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(-) Description

Title :  CRYSTAL STRUCTURE OF DIHYDRODIPICOLINATE SYNTHASE DAPA-2 (BA3935) FROM BACILLUS ANTHRACIS AT 1.94A RESOLUTION.
 
Authors :  V. Levdikov, E. Blagova, M. J. Fogg, J. A. Brannigan, N. Milioti, A. J. Wilkinson, K. S. Wilson
Date :  30 Sep 04  (Deposition) - 04 Oct 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.94
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Dihydrodipicolinate Synthase; Tim Barrel; Crystal Structure; Lysine Biosynthesis; Spine, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Blagova, V. Levdikov, N. Milioti, M. J. Fogg, A. K. Kalliomaa, J. A. Brannigan, K. S. Wilson, A. J. Wilkinson
Crystal Structure Of Dihydrodipicolinate Synthase (Ba3935) From Bacillus Anthracis At 1. 94 A Resolution
Proteins V. 62 297 2006
PubMed-ID: 16287120  |  Reference-DOI: 10.1002/PROT.20684
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DIHYDRODIPICOLINATE SYNTHASE
    Chains: A, B, C, D
    EC Number: 4.2.1.52
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-YSBLIC
    Expression System Strain: B834
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DAPA-2
    Organism Scientific: BACILLUS ANTHRACIS
    Organism Taxid: 1392

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 10)
No.NameCountTypeFull Name
1K10Ligand/IonPOTASSIUM ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER C:154 , ILE C:156 , GLU C:157 , ILE C:159 , HOH C:1971 , HOH C:2132BINDING SITE FOR RESIDUE K C 1801
02AC2SOFTWAREILE B:176 , THR B:179 , ALA B:180 , PHE B:183 , HOH B:1888 , HOH B:1910BINDING SITE FOR RESIDUE K B 1802
03AC3SOFTWARESER B:154 , ILE B:156 , GLU B:157 , ILE B:159 , HOH B:1942 , HOH B:1946BINDING SITE FOR RESIDUE K B 1803
04AC4SOFTWAREILE D:176 , THR D:179 , ALA D:180 , PHE D:183 , HOH D:1911 , HOH D:1965BINDING SITE FOR RESIDUE K D 1804
05AC5SOFTWAREILE C:176 , THR C:179 , ALA C:180 , PHE C:183 , HOH C:1916 , HOH C:1940BINDING SITE FOR RESIDUE K C 1805
06AC6SOFTWAREILE A:176 , THR A:179 , ALA A:180 , PHE A:183 , HOH A:1896 , HOH A:1956BINDING SITE FOR RESIDUE K A 1806
07AC7SOFTWARESER A:154 , ILE A:156 , GLU A:157 , ILE A:159 , HOH A:1911 , HOH A:1917BINDING SITE FOR RESIDUE K A 1807
08AC8SOFTWARESER D:154 , ILE D:156 , GLU D:157 , ILE D:159 , HOH D:1967 , HOH D:2111BINDING SITE FOR RESIDUE K D 1808
09AC9SOFTWAREILE B:176 , GLU B:177 , THR B:179 , HOH B:1888BINDING SITE FOR RESIDUE K B 1809
10BC1SOFTWAREILE C:176 , GLU C:177 , THR C:179 , HOH C:1940BINDING SITE FOR RESIDUE K C 1810

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1XKY)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Leu A:270 -Pro A:271
2Leu B:270 -Pro B:271
3Leu C:270 -Pro C:271
4Leu D:270 -Pro D:271

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1XKY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1XKY)

(-) Exons   (0, 0)

(no "Exon" information available for 1XKY)

(-) 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:292
 aligned with Q81WN7_BACAN | Q81WN7 from UniProtKB/TrEMBL  Length:292

