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(-) Description

Title :  CRYSTAL STRUCTURE OF DIHYDRODIPICOLINATE SYNTHASE FROM RHODOPSEUDOMONAS PALUSTRIS AT 2.0A RESOLUTION
 
Authors :  L. Satyanarayana, S. Eswaramoorthy, S. K. Burley, S. Swaminathan, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  26 Aug 08  (Deposition) - 02 Sep 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.04
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Lysine Biosynthesis, Pyruvate, Tim Barrel, Nysgxrc, 11102O, Psi2. , Structural Genomics, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Satyanarayana, S. Eswaramoorthy, S. K. Burley, S. Swaminathan
Crystal Structure Of Dihydrodipicolinate Synthase From Rhodopseudomonas Palustris At 2. 0A Resolution
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUTATIVE DIHYDRODIPICOLINATE SYNTHETASE
    Chains: A, B, C, D
    EC Number: 4.2.1.52
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BC-PSGX3(BC)
    Expression System Strain: BL21 (DE3) CODON+RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DAPA1, RPA1571
    Organism Scientific: RHODOPSEUDOMONAS PALUSTRIS
    Organism Taxid: 1076
    Strain: PALUSTRIS

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1PGE2Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE B:141 , GLN B:142 , ARG B:143BINDING SITE FOR RESIDUE PGE B 999
2AC2SOFTWAREPHE A:141 , ARG A:143 , PHE C:141 , ARG C:143BINDING SITE FOR RESIDUE PGE A 888

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3EB2)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Pro A:271 -Pro A:272
2Pro B:271 -Pro B:272
3Pro C:271 -Pro C:272
4Pro D:271 -Pro D:272

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3EB2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3EB2)

(-) Exons   (0, 0)

(no "Exon" information available for 3EB2)

(-) 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:288
 aligned with Q6N9H8_RHOPA | Q6N9H8 from UniProtKB/TrEMBL  Length:292

    Alignment length:288
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283        
         Q6N9H8_RHOPA     4 DFHGVFPYLVSPVDAEGRVRADVMGRLCDDLIQAGVHGLTPLGSTGEFAYLGTAQREAVVRATIEAAQRRVPVVAGVASTSVADAVAQAKLYEKLGADGILAILEAYFPLKDAQIESYFRAIADAVEIPVVIYTNPQFQRSDLTLDVIARLAEHPRIRYIKDASTNTGRLLSIINRCGDALQVFSASAHIPAAVMLIGGVGWMAGPACIAPRQSVALYELCKAQRWDEALMLQRKLWRVNEAFAKFNLAACIKAGLALQGYDVGDPIPPQAALTAEERKAVEKVLAEI 291
               SCOP domains d3eb2a_ A: automated matches                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee............hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhh..eeeeee......hhhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhheeee....hhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..............hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3eb2 A   4 DFHGVFPYLVSPVDAEGRVRADVMGRLCDDLIQAGVHGLTPLGSTGEFAYLGTAQREAVVRATIEAAQRRVPVVAGVASTSVADAVAQAKLYEKLGADGILAILEAYFPLKDAQIESYFRAIADAVEIPVVIYTNPQFQRSDLTLDVIARLAEHPRIRYIKDASTNTGRLLSIINRCGDALQVFSASAHIPAAVMLIGGVGWMAGPACIAPRQSVALYELCKAQRWDEALMLQRKLWRVNEAFAKFNLAACIKAGLALQGYDVGDPIPPQAALTAEERKAVEKVLAEI 291
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283        


Chain B from PDB  Type:PROTEIN  Length:291
 aligned with Q6N9H8_RHOPA | Q6N9H8 from UniProtKB/TrEMBL  Length:292

    Alignment length:291
                                                                                                                                                                                                                                                                                                                           292 
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292 
         Q6N9H8_RHOPA     3 ADFHGVFPYLVSPVDAEGRVRADVMGRLCDDLIQAGVHGLTPLGSTGEFAYLGTAQREAVVRATIEAAQRRVPVVAGVASTSVADAVAQAKLYEKLGADGILAILEAYFPLKDAQIESYFRAIADAVEIPVVIYTNPQFQRSDLTLDVIARLAEHPRIRYIKDASTNTGRLLSIINRCGDALQVFSASAHIPAAVMLIGGVGWMAGPACIAPRQSVALYELCKAQRWDEALMLQRKLWRVNEAFAKFNLAACIKAGLALQGYDVGDPIPPQAALTAEERKAVEKVLAEIA-   -
               SCOP domains d3eb2b_ B: automated matches                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee............hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhh..eeeeee......hhhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhheeee....hhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..............hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3eb2 B   3 LDFHGVFPYLVSPVDAEGRVRADVMGRLCDDLIQAGVHGLTPLGSTGEFAYLGTAQREAVVRATIEAAQRRVPVVAGVASTSVADAVAQAKLYEKLGADGILAILEAYFPLKDAQIESYFRAIADAVEIPVVIYTNPQFQRSDLTLDVIARLAEHPRIRYIKDASTNTGRLLSIINRCGDALQVFSASAHIPAAVMLIGGVGWMAGPACIAPRQSVALYELCKAQRWDEALMLQRKLWRVNEAFAKFNLAACIKAGLALQGYDVGDPIPPQAALTAEERKAVEKVLAEIAE 293
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292 


