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(-) Description

Title :  DIHYDRODIPICOLINATE SYNTHASE FROM SHEWANELLA BENTHICA
 
Authors :  J. M. Wubben, J. J. Paxman, C. Dogovski, M. W. Parker, M. A. Perugini
Date :  10 Dec 12  (Deposition) - 11 Dec 13  (Release) - 11 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
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, M. W. Parker, M. A. Perugini
Cold Enzymology Offers Insight Into Molecular Evolution In Quaternary Structure
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DIHYDRODIPICOLINATE SYNTHASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DAPA
    Organism Scientific: SHEWANELLA BENTHICA
    Organism Taxid: 43661
    Strain: ATCC 43992

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2GOL3Ligand/IonGLYCEROL
3SO42Ligand/IonSULFATE ION
4TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:275 , THR A:276 , GLU A:277 , LYS B:113BINDING SITE FOR RESIDUE TRS A 301
2AC2SOFTWAREALA A:8 , GLY A:43 , THR A:44 , THR A:45 , GLY A:46 , TYR A:133 , LYS A:161 , SO4 A:304BINDING SITE FOR RESIDUE GOL A 302
3AC3SOFTWARETYR A:30 , GLU A:34 , ILE A:209 , VAL A:210 , PRO A:211 , LYS A:212 , LEU A:213BINDING SITE FOR RESIDUE GOL A 303
4AC4SOFTWAREARG A:138 , PHE A:244 , ASN A:248 , GOL A:302 , CL A:305BINDING SITE FOR RESIDUE SO4 A 304
5AC5SOFTWARESO4 A:304BINDING SITE FOR RESIDUE CL A 305
6AC6SOFTWAREALA B:8 , GLY B:43 , THR B:44 , THR B:45 , GLY B:46 , LEU B:101 , TYR B:133 , LYS B:161BINDING SITE FOR RESIDUE GOL B 301
7AC7SOFTWARELYS A:109 , ARG B:138 , PHE B:244 , ALA B:247 , ASN B:248BINDING SITE FOR RESIDUE SO4 B 302
8AC8SOFTWAREARG B:138BINDING SITE FOR RESIDUE CL B 303

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Ser A:-5 -Trp A:-4
2Asn A:248 -Pro A:249
3Met A:259 -Gly A:260
4Leu A:269 -Pro A:270
5Val A:293 -Lys A:294
6Asn B:248 -Pro B:249
7Leu B:269 -Pro B:270
8Val B:293 -Lys B:294

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ICN)

(-) 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:300
                                                                                                                                                                                                                                                                                                                                            
               SCOP domains d4icna_ A: automated matches                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeeee...........hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhh.......eeeee.......hhhhhhhhhhhhhh.....eeeeehhhhhh...hhhhhhhhh....eeeeee....hhhhhhhhhhh....eeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh...............hhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4icn A  -6 ESWGSHMINGSIVALITPLNSDGTVDYTSLEKLVEYHITEGTDAIVAVGTTGESATLPISEHIAVVGQTVKFASGRIPVIGGNGANATAEAIELTKAQNKLGVAAMLGVTPYYNKPSPKGLIAHYTAVAASTDIPQILYNVPGRTAVDMLPETIAQLVEVPNIIGVKDATGDVARVKQLRDLCGNDFLLYSGDDATAREFLTLGGDGVISVANNIVPKLFKLMCDAALAGDTQAAMAAEDQIKGLFSALFCEANPIPVKWAAHKMGLISQGDIRLPLTELSTEFHGLLLDAMKNARIEVK 294
                                 ||  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294
                                -1|                                                                                                                                                                                                                                                                                                     
                                  1                                                                                                                                                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:295
                                                                                                                                                                                                                                                                                                                                       
               SCOP domains d4icnb_ B: automated matches                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee...........hhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhh.......eeeee.......hhhhhhhhhhhhhh.....eeeeehhhhhh...hhhhhhh......eeeeee.....hhhhhhhhhh....eeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh..............hhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4icn B  -1 HMINGSIVALITPLNSDGTVDYTSLEKLVEYHITEGTDAIVAVGTTGESATLPISEHIAVVGQTVKFASGRIPVIGGNGANATAEAIELTKAQNKLGVAAMLGVTPYYNKPSPKGLIAHYTAVAASTDIPQILYNVPGRTAVDMLPETIAQLVEVPNIIGVKDATGDVARVKQLRDLCGNDFLLYSGDDATAREFLTLGGDGVISVANNIVPKLFKLMCDAALAGDTQAAMAAEDQIKGLFSALFCEANPIPVKWAAHKMGLISQGDIRLPLTELSTEFHGLLLDAMKNARIEVK 294
                            ||       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     
                           -1|                                                                                                                                                                                                                                                                                                     
                             1
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 ]  
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    Met A:259 - Gly A:260   [ RasMol ]  
    Ser A:-5 - Trp A:-4   [ RasMol ]  
    Val A:293 - Lys A:294   [ RasMol ]  
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