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(-) Description

Title :  CRYSTAL STRUCTURE OF DIHYDRODIPICOLINATE SYNTHASE FROM AQUIFEX AEOLICUS
 
Authors :  T. S. Kumarevel, P. Karthe, S. Kuramitsu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  06 Mar 07  (Deposition) - 01 May 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,C,D,E
Keywords :  Dihydrodipicolinate Synthase, Aquifex Aeolicus, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. S. Kumarevel, P. Karthe, S. Kuramitsu, S. Yokoyama
Crystal Structure Of Dihydrodipicolinate Synthase From Aquifex Aeolicus
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DIHYDRODIPICOLINATE SYNTHASE
    Chains: A, C, D, E
    EC Number: 4.2.1.52
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: BL21(DE3)CODONPLUS-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AQ_1143
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 63363
    Synonym: DHDPS

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ACDE

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1PO42Ligand/IonPHOSPHATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:105 , HOH A:1003 , HOH A:1077 , HOH A:1083 , ASN C:79 , TYR C:105BINDING SITE FOR RESIDUE PO4 A 1001
2AC2SOFTWAREASN D:79 , TYR D:105 , TYR E:105 , HOH E:1004 , HOH E:1084BINDING SITE FOR RESIDUE PO4 E 1002

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:139 -C:139
2D:139 -E:139

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Asn A:248 -Pro A:249
2Leu A:268 -Pro A:269
3Asn C:248 -Pro C:249
4Leu C:268 -Pro C:269
5Asn D:248 -Pro D:249
6Leu D:268 -Pro D:269
7Asn E:248 -Pro E:249
8Leu E:268 -Pro E:269

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2EHH)

(-) PROSITE Motifs  (2, 8)

Asymmetric/Biological Unit (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DHDPS_1PS00665 Dihydrodipicolinate synthase signature 1.DAPA_AQUAE37-54
 
 
 		  4A:37-54
C:37-54
D:37-54
E:37-54
2DHDPS_2PS00666 Dihydrodipicolinate synthase signature 2.DAPA_AQUAE132-163
 
 
 		  4A:132-163
C:132-163
D:132-163
E:132-163

(-) Exons   (0, 0)

(no "Exon" information available for 2EHH)

(-) 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:294
 aligned with DAPA_AQUAE | O67216 from UniProtKB/Swiss-Prot  Length:294

    Alignment length:294
                                    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    
           DAPA_AQUAE     1 MFQGSIVALITPFKEGEVDYEALGNLIEFHVDNGTDAILVCGTTGESPTLTFEEHEKVIEFAVKRAAGRIKVIAGTGGNATHEAVHLTAHAKEVGADGALVVVPYYNKPTQRGLYEHFKTVAQEVDIPIIIYNIPSRTCVEISVDTMFKLASECENIVASKESTPNMDRISEIVKRLGESFSVLSGDDSLTLPMMALGAKGVISVANNVMPREVKELIRAALEGDFRRAREIHYYLHDLFKVLFIETNPIPVKTACWMLGMCEKEFRLPLTEMSPENENKLREVLKKYNLPLKN 294
               SCOP domains d2ehha_ A: automated matches                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 2ehhA00 A:1-294 Aldolase class I                                                                                                                                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee....ee..eehhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhh...eeeeehhhhhh...hhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhh...eeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh..............hhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------DHDPS_1           -----------------------------------------------------------------------------DHDPS_2  PDB: A:132-163         ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ehh A   1 MFQGSIVALITPFKEGEVDYEALGNLIEFHVDNGTDAILVCGTTGESPTLTFEEHEKVIEFAVKRAAGRIKVIAGTGGNATHEAVHLTAHAKEVGADGALVVVPYYNKPTQRGLYEHFKTVAQEVDIPIIIYNIPSRTCVEISVDTMFKLASECENIVASKESTPNMDRISEIVKRLGESFSVLSGDDSLTLPMMALGAKGVISVANNVMPREVKELIRAALEGDFRRAREIHYYLHDLFKVLFIETNPIPVKTACWMLGMCEKEFRLPLTEMSPENENKLREVLKKYNLPLKN 294
                                    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:293
 aligned with DAPA_AQUAE | O67216 from UniProtKB/Swiss-Prot  Length:294

