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(-) Description

Title :  1.95 ANGSTROM CRYSTAL STRUCTURE OF A BIFUNCTIONAL 3-DEOXY-7-PHOSPHOHEPTULONATE SYNTHASE/CHORISMATE MUTASE (AROA) FROM LISTERIA MONOCYTOGENES EGD-E
 
Authors :  A. S. Halavaty, S. H. Light, G. Minasov, L. Shuvalova, K. Kwon, W. F. Ande Center For Structural Genomics Of Infectious Diseases (Csgi
Date :  08 Jul 10  (Deposition) - 28 Jul 10  (Release) - 30 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Bifunctional 3-Deoxy-7-Phosphoheptulonate Synthase/Chorismate Mutase, Listeria Monocytogenes Egd-E, Amino Acid Biosynthesis, Structural Genomics, Infectious Diseases, Center For Structural Genomics Of Infectious Diseases, Csgid, N-Terminal Domain: Isomerase. C-Terminal Domain: (Beta/Alpha) Barrel, Tim Barrel, Transferase, Transferase- Isomerase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. H. Light, A. S. Halavaty, G. Minasov, L. Shuvalova, W. F. Anderson
Structural Analysis Of A 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase With An N-Terminal Chorismate Mutase-Like Regulatory Domain.
Protein Sci. V. 21 887 2012
PubMed-ID: 22505283  |  Reference-DOI: 10.1002/PRO.2075

(-) Compounds

Molecule 1 - 3-DEOXY-D-ARABINO-HEPTULOSONATE 7-PHOSPHATE SYNTHASE
    Chains: A, B
    EC Number: 2.5.1.54, 5.4.99.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG19
    Expression System Strain: BL21(DE3)/MAGIC
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: AROA, LMO1600
    Organism Scientific: LISTERIA MONOCYTOGENES
    Organism Taxid: 169963
    Strain: EGD-E

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2MN2Ligand/IonMANGANESE (II) ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:126 , ARG A:150 , HIS A:296 , GLU A:322 , ASP A:333 , ACT A:363BINDING SITE FOR RESIDUE MN A 362
2AC2SOFTWAREARG A:150 , LYS A:155 , GLN A:206 , LYS A:231 , HIS A:296 , MN A:362 , HOH A:697BINDING SITE FOR RESIDUE ACT A 363
3AC3SOFTWARECYS B:126 , ARG B:150 , HIS B:296 , GLU B:322 , ASP B:333BINDING SITE FOR RESIDUE MN B 362
4AC4SOFTWAREARG B:157 , THR B:158 , HOH B:415 , HOH B:651BINDING SITE FOR RESIDUE ACT B 363

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:64 -Pro A:65
2Gly B:64 -Pro B:65

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3NVT)

(-) 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:345
 aligned with Q8Y6T2_LISMO | Q8Y6T2 from UniProtKB/TrEMBL  Length:361

    Alignment length:350
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357
         Q8Y6T2_LISMO     8 ELRTQVDQLNIDLLELISKRANLVQEIGKIKGTQGSLRFDPLREREMLNTILAANEGPFEDSTVQKLFKEIFKAGLELQEEDHSKALLVSRKNKKEDTIVTVKGLPIGNGEPVFVFGPCSVESYEQVAAVAESIKAKGLKLIRGGAFKPRTSPYDFQGLGLEGLKILKRVSDEYGLGVISEIVTPADIEVALDYVDVIQIGARNMQNFELLKAAGRVDKPILLKRGLSATIEEFIGAAEYIMSQGNGKIILCERGIRTYEKATRNTLDISAVPILKKETHLPVMVDVTHSTGRKDLLLPCAKAALAIEADGVMAEVHPDPAVALSDSAQQMDIPEFEEFWNAILASNLVP 357
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhhhhh.-----..hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh......................eee..eee.....eeeee.....hhhhhhhhhhhhhhh...eee................hhhhhhhhhhhhhhhh.eeeee..hhhhhhhhh....eeeehhhhh.hhhhhhhhhh....eeee.....hhhhhhhhhhhhhh.....eeeee................hhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhh........hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nvt A   8 ELRTQVDQLNIDLLELISKRANLVQEIGKIKG-----RFDPLREREMLNTILAANEGPFEDSTVQKLFKEIFKAGLELQEEDHSKALLVSRKNKKEDTIVTVKGLPIGNGEPVFVFGPCSVESYEQVAAVAESIKAKGLKLIRGGAFKPRTSPYDFQGLGLEGLKILKRVSDEYGLGVISEIVTPADIEVALDYVDVIQIGARNMQNFELLKAAGRVDKPILLKRGLSATIEEFIGAAEYIMSQGNGKIILCERGIRTYEKATRNTLDISAVPILKKETHLPVMVDVTHSTGRKDLLLPCAKAALAIEADGVMAEVHPDPAVALSDSAQQMDIPEFEEFWNAILASNLVP 357
                                    17        27        37 |     |47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357
                                                          39    45                                                                                                                                                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:327
 aligned with Q8Y6T2_LISMO | Q8Y6T2 from UniProtKB/TrEMBL  Length:361

