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(-) Description

Title :  LEGIONELLA PNEUMOPHILA DIHYDRODIPICOLINATE SYNTHASE WITH FIRST SUBSTRATE PYRUVATE BOUND IN THE ACTIVE SITE
 
Authors :  T. Siddiqui, J. J. Paxman
Date :  23 Nov 13  (Deposition) - 01 Jan 14  (Release) - 01 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tim Barrel, Lysine Biosynthesis, Dihydrodipicolinate Synthesis, Pyruvate, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Siddiqui, J. J. Paxman, C. Dogovski, S. Panjikar, M. A. Perugini
Legionella Pneumophila Dhdps: The First Case Of Non-Lysine Inhibition In A Gram-Negative Pathogen
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 4-HYDROXY-TETRAHYDRODIPICOLINATE 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, LPA_03319
    Organism Scientific: LEGIONELLA PNEUMOPHILA
    Organism Taxid: 423212
    Strain: 2300/99 ALCOY
    Synonym: HTPA SYNTHASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 15)

Asymmetric/Biological Unit (5, 15)
No.NameCountTypeFull Name
1CL6Ligand/IonCHLORIDE ION
2KPI2Mod. Amino Acid(2S)-2-AMINO-6-[(1-HYDROXY-1-OXO-PROPAN-2-YLIDENE)AMINO]HEXANOIC ACID
3MG5Ligand/IonMAGNESIUM ION
4MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
5MRD1Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH B:481BINDING SITE FOR RESIDUE MRD A 301
02AC2SOFTWAREPRO A:12 , MET A:13 , LYS A:252 , GLY A:263 , GLU A:264BINDING SITE FOR RESIDUE CL A 302
03AC3SOFTWAREVAL A:134 , PRO A:135 , GLY A:136 , HOH A:536BINDING SITE FOR RESIDUE CL A 303
04AC4SOFTWARELEU A:188 , THR A:189 , ALA A:191 , GLN A:192 , GLN A:232 , HOH A:574 , HOH A:577BINDING SITE FOR RESIDUE CL A 304
05AC5SOFTWAREHOH A:628 , HOH A:631 , HOH A:825 , HOH A:826 , HOH A:827 , HOH A:838 , HOH B:619 , HOH B:858 , HOH B:859 , HOH B:860 , HOH B:861 , HOH B:862BINDING SITE FOR RESIDUE MG A 305
06AC6SOFTWAREHOH A:828 , HOH A:829 , HOH A:830 , HOH A:831 , HOH A:839 , HOH A:840 , HOH B:666 , HOH B:863 , HOH B:873 , HOH B:874 , HOH B:875 , HOH B:877BINDING SITE FOR RESIDUE MG A 306
07AC7SOFTWARETHR B:81 , LYS B:82 , ILE B:85 , HIS B:120 , HOH B:542 , HOH B:616 , HOH B:741BINDING SITE FOR RESIDUE MPD B 301
08AC8SOFTWAREHOH A:594 , VAL B:134 , PRO B:135 , GLY B:136 , HOH B:498BINDING SITE FOR RESIDUE CL B 302
09AC9SOFTWARELEU B:188 , THR B:189 , ALA B:191 , GLN B:192 , GLN B:232 , HOH B:599BINDING SITE FOR RESIDUE CL B 303
10BC1SOFTWAREPRO B:12 , MET B:13 , LYS B:252 , GLY B:263 , GLU B:264BINDING SITE FOR RESIDUE CL B 304
11BC2SOFTWAREHOH A:628 , HOH A:631 , HOH A:825 , HOH A:826 , HOH A:827 , HOH A:838 , HOH B:619 , HOH B:858 , HOH B:859 , HOH B:860 , HOH B:861 , HOH B:862BINDING SITE FOR RESIDUE MG B 305
12BC3SOFTWAREHOH A:828 , HOH A:829 , HOH A:830 , HOH A:831 , HOH A:839 , HOH A:840 , HOH B:666 , HOH B:863 , HOH B:873 , HOH B:874 , HOH B:875 , HOH B:877BINDING SITE FOR RESIDUE MG B 306
13BC4SOFTWAREHOH A:547 , HOH B:474 , HOH B:536 , HOH B:620 , HOH B:664 , HOH B:665BINDING SITE FOR RESIDUE MG B 307

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4NQ1)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Asn A:247 -Pro A:248
2Leu A:267 -Pro A:268
3Asn B:247 -Pro B:248
4Leu B:267 -Pro B:268

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NQ1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NQ1)

(-) Exons   (0, 0)

(no "Exon" information available for 4NQ1)

(-) Sequences/Alignments

Asymmetric/Biological 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:290
                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4nq1a_ A: automated matches                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee....ee..eehhhhhhhhhhhhhhhh..eeee.hhhhh....hhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhh...eeeeehhhhhh...hhhhhhhhhh...eeeeee...hhhhhhhhhhhhh...eeee.hhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh..............hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nq1 A   1 MFSGSIVALVTPMRNDSVDVHHLRELVEFHIAKGTHALVAAGTTGEAGTLSHSEKLLVIKTVIEQAKERVPVIAGTAMNATKDCIELTQQAMEYGAHAALIMTPAYIKPTQEGLYLHYSHIAQSVAIPIILYNVPGRTACDMLPETVARLAKISNIIGIkEATGQMTRLQQILRLCEGSIDVYSGDDLTAAQWLLSGAKGVISVTANVAAKLMAKMCDLAMDDDQAGCLRIQEQLMPLHELLFVESNPIPVKWAMKKMGLIGGELRLPMTELSEKHHQALEKVLKNLELI 290
                                    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
                                                                                                                                                                                         160-KPI                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:290
                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4nq1b_ B: automated matches                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee....ee..eehhhhhhhhhhhhhhhh..eeee.hhhhh....hhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhh...eeeeehhhhhh...hhhhhhhhhh...eeeeee...hhhhhhhhhhhhh...eeee.hhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh..............hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nq1 B   1 MFSGSIVALVTPMRNDSVDVHHLRELVEFHIAKGTHALVAAGTTGEAGTLSHSEKLLVIKTVIEQAKERVPVIAGTAMNATKDCIELTQQAMEYGAHAALIMTPAYIKPTQEGLYLHYSHIAQSVAIPIILYNVPGRTACDMLPETVARLAKISNIIGIkEATGQMTRLQQILRLCEGSIDVYSGDDLTAAQWLLSGAKGVISVTANVAAKLMAKMCDLAMDDDQAGCLRIQEQLMPLHELLFVESNPIPVKWAMKKMGLIGGELRLPMTELSEKHHQALEKVLKNLELI 290
                                    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
                                                                                                                                                                                         160-KPI
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NQ1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NQ1)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asn A:247 - Pro A:248   [ RasMol ]  
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