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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE DIHYDRODIPICOLINATE SYNTHETASE FROM PSEUDOMONAS AERUGINOSA
 
Authors :  W. Qiu, R. Lam, V. Romanov, K. Jones, E. F. Pai, N. Y. Chirgadze
Date :  01 Jun 10  (Deposition) - 01 Jun 11  (Release) - 15 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Qiu, R. Lam, V. Romanov, K. Jones, E. F. Pai, N. Y. Chirgadze
Crystal Structure Of A Putative Dihydrodipicolinate Synthetase From Pseudomonas Aeruginosa
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE DIHYDRODIPICOLINATE SYNTHETASE
    Chains: A, B, C, D
    EC Number: 4.2.1.52
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PA0223
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 31)

Asymmetric/Biological Unit (4, 31)
No.NameCountTypeFull Name
1CSO4Mod. Amino AcidS-HYDROXYCYSTEINE
2MG4Ligand/IonMAGNESIUM ION
3MLT3Ligand/IonD-MALATE
4MSE20Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:175 , VAL A:178 , ASP A:179 , VAL A:181 , HOH A:324 , HOH A:399BINDING SITE FOR RESIDUE MG A 316
2AC2SOFTWAREARG A:53 , LEU A:233 , ILE A:234 , PRO A:235 , THR A:236 , ARG A:313 , HOH A:347 , HOH A:771BINDING SITE FOR RESIDUE MLT A 317
3AC3SOFTWAREVAL B:175 , VAL B:178 , ASP B:179 , VAL B:181 , HOH B:361 , HOH B:602BINDING SITE FOR RESIDUE MG B 316
4AC4SOFTWAREVAL C:175 , VAL C:178 , ASP C:179 , VAL C:181 , HOH C:334 , HOH C:829BINDING SITE FOR RESIDUE MG C 316
5AC5SOFTWAREARG C:53 , LEU C:233 , ILE C:234 , PRO C:235 , THR C:236 , ARG C:313 , HOH C:449BINDING SITE FOR RESIDUE MLT C 317
6AC6SOFTWAREVAL D:175 , VAL D:178 , ASP D:179 , VAL D:181 , HOH D:332 , HOH D:1029BINDING SITE FOR RESIDUE MG D 316
7AC7SOFTWARELEU D:233 , ILE D:234 , PRO D:235 , THR D:236 , LEU D:237 , ARG D:313BINDING SITE FOR RESIDUE MLT D 317

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NA8)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Leu A:292 -Pro A:293
2Leu B:292 -Pro B:293
3Leu C:292 -Pro C:293
4Leu D:292 -Pro D:293

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3NA8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3NA8)

(-) Exons   (0, 0)

(no "Exon" information available for 3NA8)

(-) 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 Q9I6R5_PSEAE | Q9I6R5 from UniProtKB/TrEMBL  Length:293

    Alignment length:291
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292 
         Q9I6R5_PSEAE     3 ASIHGIIGYTITPFAADGGLDLPALGRSIERLIDGGVHAIAPLGSTGEGAYLSDPEWDEVVDFTLKTVAHRVPTIVSVSDLTTAKTVRRAQFAESLGAEAVMVLPISYWKLNEAEVFQHYRAVGEAIGVPVMLYNNPGTSGIDMSVELILRIVREVDNVTMVKESTGDIQRMHKLRLLGEGRVPFYNGCNPLALEAFVAGAKGWCSAAPNLIPTLNGQLYQAVLDGDLEKARALFYRQLPLLDFILRRGLPTTIKAGLGLSGLEVGAPRLPVQALDTEGCRYLQGLLEELR 293
               SCOP domains d3na8a_ A: automated matches                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee...........hhhhhhhhhhhhhhh...eee..hhhhhhhhhhhhhhhhhhhhhhhhhh.....eee....hhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhh...eeeeehhhhhh...hhhhhhhhhhhh..eeeeee...hhhhhhhhhhhh.....eee.hhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3na8 A  23 ASIHGIIGYTITPFAADGGLDLPALGRSIERLIDGGVHAIAPLGSTGEGAYLSDPEWDEVVDFTLKTVAHRVPTIVSVSDLTTAKTVRRAQFAESLGAEAVmVLPISYWKLNEAEVFQHYRAVGEAIGVPVmLYNNPGTSGIDmSVELILRIVREVDNVTmVKESTGDIQRmHKLRLLGEGRVPFYNGcNPLALEAFVAGAKGWCSAAPNLIPTLNGQLYQAVLDGDLEKARALFYRQLPLLDFILRRGLPTTIKAGLGLSGLEVGAPRLPVQALDTEGCRYLQGLLEELR 313
                                    32        42        52        62        72        82        92       102       112       122 |     132       142       152 |     162   |   172       182|      192 |     202       212       222       232       242       252       262       272       282       292       302       312 
                                                                                                                               124-MSE                       154-MSE     166-MSE          183-MSE    194-MSE          211-CSO                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:290
 aligned with Q9I6R5_PSEAE | Q9I6R5 from UniProtKB/TrEMBL  Length:293