    Alignment length:351
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355 
         Q8Y6T2_LISMO     6 LEELRTQVDQLNIDLLELISKRANLVQEIGKIKGTQGSLRFDPLREREMLNTILAANEGPFEDSTVQKLFKEIFKAGLELQEEDHSKALLVSRKNKKEDTIVTVKGLPIGNGEPVFVFGPCSVESYEQVAAVAESIKAKGLKLIRGGAFKPRTSPYDFQGLGLEGLKILKRVSDEYGLGVISEIVTPADIEVALDYVDVIQIGARNMQNFELLKAAGRVDKPILLKRGLSATIEEFIGAAEYIMSQGNGKIILCERGIRTYEKATRNTLDISAVPILKKETHLPVMVDVTHSTGRKDLLLPCAKAALAIEADGVMAEVHPDPAVALSDSAQQMDIPEFEEFWNAILASNLV 356
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----CM_2-3nvtB03 B:10-86                                                             -----DAHP_synth_1-3nvtB01 B:96-354                                                                                                                                                                                                                                      -- Pfam domains (1)
           Pfam domains (2) ----CM_2-3nvtB04 B:10-86                                                             -----DAHP_synth_1-3nvtB02 B:96-354                                                                                                                                                                                                                                      -- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhh--------------------.hhhhhhhh.....hhhhhhhhhhhhhhhh....----................eee..eee.....eeeee.....hhhhhhhhhhhhhhh...eee................hhhhhhhhhhhhhhhh.eeeee...hhhhhhhh....eeeehhhhh.hhhhhhhhhh....eeee.....hhhhhhhhhhhhhh.....eeeee................hhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhh........hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nvt B   6 LEELRTQVDQLNIDLLELISKRANLVQ--------------------EMLNTILAANEGPFEDSTVQKLFKEIFKAGLELQ----SKALLVSRKNKKEDTIVTVKGLPIGNGEPVFVFGPCSVESYEQVAAVAESIKAKGLKLIRGGAFKPRTSPYDFQGLGLEGLKILKRVSDEYGLGVISEIVTPADIEVALDYVDVIQIGARNMQNFELLKAAGRVDKPILLKRGLSATIEEFIGAAEYIMSQGNGKIILCERGIRTYEKATRNTLDISAVPILKKETHLPVMVDVTHSTGRKDLLLPCAKAALAIEADGVMAEVHPDPAVALSDSAQQMDIPEFEEFWNAILASNLV 356
                                    15        25      |  -         -       |55        65        75        85|    |  95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355 
                                                     32                   53                               86   91
   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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: TIM_barrel (694)
(-)
Clan: no clan defined [family: CM_2] (2)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8Y6T2_LISMO | Q8Y6T2)
molecular function
    GO:0016832    aldehyde-lyase activity    Catalysis of the cleavage of a C-C bond in a molecule containing a hydroxyl group and a carbonyl group to form two smaller molecules, each being an aldehyde or a ketone.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0009073    aromatic amino acid family biosynthetic process    The chemical reactions and pathways resulting in the formation of aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan).
    GO:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
    GO:0046417    chorismate metabolic process    The chemical reactions and pathways involving chorismate, the anion of (3R-trans)-3-((1-carboxyethenyl)oxy)-4-hydroxy-1,5-cyclohexadiene-1-carboxylic acid.

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        Q8Y6T2_LISMO | Q8Y6T2: 3tfc

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