharing at Least One Protein Chain" available for 4FHA)

(-) Related Entries Specified in the PDB File

3daq CRYSTAL STRUCTURE OF DIHYDRODIPICOLINATE SYNTHASE FROM METHICILLIN-RESISTANT STAPHYLOCOCCUS AUREUS
3h5d DIHYDRODIPICOLINATE SYNTHASE FROM DRUG-RESISTANT STREPTOCOCCUS PNEUMONIAE
3i7s DIHYDRODIPICOLINATE SYNTHASE MUTANT