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(-) Description

Title :  CRYSTAL STRUCTURE OF E. COLI DIHYDRODIPICOLINATE SYNTHASE WITH PYRUVATE AND SUCCINIC SEMI-ALDEHYDE BOUND IN ACTIVE SITE
 
Authors :  B. A. Boughton, R. C. J. Dobson, C. A. Hutton
Date :  15 Apr 12  (Deposition) - 25 Apr 12  (Release) - 25 Jul 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Alpha/Beta Barrel, Tim Barrel, Amino-Acid Biosynthesis, Schiff Base, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. A. Boughton, R. C. Dobson, C. A. Hutton
The Crystal Structure Of Dihydrodipicolinate Synthase From Escherichia Coli With Bound Pyruvate And Succinic Acid Semialdehyde: Unambiguous Resolution Of The Stereochemistry Of The Condensation Product.
Proteins V. 80 2117 2012
PubMed-ID: 22552955  |  Reference-DOI: 10.1002/PROT.24106

(-) Compounds

Molecule 1 - DIHYDRODIPICOLINATE SYNTHASE
    Chains: A, B
    EC Number: 4.2.1.52
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: HARBORING PLASMID PJG001
    Strain: XL1-BLUE
    Synonym: DHDPS

 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, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2K4Ligand/IonPOTASSIUM ION
3LYF2Mod. Amino Acid(2E,4S)-2-{[(5S)-5-AMINO-5-CARBOXYPENTYL]IMINO}-4-HYDROXYHEPTANEDIOIC ACID
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2K-1Ligand/IonPOTASSIUM ION
3LYF4Mod. Amino Acid(2E,4S)-2-{[(5S)-5-AMINO-5-CARBOXYPENTYL]IMINO}-4-HYDROXYHEPTANEDIOIC ACID

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:152 , VAL A:154 , LYS A:155 , ILE A:157 , HOH A:514 , HOH A:568BINDING SITE FOR RESIDUE K A 301
2AC2SOFTWARESER A:48 , ALA A:49 , TYR A:106 , HOH A:462 , HOH A:585 , ASN B:80 , TYR B:107BINDING SITE FOR RESIDUE GOL A 302
3AC3SOFTWAREALA A:123 , GLU A:124 , THR A:126 , HOH A:512BINDING SITE FOR RESIDUE K A 303
4AC4SOFTWAREALA B:152 , VAL B:154 , LYS B:155 , ILE B:157 , HOH B:561BINDING SITE FOR RESIDUE K B 301
5AC5SOFTWAREASN A:80 , SER B:48 , ALA B:49 , GLY B:78 , VAL B:103 , TYR B:106 , HOH B:411 , HOH B:431 , HOH B:547BINDING SITE FOR RESIDUE GOL B 302
6AC6SOFTWAREALA B:123 , THR B:126 , HOH B:500BINDING SITE FOR RESIDUE K B 303

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Asn A:248 -Pro A:249
2Leu A:269 -Pro A:270
3Asn B:248 -Pro B:249
4Leu B:269 -Pro B:270

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4EOU)

(-) 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:292
                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d4eoua_ A: Dihydrodipicolinate synthase                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...........hhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhh......eeeee.......hhhhhhhhhhhhhhh....eeeeehhhhhh...hhhhhhhhh....eeeeee.....hhhhhhhh......eeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh...............hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eou A   1 MFTGSIVAIVTPMDEKGNVCRASLKKLIDYHVASGTSAIVSVGTTGESATLNHDEHADVVMMTLDLADGRIPVIAGTGANATAEAISLTQRFNDSGIVGCLTVTPYYNRPSQEGLYQHFKAIAEHTDLPQILYNVPSRTGCDLLPETVGRLAKVKNIIGIkEATGNLTRVNQIKELVSDDFVLLSGDDASALDFMQLGGHGVISVTANVAARDMAQMCKLAAEGHFAEARVINQRLMPLHNKLFVEPNPIPVKWACKELGLVATDTLRLPMTPITDSGRETVRAALKHAGLL 292
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160|      170       180       190       200       210       220       230       240       250       260       270       280       290  
                                                                                                                                                                                          161-LYF                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:292
                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d4eoub_ B: Dihydrodipicolinate synthase                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...........hhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhh.......eeeee.......hhhhhhhhhhhhhhh....eeeeehhhhhh...hhhhhhhhh....eeeeee.....hhhhhhhh......eeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh...............hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eou B   1 MFTGSIVAIVTPMDEKGNVCRASLKKLIDYHVASGTSAIVSVGTTGESATLNHDEHADVVMMTLDLADGRIPVIAGTGANATAEAISLTQRFNDSGIVGCLTVTPYYNRPSQEGLYQHFKAIAEHTDLPQILYNVPSRTGCDLLPETVGRLAKVKNIIGIkEATGNLTRVNQIKELVSDDFVLLSGDDASALDFMQLGGHGVISVTANVAARDMAQMCKLAAEGHFAEARVINQRLMPLHNKLFVEPNPIPVKWACKELGLVATDTLRLPMTPITDSGRETVRAALKHAGLL 292
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160|      170       180       190       200       210       220       230       240       250       260       270       280       290  
                                                                                                                                                                                          161-LYF
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 4EOU)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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UniProtKB/Swiss-Prot
        DAPA_ECOLI | P0A6L2: 1dhp 1s5t 1s5v 1s5w 1yxc 1yxd 2a6l 2a6n 2ats 2ojp 2pur 3c0j 3den 3du0 3i7q 3i7r 3i7s 5t25 5t26

(-) Related Entries Specified in the PDB File

1dhp 1yxc 3du0