Chain C from PDB  Type:PROTEIN  Length:288
 aligned with Q6N9H8_RHOPA | Q6N9H8 from UniProtKB/TrEMBL  Length:292

    Alignment length:288
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283        
         Q6N9H8_RHOPA     4 DFHGVFPYLVSPVDAEGRVRADVMGRLCDDLIQAGVHGLTPLGSTGEFAYLGTAQREAVVRATIEAAQRRVPVVAGVASTSVADAVAQAKLYEKLGADGILAILEAYFPLKDAQIESYFRAIADAVEIPVVIYTNPQFQRSDLTLDVIARLAEHPRIRYIKDASTNTGRLLSIINRCGDALQVFSASAHIPAAVMLIGGVGWMAGPACIAPRQSVALYELCKAQRWDEALMLQRKLWRVNEAFAKFNLAACIKAGLALQGYDVGDPIPPQAALTAEERKAVEKVLAEI 291
               SCOP domains d3eb2c_ C: automated matches                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee............hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhh..eeeeee......hhhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhheeee....hhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..............hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3eb2 C   4 DFHGVFPYLVSPVDAEGRVRADVMGRLCDDLIQAGVHGLTPLGSTGEFAYLGTAQREAVVRATIEAAQRRVPVVAGVASTSVADAVAQAKLYEKLGADGILAILEAYFPLKDAQIESYFRAIADAVEIPVVIYTNPQFQRSDLTLDVIARLAEHPRIRYIKDASTNTGRLLSIINRCGDALQVFSASAHIPAAVMLIGGVGWMAGPACIAPRQSVALYELCKAQRWDEALMLQRKLWRVNEAFAKFNLAACIKAGLALQGYDVGDPIPPQAALTAEERKAVEKVLAEI 291
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283        


Chain D from PDB  Type:PROTEIN  Length:290
 aligned with Q6N9H8_RHOPA | Q6N9H8 from UniProtKB/TrEMBL  Length:292

    Alignment length:290
                                                                                                                                                                                                                                                                                                                          292 
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283        |-
         Q6N9H8_RHOPA     4 DFHGVFPYLVSPVDAEGRVRADVMGRLCDDLIQAGVHGLTPLGSTGEFAYLGTAQREAVVRATIEAAQRRVPVVAGVASTSVADAVAQAKLYEKLGADGILAILEAYFPLKDAQIESYFRAIADAVEIPVVIYTNPQFQRSDLTLDVIARLAEHPRIRYIKDASTNTGRLLSIINRCGDALQVFSASAHIPAAVMLIGGVGWMAGPACIAPRQSVALYELCKAQRWDEALMLQRKLWRVNEAFAKFNLAACIKAGLALQGYDVGDPIPPQAALTAEERKAVEKVLAEIA-   -
               SCOP domains d3eb2d_ D: automated matches                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee............hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhh..eeeeee......hhhhhhhhhhhhhh.....eeeee.........hhhhhhhhh....eeeeee...hhhhhhhhhhhhhhhheeee....hhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..............hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3eb2 D   4 DFHGVFPYLVSPVDAEGRVRADVMGRLCDDLIQAGVHGLTPLGSTGEFAYLGTAQREAVVRATIEAAQRRVPVVAGVASTSVADAVAQAKLYEKLGADGILAILEAYFPLKDAQIESYFRAIADAVEIPVVIYTNPQFQRSDLTLDVIARLAEHPRIRYIKDASTNTGRLLSIINRCGDALQVFSASAHIPAAVMLIGGVGWMAGPACIAPRQSVALYELCKAQRWDEALMLQRKLWRVNEAFAKFNLAACIKAGLALQGYDVGDPIPPQAALTAEERKAVEKVLAEIAE 293
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293
   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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3EB2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3EB2)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q6N9H8_RHOPA | Q6N9H8)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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 Related Entries

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(-) Related Entries Specified in the PDB File

3doc CRYSTAL STRUCTURE OF DIHYDRODIPICOLINATE SYNTHASE FROM OCEANOBACILLUS IHEYENSIS AT 1.9 A RESOLUTION
3dz1 CRYSTAL STRUCTURE OF DIHYDRODIPICOLINATE SYNTHASE FROM RHODOPSEUDOMONAS PALUSTRIS AT 1.87A RESOLUTION RELATED ID: NYSGXRC-11102N RELATED DB: TARGETDB