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(-) Description

Title :  HIGH-RESOLUTION STRUCTURE OF DHDPS FROM CLOSTRIDIUM BOTULINUM IN COMPLEX WITH PYRUVATE
 
Authors :  S. C. Atkinson, R. C. J. Dobson, M. A. Perugini
Date :  06 Aug 09  (Deposition) - 30 Jun 10  (Release) - 26 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.19
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Tim Barrel, Enzyme, Amino-Acid Biosynthesis, Diaminopimelate Biosynthesis, Lyase, Lysine Biosynthesis, Schiff Base (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. C. J. Dobson, S. C. Atkinson
The High Resolution Structure Of Dhdps From Clostridium Botulinum
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 Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: DAPA
    Organism Scientific: CLOSTRIDIUM BOTULINUM A
    Organism Taxid: 441770

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2KPI2Mod. Amino Acid(2S)-2-AMINO-6-[(1-HYDROXY-1-OXO-PROPAN-2-YLIDENE)AMINO]HEXANOIC ACID
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2KPI4Mod. Amino Acid(2S)-2-AMINO-6-[(1-HYDROXY-1-OXO-PROPAN-2-YLIDENE)AMINO]HEXANOIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:258 , ASP A:266 , LEU A:267 , HOH A:329 , HOH A:366 , HOH A:911BINDING SITE FOR RESIDUE GOL A 293
2AC2SOFTWAREASN B:258 , ASP B:266 , LEU B:267 , HOH B:341 , HOH B:353 , HOH B:747BINDING SITE FOR RESIDUE GOL B 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3A5F)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Asn A:249 -Pro A:250
2Leu A:269 -Pro A:270
3Asn B:249 -Pro B:250
4Leu B:269 -Pro B:270

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3A5F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3A5F)

(-) Exons   (0, 0)

(no "Exon" information available for 3A5F)

(-) 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:291
                                                                                                                                                                                                                                                                                                                                   
               SCOP domains d3a5fa_ A: Dihydrodipicolinate synthase                                                                                                                                                                                                                                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..........hhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhh....eeeeehhhhhh...hhhhhhhhh....eeeeee...hhhhhhhhhhhhhhhheeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh..............hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a5f A   2 SIFKGSGVAIITPFTNTGVDFDKLSELIEWHIKSKTDAIIVCGTTGEATTMTETERKETIKFVIDKVNKRIPVIAGTGSNNTAASIAMSKWAESIGVDGLLVITPYYNKTTQKGLVKHFKAVSDAVSTPIIIYNVPGRTGLNITPGTLKELCEDKNIVAVkEASGNISQIAQIKALCGDKLDIYSGNDDQIIPILALGGIGVISVLANVIPEDVHNMCELYLNGKVNEALKIQLDSLALTNALFIETNPIPVKTAMNLMNMKVGDLRLPLCEMNENNLEILKKELKAYNLM 292
                                    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 
                                                                                                                                                                                          162-KPI                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:291
                                                                                                                                                                                                                                                                                                                                   
               SCOP domains d3a5fb_ B: Dihydrodipicolinate synthase                                                                                                                                                                                                                                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee....ee..eehhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhh....eeeeehhhhhh...hhhhhhhhh....eeeeee...hhhhhhhhhhhhhhhheeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh..............hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a5f B   2 SIFKGSGVAIITPFTNTGVDFDKLSELIEWHIKSKTDAIIVCGTTGEATTMTETERKETIKFVIDKVNKRIPVIAGTGSNNTAASIAMSKWAESIGVDGLLVITPYYNKTTQKGLVKHFKAVSDAVSTPIIIYNVPGRTGLNITPGTLKELCEDKNIVAVkEASGNISQIAQIKALCGDKLDIYSGNDDQIIPILALGGIGVISVLANVIPEDVHNMCELYLNGKVNEALKIQLDSLALTNALFIETNPIPVKTAMNLMNMKVGDLRLPLCEMNENNLEILKKELKAYNLM 292
                                    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 
                                                                                                                                                                                          162-KPI
   Legend:   → Mismatch (orange background)
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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  (1, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3A5F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3A5F)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3A5F)

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 Related Entries

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