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(-) Description

Title :  CRYSTAL STRUCTURE OF THE COMPLEX OF DHYDRODIPICOLINATE SYNTHASE FROM ACINETOBACTER BAUMANNII WITH LYSINE AT 2.3A RESOLUTION
 
Authors :  O. Jithesh, S. Yamini, N. Kaur, A. Gautam, R. Tewari, G. S. Kushwaha, P. K A. Srinivasan, S. Sharma, T. P. Singh
Date :  06 Dec 10  (Deposition) - 29 Dec 10  (Release) - 29 Dec 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tim Barrel, Beta-Alpha-Barrel, Diaminopimelate Biosynthesis, Lysine Biosynthesis, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Jithesh, S. Yamini, N. Kaur, A. Gautam, R. Tewari, G. S. Kushwaha, P. Kaur, A. Srinivasan, S. Sharma, T. P. Singh
Crystal Structure Of The Complex Of Dhydrodipicolinate Synthase From Acinetobacter Baumannii With Lysine At 2. 3A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DIHYDRODIPICOLINATE SYNTHASE
    Chains: A, B
    EC Number: 4.2.1.52
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRSETA
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: DHDPS, RESIDUES IN UNP 7-297
    Gene: DHDPS, HMPREF0010_03414
    Organism Scientific: ACINETOBACTER BAUMANNII
    Organism Taxid: 575584
    Strain: ATCC 19606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric/Biological Unit (4, 9)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL5Ligand/IonGLYCEROL
3LYS1Mod. Amino AcidLYSINE
4SO42Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:250 , LYS A:253 , TRP A:254 , HIS A:257 , ASP A:263 , THR A:264 , ILE A:266 , PRO A:272 , LEU A:273BINDING SITE FOR RESIDUE GOL A 292
2AC2SOFTWAREVAL A:135 , ARG A:138 , PHE A:244 , HOH A:313 , HOH A:346 , HOH A:385 , HOH A:418BINDING SITE FOR RESIDUE SO4 A 293
3AC3SOFTWAREASN A:80 , TYR A:106 , HOH A:311 , HOH A:405 , ASN B:80 , TYR B:106BINDING SITE FOR RESIDUE SO4 A 294
4AC4SOFTWARELYS A:109 , VAL B:135 , ARG B:138 , PHE B:244 , GLU B:246 , SER B:247 , ASN B:248 , HOH B:341BINDING SITE FOR RESIDUE LYS B 292
5AC5SOFTWARETHR A:50 , LEU A:51 , SER A:52 , SER B:81 , GLU B:84 , GLU B:87 , HOH B:410BINDING SITE FOR RESIDUE GOL B 293
6AC6SOFTWAREGLU B:189 , ASN B:233 , ALA B:237 , HIS B:240BINDING SITE FOR RESIDUE GOL B 294
7AC7SOFTWARELYS B:224 , ASP B:225 , GLU B:226 , GLN B:227BINDING SITE FOR RESIDUE GOL B 295
8AC8SOFTWAREASN A:108 , THR B:44 , GLU B:47 , ALA B:48 , SER B:49 , ARG B:138 , ASN B:248 , PRO B:249 , LEU B:270BINDING SITE FOR RESIDUE GOL B 296
9AC9SOFTWAREALA B:8 , GLY B:43 , THR B:44 , THR B:45 , LEU B:101 , TYR B:133 , LYS B:161 , ILE B:203BINDING SITE FOR RESIDUE ACT B 297

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Asn A:248 -Pro A:249
2Leu A:268 -Pro A:269
3Asn B:248 -Pro B:249
4Leu B:268 -Pro B:269

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3PUL)

(-) 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:291
 aligned with D0CFC3_ACIB2 | D0CFC3 from UniProtKB/TrEMBL  Length:297