    Alignment length: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  
         Q81WN7_BACAN     1 MIDFGTIATAMVTPFDINGNIDFAKTTKLVNYLIDNGTTAIVVGGTTGESPTLTSEEKVALYRHVVSVVDKRVPVIAGTGSNNTHASIDLTKKATEVGVDAVMLVAPYYNKPSQEGMYQHFKAIAESTPLPVMLYNVPGRSIVQISVDTVVRLSEIENIVAIKDAGGDVLTMTEIIEKTADDFAVYSGDDGLTLPAMAVGAKGIVSVASHVIGNEMQEMIAAFQAGEFKKAQKLHQLLVRVTDSLFMAPSPTPVKTALQMVGLDVGSVRLPLLPLTEEERVTLQSVMQSIPR 292
               SCOP domains d1xkya1 A:1-292 Dihydrodipicolinate synthase                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1xkyA00 A:1-292 Aldolase class I                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee...........hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhh....eeeeehhhhhh...hhhhhhhhhh...eeeeee...hhhhhhhhhhhh....eeee.hhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh..............hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xky A   1 MIDFGTIATAMVTPFDINGNIDFAKTTKLVNYLIDNGTTAIVVGGTTGESPTLTSEEKVALYRHVVSVVDKRVPVIAGTGSNNTHASIDLTKKATEVGVDAVMLVAPYYNKPSQEGMYQHFKAIAESTPLPVMLYNVPGRSIVQISVDTVVRLSEIENIVAIKDAGGDVLTMTEIIEKTADDFAVYSGDDGLTLPAMAVGAKGIVSVASHVIGNEMQEMIAAFQAGEFKKAQKLHQLLVRVTDSLFMAPSPTPVKTALQMVGLDVGSVRLPLLPLTEEERVTLQSVMQSIPR 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  


Chain B from PDB  Type:PROTEIN  Length:292
 aligned with Q81WN7_BACAN | Q81WN7 from UniProtKB/TrEMBL  Length:292

    Alignment length: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  
         Q81WN7_BACAN     1 MIDFGTIATAMVTPFDINGNIDFAKTTKLVNYLIDNGTTAIVVGGTTGESPTLTSEEKVALYRHVVSVVDKRVPVIAGTGSNNTHASIDLTKKATEVGVDAVMLVAPYYNKPSQEGMYQHFKAIAESTPLPVMLYNVPGRSIVQISVDTVVRLSEIENIVAIKDAGGDVLTMTEIIEKTADDFAVYSGDDGLTLPAMAVGAKGIVSVASHVIGNEMQEMIAAFQAGEFKKAQKLHQLLVRVTDSLFMAPSPTPVKTALQMVGLDVGSVRLPLLPLTEEERVTLQSVMQSIPR 292
               SCOP domains d1xkyb_ B: Dihydrodipicolinate synthase                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1xkyB00 B:1-292 Aldolase class I                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee...........hhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhh....eee.....hhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhh....eeeeehhhhhh...hhhhhhhhhh...eeeeee...hhhhhhhhhhhh....eeee.hhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh..............hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xky B   1 MIDFGTIATAMVTPFDINGNIDFAKTTKLVNYLIDNGTTAIVVGGTTGESPTLTSEEKVALYRHVVSVVDKRVPVIAGTGSNNTHASIDLTKKATEVGVDAVMLVAPYYNKPSQEGMYQHFKAIAESTPLPVMLYNVPGRSIVQISVDTVVRLSEIENIVAIKDAGGDVLTMTEIIEKTADDFAVYSGDDGLTLPAMAVGAKGIVSVASHVIGNEMQEMIAAFQAGEFKKAQKLHQLLVRVTDSLFMAPSPTPVKTALQMVGLDVGSVRLPLLPLTEEERVTLQSVMQSIPR 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  


Chain C from PDB  Type:PROTEIN  Length:292
 aligned with Q81WN7_BACAN | Q81WN7 from UniProtKB/TrEMBL  Length:292

