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Title :  CRYSTAL STRUCTURE OF DIHYDRODIPICOLINATE SYNTHASE FROM RHODOPSEUDOMONAS PALUSTRIS AT 1.87A RESOLUTION
 
Authors :  L. Satyanarayana, S. Eswaramoorthy, S. K. Burley, S. Swaminathan, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  29 Jul 08  (Deposition) - 12 Aug 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.87
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
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 1. 87A Resolution
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DIHYDRODIPICOLINATE SYNTHASE
    Chains: A
    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: RPA3190
    Organism Scientific: RHODOPSEUDOMONAS PALUSTRIS
    Organism Taxid: 1076
    Strain: PALUSTRIS

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 10)

Asymmetric Unit (1, 10)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 40)
No.NameCountTypeFull Name
1MSE40Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3DZ1)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3DZ1)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Trp A:171 -Pro A:172
2Lys A:280 -Pro A:281

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3DZ1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3DZ1)

(-) Exons   (0, 0)

(no "Exon" information available for 3DZ1)

(-) 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:301
 aligned with Q6N4Z3_RHOPA | Q6N4Z3 from UniProtKB/TrEMBL  Length:317

    Alignment length:301
                             1                                                                                                                                                                                                                                                                                                           
                             |       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       299 
         Q6N4Z3_RHOPA     - -MKLTPEAAGTFAIAPTPFHDDGKIDDVSIDRLTDFYAEVGCEGVTVLGILGEAPKLDAAEAEAVATRFIKRAKSMQVIVGVSAPGFAAMRRLARLSMDAGAAGVMIAPPPSLRTDEQITTYFRQATEAIGDDVPWVLQDYPLTLSVVMTPKVIRQIVMDSASCVMLKHEDWPGLEKITTLRGFQKDGSLRPLSILCGNGGLFLDFEMERGADGAMTGYCFPDMLVDVVKLSKAGQRDLAHNLFDAHLPLIRYEHQQGVGLSVRKYVLKKRGLLSSSAQRKPGASLTDTAREEVDYLLSRL 300
               SCOP domains d3dz1a_ A: automated matches                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeee...........hhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhhhh....eeeeehhhhhh...hhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhh......eeee.hhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh...............hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dz1 A  -2 SLKLTPEAAGTFAIAPTPFHDDGKIDDVSIDRLTDFYAEVGCEGVTVLGILGEAPKLDAAEAEAVATRFIKRAKSmQVIVGVSAPGFAAmRRLARLSmDAGAAGVmIAPPPSLRTDEQITTYFRQATEAIGDDVPWVLQDYPLTLSVVmTPKVIRQIVmDSASCVmLKHEDWPGLEKITTLRGFQKDGSLRPLSILCGNGGLFLDFEmERGADGAmTGYCFPDmLVDVVKLSKAGQRDLAHNLFDAHLPLIRYEHQQGVGLSVRKYVLKKRGLLSSSAQRKPGASLTDTAREEVDYLLSRL 300
                             ||      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       299 
                             ||                                                                       75-MSE        89-MSE  97-MSE 105-MSE                                    148-MSE   158-MSE  |                                       207-MSE 215-MSE 223-MSE                                                                         
                            -1|                                                                                                                                                                165-MSE                                                                                                                                   
                              2
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3DZ1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DZ1)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q6N4Z3_RHOPA | Q6N4Z3)
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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  Cis Peptide Bonds
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3d0c CRYSTAL STRUCTURE OF DIHYDRODIPICOLINATE SYNTHASE FROM OCEANOBACILLUS IHEYENSIS AT 1.9A RESOLUTION