    Alignment length:291
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292 
         Q9I6R5_PSEAE     3 ASIHGIIGYTITPFAADGGLDLPALGRSIERLIDGGVHAIAPLGSTGEGAYLSDPEWDEVVDFTLKTVAHRVPTIVSVSDLTTAKTVRRAQFAESLGAEAVMVLPISYWKLNEAEVFQHYRAVGEAIGVPVMLYNNPGTSGIDMSVELILRIVREVDNVTMVKESTGDIQRMHKLRLLGEGRVPFYNGCNPLALEAFVAGAKGWCSAAPNLIPTLNGQLYQAVLDGDLEKARALFYRQLPLLDFILRRGLPTTIKAGLGLSGLEVGAPRLPVQALDTEGCRYLQGLLEELR 293
               SCOP domains d3na8b_ B: auto mated matches                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee......-....hhhhhhhhhhhhhhh...eee......hhhhhhhhhhhhhhhhhhhhhh.....eee....hhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhh...eeeeehhhhhh...hhhhhhhhhhhh..eeeeee...hhhhhhhhhhhh.....eee.hhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3na8 B  23 ASIHGIIGYTITPFA-DGGLDLPALGRSIERLIDGGVHAIAPLGSTGEGAYLSDPEWDEVVDFTLKTVAHRVPTIVSVSDLTTAKTVRRAQFAESLGAEAVmVLPISYWKLNEAEVFQHYRAVGEAIGVPVmLYNNPGTSGIDmSVELILRIVREVDNVTmVKESTGDIQRmHKLRLLGEGRVPFYNGcNPLALEAFVAGAKGWCSAAPNLIPTLNGQLYQAVLDGDLEKARALFYRQLPLLDFILRRGLPTTIKAGLGLSGLEVGAPRLPVQALDTEGCRYLQGLLEELR 313
                                    32    | | 42        52        62        72        82        92       102       112       122 |     132       142       152 |     162   |   172       182|      192 |     202       212       222       232       242       252       262       272       282       292       302       312 
                                         37 |                                                                                  124-MSE                       154-MSE     166-MSE          183-MSE    194-MSE          211-CSO                                                                                                  
                                           39                                                                                                                                                                                                                                                                                  


Chain C from PDB  Type:PROTEIN  Length:291
 aligned with Q9I6R5_PSEAE | Q9I6R5 from UniProtKB/TrEMBL  Length:293

