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(-) Description

Title :  CRYSTAL STRUCTURE OF DIHYDRODIPICOLINATE SYNTHASE FROM OCEANOBACILLUS IHEYENSIS AT 1.9 A RESOLUTION
 
Authors :  L. Satyanarayana, S. Eswaramoorthy, J. M. Sauder, S. K. Burley, S. Swaminathan, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  01 May 08  (Deposition) - 13 May 08  (Release) - 09 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Lysine Biosynthesis, Pyruvate, Tim Barrel, Nysgxrc, 9375O, Psi-2, 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, J. M. Sauder, S. K. Burley, S. Swaminathan
Crystal Structure Of Dihydrodipicolinate Synthase From Oceanobacillus Iheyensis At 1. 9 A Resolution.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DIHYDRODIPICOLINATE SYNTHASE
    Chains: A, B
    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: PSGX3
    Expression System Vector Type: PLASMID
    Gene: OB2845, DHDPS
    Organism Scientific: OCEANOBACILLUS IHEYENSIS HTE831
    Organism Taxid: 221109
    Strain: HTE831 / DSM 14371 / JCM 11309 / KCTC 3954 /

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric/Biological Unit (1, 6)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3D0C)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3D0C)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:278 -Pro A:279
2Glu B:278 -Pro B:279

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3D0C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3D0C)

(-) Exons   (0, 0)

(no "Exon" information available for 3D0C)

(-) 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:302
 aligned with Q8EMJ7_OCEIH | Q8EMJ7 from UniProtKB/TrEMBL  Length:304

    Alignment length:302
                                    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       300  
         Q8EMJ7_OCEIH     1 MDYGEFSKRFSTISGINIVPFLEGTREIDWKGLDDNVEFLLQNGIEVIVPNGNTGEFYALTIEEAKQVATRVTELVNGRATVVAGIGYSVDTAIELGKSAIDSGADCVMIHQPVHPYITDAGAVEYYRNIIEALDAPSIIYFKDAHLSDDVIKELAPLDKLVGIKYAINDIQRVTQVIRAVPKSSNVAFICGTAEKWAPFFYHAGAVGFTSGLVNVFPQKSFALLEALEEGNQEKIWDVWEDVVPFEDLRAKHNNGNNVVIIKEAMEQLGLRAGVTREPVNPLSPNDRLELEELLKSWNTQE 302
               SCOP domains d3d0ca_ A: automated matches                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 3d0cA00 A:1-302 Aldolase class I                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh.eee.............hhhhhhhhhhhhhhh...ee...hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhh...eeeee......hhhhhhhh....eeeeee...hhhhhhhhhhhhhhhhh.eeee.hhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d0c A   1 LDYGEFSKRFSTISGINIVPFLEGTREIDWKGLDDNVEFLLQNGIEVIVPNGNTGEFYALTIEEAKQVATRVTELVNGRATVVAGIGYSVDTAIELGKSAIDSGADCVmIHQPVHPYITDAGAVEYYRNIIEALDAPSIIYFKDAHLSDDVIKELAPLDKLVGIKYAINDIQRVTQVmRAVPKSSNVAFICGTAEKWAPFFYHAGAVGFTSGLVNVFPQKSFALLEALEEGNQEKIWDVWEDVVPFEDLRAKHNNGNNVVIIKEAmEQLGLRAGVTREPVNPLSPNDRLELEELLKSWNTQE 302
                                    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       300  
                                                                                                                                      109-MSE                                                              178-MSE                                                                                 266-MSE                                


Chain B from PDB  Type:PROTEIN  Length:300
 aligned with Q8EMJ7_OCEIH | Q8EMJ7 from UniProtKB/TrEMBL  Length:304

    Alignment length:300
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301
         Q8EMJ7_OCEIH     2 DYGEFSKRFSTISGINIVPFLEGTREIDWKGLDDNVEFLLQNGIEVIVPNGNTGEFYALTIEEAKQVATRVTELVNGRATVVAGIGYSVDTAIELGKSAIDSGADCVMIHQPVHPYITDAGAVEYYRNIIEALDAPSIIYFKDAHLSDDVIKELAPLDKLVGIKYAINDIQRVTQVIRAVPKSSNVAFICGTAEKWAPFFYHAGAVGFTSGLVNVFPQKSFALLEALEEGNQEKIWDVWEDVVPFEDLRAKHNNGNNVVIIKEAMEQLGLRAGVTREPVNPLSPNDRLELEELLKSWNTQ 301
               SCOP domains d3d0cb_ B: automated matches                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 3d0cB00 B:2-301 Aldolase class I                                                                                                                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhh.eee.............hhhhhhhhhhhhhhh...ee...hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhh...eeeee......hhhhhhhh....eeeeee...hhhhhhhhhhhhhhhhh.eeee.hhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3d0c B   2 DYGEFSKRFSTISGINIVPFLEGTREIDWKGLDDNVEFLLQNGIEVIVPNGNTGEFYALTIEEAKQVATRVTELVNGRATVVAGIGYSVDTAIELGKSAIDSGADCVmIHQPVHPYITDAGAVEYYRNIIEALDAPSIIYFKDAHLSDDVIKELAPLDKLVGIKYAINDIQRVTQVmRAVPKSSNVAFICGTAEKWAPFFYHAGAVGFTSGLVNVFPQKSFALLEALEEGNQEKIWDVWEDVVPFEDLRAKHNNGNNVVIIKEAmEQLGLRAGVTREPVNPLSPNDRLELEELLKSWNTQ 301
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171      |181       191       201       211       221       231       241       251       261    |  271       281       291       301
                                                                                                                                     109-MSE                                                              178-MSE                                                                                 266-MSE
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3D0C)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q8EMJ7_OCEIH | Q8EMJ7)
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
    Glu A:278 - Pro A:279   [ RasMol ]  
    Glu B:278 - Pro B:279   [ RasMol ]  
 

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