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(-) Description

Title :  CRYSTAL STRUCTURE OF 2-DEHYDRO-3-DEOXYPHOSPHOGLUCONATE ALDOLASE FROM VIBRIO FISCHERI ES114
 
Authors :  B. Nocek, N. Marshall, B. Feldmann, A. Joachimiak, Midwest Center Fo Structural Genomics (Mcsg)
Date :  16 Jul 10  (Deposition) - 08 Sep 10  (Release) - 08 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Kdpg Aldolase, , Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Nocek, N. Marshall, B. Feldmann, A. Joachimiak
Crystal Structure Of 2-Dehydro-3-Deoxyphosphogluconate Aldolase From Vibrio Fischeri Es114
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 2-DEHYDRO-3-DEOXYPHOSPHOGLUCONATE ALDOLASE
    Chains: A, B, C, D
    EC Number: 4.1.2.14, 4.1.3.16
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG19
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: VF_2509
    Organism Scientific: VIBRIO FISCHERI
    Organism Taxid: 312309
    Strain: ES114

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 38)

Asymmetric Unit (2, 38)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2MSE36Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 18)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2MSE18Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 18)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2MSE18Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:34 , HOH A:1217 , HOH A:1218 , HOH A:1219 , HOH A:1220 , HOH A:1221BINDING SITE FOR RESIDUE MG A 601
2AC2SOFTWAREASP A:194 , HOH A:325 , HOH A:1213 , HOH A:1225 , HOH A:1226 , HOH A:1227BINDING SITE FOR RESIDUE MG A 247

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Phe A:162 -Pro A:163
2Phe B:162 -Pro B:163
3Phe C:162 -Pro C:163
4Phe D:162 -Pro D:163

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3NZR)

(-) Sequences/Alignments

Asymmetric 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:245
 aligned with Q5E1U2_VIBF1 | Q5E1U2 from UniProtKB/TrEMBL  Length:246

    Alignment length:245
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241     
         Q5E1U2_VIBF1     2 SLKANFYKNRVCLNVLAGSVDNAADIYDAAEGHVLVGVLSKNYPDVDTAVEDMKKYSEVTNNAVSVGLGAGDPNQSMMVSLISQHVQPQHINQVFTGVATSRALAGQDKSIVNGLISPTGTVGMVKISTGPLSSRSEDAIVPVETAIAMLKDMGGSSVKYFPMGGLETREEFACVAKACADKDFWLEPTGGIDLENYEEIMQIALDAGVSKIIPHIYSSIIDKATGNTRPEDVKTLLDMTKKLLN 246
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh..eeee..hhhhhhhhhhhh...eeeeee.hhh.hhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhh..ee..hhhhhhhhhhhhh....eeeeee.......eee.....hhhhh...eeehhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhhh.........hhh.ee....eehhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nzr A   2 SLKANFYKNRVCLNVLAGSVDNAADIYDAAEGHVLVGVLSKNYPDVDTAVEDmKKYSEVTNNAVSVGLGAGDPNQSmmVSLISQHVQPQHINQVFTGVATSRALAGQDKSIVNGLISPTGTVGmVKISTGPLSSRSEDAIVPVETAIAmLKDmGGSSVKYFPmGGLETREEFACVAKACADKDFWLEPTGGIDLENYEEImQIALDAGVSKIIPHIYSSIIDKATGNTRPEDVKTLLDmTKKLLL 246
                                    11        21        31        41        51  |     61        71      ||81        91       101       111       121   |   131       141       151  |    161  |    171       181       191       201|      211       221       231       241     
                                                                               54-MSE                  78-MSE                                        125-MSE                  150-MSE       164-MSE                               202-MSE                               240-MSE  
                                                                                                        79-MSE                                                                    154-MSE                                                                                        


Chain B from PDB  Type:PROTEIN  Length:245
 aligned with Q5E1U2_VIBF1 | Q5E1U2 from UniProtKB/TrEMBL  Length:246

    Alignment length:245
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241     
         Q5E1U2_VIBF1     2 SLKANFYKNRVCLNVLAGSVDNAADIYDAAEGHVLVGVLSKNYPDVDTAVEDMKKYSEVTNNAVSVGLGAGDPNQSMMVSLISQHVQPQHINQVFTGVATSRALAGQDKSIVNGLISPTGTVGMVKISTGPLSSRSEDAIVPVETAIAMLKDMGGSSVKYFPMGGLETREEFACVAKACADKDFWLEPTGGIDLENYEEIMQIALDAGVSKIIPHIYSSIIDKATGNTRPEDVKTLLDMTKKLLN 246
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh..eeee..hhhhhhhhhhhh...eeeeee.hhh.hhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhh..ee..hhhhhhhhhhhhh....eeeeee.......eee.....hhhhh...eeehhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhh........hhhhh.......hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nzr B   2 SLKANFYKNRVCLNVLAGSVDNAADIYDAAEGHVLVGVLSKNYPDVDTAVEDmKKYSEVTNNAVSVGLGAGDPNQSmmVSLISQHVQPQHINQVFTGVATSRALAGQDKSIVNGLISPTGTVGmVKISTGPLSSRSEDAIVPVETAIAmLKDmGGSSVKYFPmGGLETREEFACVAKACADKDFWLEPTGGIDLENYEEImQIALDAGVSKIIPHIYSSIIDKATGNTRPEDVKTLLDmTKKLLL 246
                                    11        21        31        41        51  |     61        71      ||81        91       101       111       121   |   131       141       151  |    161  |    171       181       191       201|      211       221       231       241     
                                                                               54-MSE                  78-MSE                                        125-MSE                  150-MSE       164-MSE                               202-MSE                               240-MSE  
                                                                                                        79-MSE                                                                    154-MSE                                                                                        


