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(-) Description

Title :  SHEWANELLA BENTHICA DHDPS WITH LYSINE AND PYRUVATE
 
Authors :  J. M. Wubben, J. J. Paxman, C. Dogovski, S. Panjikar, M. A. Perugini
Date :  30 Apr 14  (Deposition) - 06 May 15  (Release) - 06 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.33
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dihydrodipicolinate Synthase, Lysine Biosynthesis, Tim Barrel, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. M. Wubben, J. J. Paxman, C. Dogovski, S. Panjikar, M. A. Perugini
Defining A Molecular Determinant Of Lysine-Mediated Allosteric Inhibition Of Dhdps.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 4-HYDROXY-TETRAHYDRODIPICOLINATE SYNTHASE
    Chains: A, B
    EC Number: 4.3.3.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: DAPA, KT99_11964
    Organism Scientific: SHEWANELLA BENTHICA KT99
    Organism Taxid: 314608
    Synonym: HTPA SYNTHASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 10)

Asymmetric/Biological Unit (5, 10)
No.NameCountTypeFull Name
1FLC1Ligand/IonCITRATE ANION
2GOL2Ligand/IonGLYCEROL
3KPI2Mod. Amino Acid(2S)-2-AMINO-6-[(1-HYDROXY-1-OXO-PROPAN-2-YLIDENE)AMINO]HEXANOIC ACID
4LYS3Mod. Amino AcidLYSINE
5NA2Ligand/IonSODIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:48 , ALA A:49 , LEU A:51 , HIS A:56 , TYR A:106 , LYS A:302 , HOH A:428 , HOH A:470 , ASN B:80 , GLU B:84binding site for residue LYS A 301
2AC2SOFTWAREASN A:80 , GLU A:84 , LYS A:301 , HOH A:403 , SER B:48 , ALA B:49 , LEU B:51 , HIS B:56 , TYR B:106binding site for residue LYS A 302
3AC3SOFTWAREGLU A:146 , ASP A:166 , ARG A:169 , GLN A:172binding site for residue GOL A 303
4AC4SOFTWAREVAL A:152 , VAL A:154 , ILE A:157 , HOH A:538binding site for residue NA A 304
5AC5SOFTWAREPRO A:52 , ALA B:81 , GLU B:84 , GLU B:87binding site for residue LYS B 301
6AC6SOFTWARETRP B:254 , HIS B:279 , HOH B:413binding site for residue FLC B 302
7AC7SOFTWARELYS B:94binding site for residue GOL B 303
8AC8SOFTWAREVAL B:152 , VAL B:154 , PRO B:155 , ILE B:157 , HOH B:540binding site for residue NA B 304

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Asn A:248 -Pro A:249
2Leu A:269 -Pro A:270
3Val A:293 -Lys A:294
4Asn B:248 -Pro B:249
5Leu B:269 -Pro B:270

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4PFM)

(-) 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:297
                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee..........hhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhh.....eeeee.......hhhhhhhhhhhhhhh....eeeeehhhhhh...hhhhhhhhh....eeeeee.....hhhhhhhhhhh...eeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh...............hhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pfm A   0 HMINGSIVALITPLNSDGTVDYTSLEKLVEYHITEGTDAIVAVGTTGESATLPISEHIAVVGQTVKFASGRIPVIGGNGANATAEAIELTKAQNKLGVAAMLGVTPYYNKPSPKGLIAHYTAVAASTDIPQILYNVPGRTAVDMLPETIAQLVEVPNIIGVkDATGDVARVKQLRDLCGNDFLLYSGDDATAREFLTLGGDGVISVANNIVPKLFKLMCDAALAGDTQAAMAAEDQIKGLFSALFCEANPIPVKWAAHKMGLISQGDIRLPLTELSTEFHGLLLDAMKNARIEVKKK 302
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159 |     169       179       189       199       209       219       229       239       249       259       269       279       289    || 
                                                                                                                                                                                           161-KPI                                                                                                                              294| 
                                                                                                                                                                                                                                                                                                                                 301 


Chain B from PDB  Type:PROTEIN  Length:296
                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee...........hhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhh.....eeeee.......hhhhhhhhhhhhhh.....eeeeehhhhhh...hhhhhhhhh....eeeeee.....hhhhhhhhhhh...eeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh...............hhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pfm B   0 HMINGSIVALITPLNSDGTVDYTSLEKLVEYHITEGTDAIVAVGTTGESATLPISEHIAVVGQTVKFASGRIPVIGGNGANATAEAIELTKAQNKLGVAAMLGVTPYYNKPSPKGLIAHYTAVAASTDIPQILYNVPGRTAVDMLPETIAQLVEVPNIIGVkDATGDVARVKQLRDLCGNDFLLYSGDDATAREFLTLGGDGVISVANNIVPKLFKLMCDAALAGDTQAAMAAEDQIKGLFSALFCEANPIPVKWAAHKMGLISQGDIRLPLTELSTEFHGLLLDAMKNARIEVKK 301
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159 |     169       179       189       199       209       219       229       239       249       259       269       279       289    ||
                                                                                                                                                                                           161-KPI                                                                                                                              294|
                                                                                                                                                                                                                                                                                                                                 301
   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  (0, 0)

(no "SCOP Domain" information available for 4PFM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asn A:248 - Pro A:249   [ RasMol ]  
    Asn B:248 - Pro B:249   [ RasMol ]  
    Leu A:269 - Pro A:270   [ RasMol ]  
    Leu B:269 - Pro B:270   [ RasMol ]  
    Val A:293 - Lys A:294   [ RasMol ]  
 

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