    Alignment length: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  
         Q81WN7_BACAN     1 MIDFGTIATAMVTPFDINGNIDFAKTTKLVNYLIDNGTTAIVVGGTTGESPTLTSEEKVALYRHVVSVVDKRVPVIAGTGSNNTHASIDLTKKATEVGVDAVMLVAPYYNKPSQEGMYQHFKAIAESTPLPVMLYNVPGRSIVQISVDTVVRLSEIENIVAIKDAGGDVLTMTEIIEKTADDFAVYSGDDGLTLPAMAVGAKGIVSVASHVIGNEMQEMIAAFQAGEFKKAQKLHQLLVRVTDSLFMAPSPTPVKTALQMVGLDVGSVRLPLLPLTEEERVTLQSVMQSIPR 292
               SCOP domains d1xkyc_ C: Dihydrodipicolinate synthase                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1xkyC00 C:1-292 Aldolase class I                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee...........hhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhhhhhhh....eee.....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhh....eeeeehhhhhh...hhhhhhhhhh...eeeeee...hhhhhhhhhhhh....eeee.hhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh..............hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xky C   1 MIDFGTIATAMVTPFDINGNIDFAKTTKLVNYLIDNGTTAIVVGGTTGESPTLTSEEKVALYRHVVSVVDKRVPVIAGTGSNNTHASIDLTKKATEVGVDAVMLVAPYYNKPSQEGMYQHFKAIAESTPLPVMLYNVPGRSIVQISVDTVVRLSEIENIVAIKDAGGDVLTMTEIIEKTADDFAVYSGDDGLTLPAMAVGAKGIVSVASHVIGNEMQEMIAAFQAGEFKKAQKLHQLLVRVTDSLFMAPSPTPVKTALQMVGLDVGSVRLPLLPLTEEERVTLQSVMQSIPR 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  


Chain D from PDB  Type:PROTEIN  Length:292
 aligned with Q81WN7_BACAN | Q81WN7 from UniProtKB/TrEMBL  Length:292

    Alignment length: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  
         Q81WN7_BACAN     1 MIDFGTIATAMVTPFDINGNIDFAKTTKLVNYLIDNGTTAIVVGGTTGESPTLTSEEKVALYRHVVSVVDKRVPVIAGTGSNNTHASIDLTKKATEVGVDAVMLVAPYYNKPSQEGMYQHFKAIAESTPLPVMLYNVPGRSIVQISVDTVVRLSEIENIVAIKDAGGDVLTMTEIIEKTADDFAVYSGDDGLTLPAMAVGAKGIVSVASHVIGNEMQEMIAAFQAGEFKKAQKLHQLLVRVTDSLFMAPSPTPVKTALQMVGLDVGSVRLPLLPLTEEERVTLQSVMQSIPR 292
               SCOP domains d1xkyd_ D: Dihydrodipicolinate synthase                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1xkyD00 D:1-292 Aldolase class I                                                                                                                                                                                                                                                                     CATH domains
           Pfam domains (1) --DHDPS-1xkyD01 D:3-290                                                                                                                                                                                                                                                                           -- Pfam domains (1)
           Pfam domains (2) --DHDPS-1xkyD02 D:3-290                                                                                                                                                                                                                                                                           -- Pfam domains (2)
           Pfam domains (3) --DHDPS-1xkyD03 D:3-290                                                                                                                                                                                                                                                                           -- Pfam domains (3)
           Pfam domains (4) --DHDPS-1xkyD04 D:3-290                                                                                                                                                                                                                                                                           -- Pfam domains (4)
         Sec.struct. author ......eeee...........hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhhhhh....eee.....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhh....eeeeehhhhhh...hhhhhhhhhh...eeeeee...hhhhhhhhhhhh....eeee.hhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh..............hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xky D   1 MIDFGTIATAMVTPFDINGNIDFAKTTKLVNYLIDNGTTAIVVGGTTGESPTLTSEEKVALYRHVVSVVDKRVPVIAGTGSNNTHASIDLTKKATEVGVDAVMLVAPYYNKPSQEGMYQHFKAIAESTPLPVMLYNVPGRSIVQISVDTVVRLSEIENIVAIKDAGGDVLTMTEIIEKTADDFAVYSGDDGLTLPAMAVGAKGIVSVASHVIGNEMQEMIAAFQAGEFKKAQKLHQLLVRVTDSLFMAPSPTPVKTALQMVGLDVGSVRLPLLPLTEEERVTLQSVMQSIPR 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)
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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, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: TIM_barrel (694)
(-)
Family: DHDPS (40)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q81WN7_BACAN | Q81WN7)
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.
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

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q81WN7_BACAN | Q81WN7: 1xl9 3hij

(-) Related Entries Specified in the PDB File

1xl9