    Alignment length:293
                                    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   
           DAPA_AQUAE     2 FQGSIVALITPFKEGEVDYEALGNLIEFHVDNGTDAILVCGTTGESPTLTFEEHEKVIEFAVKRAAGRIKVIAGTGGNATHEAVHLTAHAKEVGADGALVVVPYYNKPTQRGLYEHFKTVAQEVDIPIIIYNIPSRTCVEISVDTMFKLASECENIVASKESTPNMDRISEIVKRLGESFSVLSGDDSLTLPMMALGAKGVISVANNVMPREVKELIRAALEGDFRRAREIHYYLHDLFKVLFIETNPIPVKTACWMLGMCEKEFRLPLTEMSPENENKLREVLKKYNLPLKN 294
               SCOP domains d2ehhc_ C: automated matches                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 2ehhC00 C:2-294 Aldolase class I                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....ee..eehhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhh...eeeeehhhhhh...hhhhhhhhhhhh..eeeeee...hhhhhhhhhhhh....eeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh..............hhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------DHDPS_1           -----------------------------------------------------------------------------DHDPS_2  PDB: C:132-163         ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ehh C   2 FQGSIVALITPFKEGEVDYEALGNLIEFHVDNGTDAILVCGTTGESPTLTFEEHEKVIEFAVKRAAGRIKVIAGTGGNATHEAVHLTAHAKEVGADGALVVVPYYNKPTQRGLYEHFKTVAQEVDIPIIIYNIPSRTCVEISVDTMFKLASECENIVASKESTPNMDRISEIVKRLGESFSVLSGDDSLTLPMMALGAKGVISVANNVMPREVKELIRAALEGDFRRAREIHYYLHDLFKVLFIETNPIPVKTACWMLGMCEKEFRLPLTEMSPENENKLREVLKKYNLPLKN 294
                                    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   


Chain D from PDB  Type:PROTEIN  Length:293
 aligned with DAPA_AQUAE | O67216 from UniProtKB/Swiss-Prot  Length:294

    Alignment length:293
                                    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   
           DAPA_AQUAE     2 FQGSIVALITPFKEGEVDYEALGNLIEFHVDNGTDAILVCGTTGESPTLTFEEHEKVIEFAVKRAAGRIKVIAGTGGNATHEAVHLTAHAKEVGADGALVVVPYYNKPTQRGLYEHFKTVAQEVDIPIIIYNIPSRTCVEISVDTMFKLASECENIVASKESTPNMDRISEIVKRLGESFSVLSGDDSLTLPMMALGAKGVISVANNVMPREVKELIRAALEGDFRRAREIHYYLHDLFKVLFIETNPIPVKTACWMLGMCEKEFRLPLTEMSPENENKLREVLKKYNLPLKN 294
               SCOP domains d2ehhd_ D: automated matches                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 2ehhD00 D:2-294 Aldolase class I                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....ee..eehhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhh...eeeeehhhhhh...hhhhhhhhhhhh..eeeeee...hhhhhhhhhhhh....eeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh..............hhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------DHDPS_1           -----------------------------------------------------------------------------DHDPS_2  PDB: D:132-163         ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ehh D   2 FQGSIVALITPFKEGEVDYEALGNLIEFHVDNGTDAILVCGTTGESPTLTFEEHEKVIEFAVKRAAGRIKVIAGTGGNATHEAVHLTAHAKEVGADGALVVVPYYNKPTQRGLYEHFKTVAQEVDIPIIIYNIPSRTCVEISVDTMFKLASECENIVASKESTPNMDRISEIVKRLGESFSVLSGDDSLTLPMMALGAKGVISVANNVMPREVKELIRAALEGDFRRAREIHYYLHDLFKVLFIETNPIPVKTACWMLGMCEKEFRLPLTEMSPENENKLREVLKKYNLPLKN 294
                                    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   


Chain E from PDB  Type:PROTEIN  Length:294
 aligned with DAPA_AQUAE | O67216 from UniProtKB/Swiss-Prot  Length:294

    Alignment length:294
                                    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    
           DAPA_AQUAE     1 MFQGSIVALITPFKEGEVDYEALGNLIEFHVDNGTDAILVCGTTGESPTLTFEEHEKVIEFAVKRAAGRIKVIAGTGGNATHEAVHLTAHAKEVGADGALVVVPYYNKPTQRGLYEHFKTVAQEVDIPIIIYNIPSRTCVEISVDTMFKLASECENIVASKESTPNMDRISEIVKRLGESFSVLSGDDSLTLPMMALGAKGVISVANNVMPREVKELIRAALEGDFRRAREIHYYLHDLFKVLFIETNPIPVKTACWMLGMCEKEFRLPLTEMSPENENKLREVLKKYNLPLKN 294
               SCOP domains d2ehhe_ E: automated matches                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 2ehhE00 E:1-294 Aldolase class I                                                                                                                                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee....ee..eehhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhh...eeeeehhhhhh...hhhhhhhhhhhh..eeeeee...hhhhhhhhhhhh....eeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh..............hhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------DHDPS_1           -----------------------------------------------------------------------------DHDPS_2  PDB: E:132-163         ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ehh E   1 MFQGSIVALITPFKEGEVDYEALGNLIEFHVDNGTDAILVCGTTGESPTLTFEEHEKVIEFAVKRAAGRIKVIAGTGGNATHEAVHLTAHAKEVGADGALVVVPYYNKPTQRGLYEHFKTVAQEVDIPIIIYNIPSRTCVEISVDTMFKLASECENIVASKESTPNMDRISEIVKRLGESFSVLSGDDSLTLPMMALGAKGVISVANNVMPREVKELIRAALEGDFRRAREIHYYLHDLFKVLFIETNPIPVKTACWMLGMCEKEFRLPLTEMSPENENKLREVLKKYNLPLKN 294
                                    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  (0, 0)

(no "Pfam Domain" information available for 2EHH)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,C,D,E   (DAPA_AQUAE | O67216)
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

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