Chain C from PDB  Type:PROTEIN  Length:245
 aligned with Q5E1U2_VIBF1 | Q5E1U2 from UniProtKB/TrEMBL  Length:246

    Alignment length:245
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241     
         Q5E1U2_VIBF1     2 SLKANFYKNRVCLNVLAGSVDNAADIYDAAEGHVLVGVLSKNYPDVDTAVEDMKKYSEVTNNAVSVGLGAGDPNQSMMVSLISQHVQPQHINQVFTGVATSRALAGQDKSIVNGLISPTGTVGMVKISTGPLSSRSEDAIVPVETAIAMLKDMGGSSVKYFPMGGLETREEFACVAKACADKDFWLEPTGGIDLENYEEIMQIALDAGVSKIIPHIYSSIIDKATGNTRPEDVKTLLDMTKKLLN 246
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh..eeee..hhhhhhhhhhhh...eeeeee.hhh.hhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhh..ee..hhhhhhhhhhhhh....eeeeee.......eee.....hhhhh...eeehhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhhh.......eehhhhh.......hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nzr C   2 SLKANFYKNRVCLNVLAGSVDNAADIYDAAEGHVLVGVLSKNYPDVDTAVEDmKKYSEVTNNAVSVGLGAGDPNQSmmVSLISQHVQPQHINQVFTGVATSRALAGQDKSIVNGLISPTGTVGmVKISTGPLSSRSEDAIVPVETAIAmLKDmGGSSVKYFPmGGLETREEFACVAKACADKDFWLEPTGGIDLENYEEImQIALDAGVSKIIPHIYSSIIDKATGNTRPEDVKTLLDmTKKLLL 246
                                    11        21        31        41        51  |     61        71      ||81        91       101       111       121   |   131       141       151  |    161  |    171       181       191       201|      211       221       231       241     
                                                                               54-MSE                  78-MSE                                        125-MSE                  150-MSE       164-MSE                               202-MSE                               240-MSE  
                                                                                                        79-MSE                                                                    154-MSE                                                                                        


Chain D from PDB  Type:PROTEIN  Length:245
 aligned with Q5E1U2_VIBF1 | Q5E1U2 from UniProtKB/TrEMBL  Length:246

    Alignment length:245
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241     
         Q5E1U2_VIBF1     2 SLKANFYKNRVCLNVLAGSVDNAADIYDAAEGHVLVGVLSKNYPDVDTAVEDMKKYSEVTNNAVSVGLGAGDPNQSMMVSLISQHVQPQHINQVFTGVATSRALAGQDKSIVNGLISPTGTVGMVKISTGPLSSRSEDAIVPVETAIAMLKDMGGSSVKYFPMGGLETREEFACVAKACADKDFWLEPTGGIDLENYEEIMQIALDAGVSKIIPHIYSSIIDKATGNTRPEDVKTLLDMTKKLLN 246
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------DUF1341-3nzrD01 D:8-225                                                                                                                                                                                                   --------------------- Pfam domains (1)
           Pfam domains (2) ------DUF1341-3nzrD02 D:8-225                                                                                                                                                                                                   --------------------- Pfam domains (2)
           Pfam domains (3) ------DUF1341-3nzrD03 D:8-225                                                                                                                                                                                                   --------------------- Pfam domains (3)
           Pfam domains (4) ------DUF1341-3nzrD04 D:8-225                                                                                                                                                                                                   --------------------- Pfam domains (4)
         Sec.struct. author .....hhhhh..eeee..hhhhhhhhhhhh...eeeeee.hhh.hhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhh..ee..hhhhhhhhhhhhh....eeeeeeee.....eee.....hhhhh...eeehhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhh......eehhhhh.......hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nzr D   2 SLKANFYKNRVCLNVLAGSVDNAADIYDAAEGHVLVGVLSKNYPDVDTAVEDmKKYSEVTNNAVSVGLGAGDPNQSmmVSLISQHVQPQHINQVFTGVATSRALAGQDKSIVNGLISPTGTVGmVKISTGPLSSRSEDAIVPVETAIAmLKDmGGSSVKYFPmGGLETREEFACVAKACADKDFWLEPTGGIDLENYEEImQIALDAGVSKIIPHIYSSIIDKATGNTRPEDVKTLLDmTKKLLL 246
                                    11        21        31        41        51  |     61        71      ||81        91       101       111       121   |   131       141       151  |    161  |    171       181       191       201|      211       221       231       241     
                                                                               54-MSE                  78-MSE                                        125-MSE                  150-MSE       164-MSE                               202-MSE                               240-MSE  
                                                                                                        79-MSE                                                                    154-MSE
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3NZR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q5E1U2_VIBF1 | Q5E1U2)
molecular function
    GO:0008675    2-dehydro-3-deoxy-phosphogluconate aldolase activity    Catalysis of the reaction: 2-dehydro-3-deoxy-D-gluconate 6-phosphate = pyruvate + D-glyceraldehyde 3-phosphate.
    GO:0008700    4-hydroxy-2-oxoglutarate aldolase activity    Catalysis of the reaction: 4-hydroxy-2-oxoglutarate = pyruvate + glyoxylate.
    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.

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