    Alignment length:291
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292 
         Q9I6R5_PSEAE     3 ASIHGIIGYTITPFAADGGLDLPALGRSIERLIDGGVHAIAPLGSTGEGAYLSDPEWDEVVDFTLKTVAHRVPTIVSVSDLTTAKTVRRAQFAESLGAEAVMVLPISYWKLNEAEVFQHYRAVGEAIGVPVMLYNNPGTSGIDMSVELILRIVREVDNVTMVKESTGDIQRMHKLRLLGEGRVPFYNGCNPLALEAFVAGAKGWCSAAPNLIPTLNGQLYQAVLDGDLEKARALFYRQLPLLDFILRRGLPTTIKAGLGLSGLEVGAPRLPVQALDTEGCRYLQGLLEELR 293
               SCOP domains d3na8c_ C: automated matches                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee...........hhhhhhhhhhhhhhh...eee..hhhhhhhhhhhhhhhhhhhhhhhhhh.....eee....hhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhh....eeeeehhhhhh...hhhhhhhhhhhh..eeeeee...hhhhhhhhhhhh.....eee.hhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3na8 C  23 ASIHGIIGYTITPFAADGGLDLPALGRSIERLIDGGVHAIAPLGSTGEGAYLSDPEWDEVVDFTLKTVAHRVPTIVSVSDLTTAKTVRRAQFAESLGAEAVmVLPISYWKLNEAEVFQHYRAVGEAIGVPVmLYNNPGTSGIDmSVELILRIVREVDNVTmVKESTGDIQRmHKLRLLGEGRVPFYNGcNPLALEAFVAGAKGWCSAAPNLIPTLNGQLYQAVLDGDLEKARALFYRQLPLLDFILRRGLPTTIKAGLGLSGLEVGAPRLPVQALDTEGCRYLQGLLEELR 313
                                    32        42        52        62        72        82        92       102       112       122 |     132       142       152 |     162   |   172       182|      192 |     202       212       222       232       242       252       262       272       282       292       302       312 
                                                                                                                               124-MSE                       154-MSE     166-MSE          183-MSE    194-MSE          211-CSO                                                                                                  


Chain D from PDB  Type:PROTEIN  Length:290
 aligned with Q9I6R5_PSEAE | Q9I6R5 from UniProtKB/TrEMBL  Length:293

    Alignment length:290
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293
         Q9I6R5_PSEAE     4 SIHGIIGYTITPFAADGGLDLPALGRSIERLIDGGVHAIAPLGSTGEGAYLSDPEWDEVVDFTLKTVAHRVPTIVSVSDLTTAKTVRRAQFAESLGAEAVMVLPISYWKLNEAEVFQHYRAVGEAIGVPVMLYNNPGTSGIDMSVELILRIVREVDNVTMVKESTGDIQRMHKLRLLGEGRVPFYNGCNPLALEAFVAGAKGWCSAAPNLIPTLNGQLYQAVLDGDLEKARALFYRQLPLLDFILRRGLPTTIKAGLGLSGLEVGAPRLPVQALDTEGCRYLQGLLEELR 293
               SCOP domains d3na8d_ D: automated matches                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) DHDPS-3na8D01 D:24-313                                                                                                                                                                                                                                                                             Pfam domains (1)
           Pfam domains (2) DHDPS-3na8D02 D:24-313                                                                                                                                                                                                                                                                             Pfam domains (2)
           Pfam domains (3) DHDPS-3na8D03 D:24-313                                                                                                                                                                                                                                                                             Pfam domains (3)
           Pfam domains (4) DHDPS-3na8D04 D:24-313                                                                                                                                                                                                                                                                             Pfam domains (4)
         Sec.struct. author ...eeeee...........hhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhhhhhhhhhhhh.....eee....hhhhhhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhh...eeeeehhhhhh...hhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhh....eee.hhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3na8 D  24 SIHGIIGYTITPFAADGGLDLPALGRSIERLIDGGVHAIAPLGSTGEGAYLSDPEWDEVVDFTLKTVAHRVPTIVSVSDLTTAKTVRRAQFAESLGAEAVmVLPISYWKLNEAEVFQHYRAVGEAIGVPVmLYNNPGTSGIDmSVELILRIVREVDNVTmVKESTGDIQRmHKLRLLGEGRVPFYNGcNPLALEAFVAGAKGWCSAAPNLIPTLNGQLYQAVLDGDLEKARALFYRQLPLLDFILRRGLPTTIKAGLGLSGLEVGAPRLPVQALDTEGCRYLQGLLEELR 313
                                    33        43        53        63        73        83        93       103       113       123|      133       143       153|      163  |    173       183       193|      203       213       223       233       243       253       263       273       283       293       303       313
                                                                                                                              124-MSE                       154-MSE     166-MSE          183-MSE    194-MSE          211-CSO
   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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NA8)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: TIM_barrel (694)
(-)
Family: DHDPS (40)
(-)
Pseudomonas aeruginosa (2)
1aDHDPS-3na8D01D:24-313
1bDHDPS-3na8D02D:24-313
1cDHDPS-3na8D03D:24-313
1dDHDPS-3na8D04D:24-313

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q9I6R5_PSEAE | Q9I6R5)
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.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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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