    Alignment length:291
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296 
         D0CFC3_ACIB2     7 TIQGSIVAIVTPMLKDGGVDWKSLEKLVEWHIEQGTNSIVAVGTTGEASTLSMEEHTQVIKEIIRVANKRIPIIAGTGANSTREAIELTKAAKDLGADAALLVTPYYNKPTQEGLYQHYKAIAEAVELPLILYNVPGRTGVDLSNDTAVRLAEIPNIVGIKDATGDVPRGKALIDALNGKMAVYSGDDETAWELMLLGADGNISVTANIAPKAMSEVCAVAIAKDEQQAKTLNNKIANLHNILFCESNPIPVKWALHEMGLIDTGIRLPLTPLAEQYREPLRNALKDAGII 297
               SCOP domains d3pula_ A: automated matches                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...........hhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhh...eeeeehhhhhh...hhhhhhhhh....eeeeee...hhhhhhhhhhhh....eeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh..............hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pul A   1 TIQGSIVAIVTPMLKDGGVDWKSLEKLVEWHIEQGTNSIVAVGTTGEASTLSMEEHTQVIKEIIRVANKRIPIIAGTGANSTREAIELTKAAKDLGADAALLVTPYYNKPTQEGLYQHYKAIAEAVELPLILYNVPGRTGVDLSNDTAVRLAEIPNIVGIKDATGDVPRGKALIDALNGKMAVYSGDDETAWELMLLGADGNISVTANIAPKAMSEVCAVAIAKDEQQAKTLNNKIANLHNILFCESNPIPVKWALHEMGLIDTGIRLPLTPLAEQYREPLRNALKDAGII 291
                                    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 


Chain B from PDB  Type:PROTEIN  Length:292
 aligned with D0CFC3_ACIB2 | D0CFC3 from UniProtKB/TrEMBL  Length:297

    Alignment length:292
                                                                                                                                                                                                                                                                                                                            297 
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296| 
         D0CFC3_ACIB2     7 TIQGSIVAIVTPMLKDGGVDWKSLEKLVEWHIEQGTNSIVAVGTTGEASTLSMEEHTQVIKEIIRVANKRIPIIAGTGANSTREAIELTKAAKDLGADAALLVTPYYNKPTQEGLYQHYKAIAEAVELPLILYNVPGRTGVDLSNDTAVRLAEIPNIVGIKDATGDVPRGKALIDALNGKMAVYSGDDETAWELMLLGADGNISVTANIAPKAMSEVCAVAIAKDEQQAKTLNNKIANLHNILFCESNPIPVKWALHEMGLIDTGIRLPLTPLAEQYREPLRNALKDAGII-   -
               SCOP domains d3pulb_ B: automated matches                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...........hhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhh...eeeeehhhhhh...hhhhhhhhh....eeeeee...hhhhhhhhhhhhh...eeee....hhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh..............hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pul B   1 TIQGSIVAIVTPMLKDGGVDWKSLEKLVEWHIEQGTNSIVAVGTTGEASTLSMEEHTQVIKEIIRVANKRIPIIAGTGANSTREAIELTKAAKDLGADAALLVTPYYNKPTQEGLYQHYKAIAEAVELPLILYNVPGRTGVDLSNDTAVRLAEIPNIVGIKDATGDVPRGKALIDALNGKMAVYSGDDETAWELMLLGADGNISVTANIAPKAMSEVCAVAIAKDEQQAKTLNNKIANLHNILFCESNPIPVKWALHEMGLIDTGIRLPLTPLAEQYREPLRNALKDAGIIK 292
                                    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
   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  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (D0CFC3_ACIB2 | D0CFC3)
molecular function
    GO:0008840    4-hydroxy-tetrahydrodipicolinate synthase    Catalysis of the reaction: pyruvate + L-aspartate-4-semialdehyde = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H2O.
    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.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0019877    diaminopimelate biosynthetic process    The chemical reactions and pathways resulting in the formation of diaminopimelate, both as an intermediate in lysine biosynthesis and as a component (as meso-diaminopimelate) of the peptidoglycan of Gram-negative bacterial cell walls.
    GO:0009085    lysine biosynthetic process    The chemical reactions and pathways resulting in the formation of lysine, 2,6-diaminohexanoic acid.
    GO:0009089    lysine biosynthetic process via diaminopimelate    The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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        D0CFC3_ACIB2 | D0CFC3: 3pud 3pue 3rk8 3tak 3tce 3tdf 3u8g 3uqn 4dxv

(-) Related Entries Specified in the PDB File

3noe 3pud 3pue