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(-) Description

Title :  2.49 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF SHIKIMATE 5-DEHYDROGENASE (AROE) FROM VIBRIO CHOLERAE O1 BIOVAR ELTOR STR. N16961 IN COMPLEX WITH SHIKIMATE
 
Authors :  A. S. Halavaty, S. H. Light, L. Shuvalova, L. Papazisi, W. F. Anderson, C Structural Genomics Of Infectious Diseases (Csgid)
Date :  02 Nov 10  (Deposition) - 24 Nov 10  (Release) - 24 Nov 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.49
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Shikimate 5-Dehydrogenase, Shikimate, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Alpha/Beta Domain, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. S. Halavaty, S. H. Light, L. Shuvalova, L. Papazisi, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
2. 49 Angstrom Resolution Crystal Structure Of Shikimate 5-Dehydrogenase (Aroe) From Vibrio Cholerae O1 Biovar Eltor Str. N16961 In Complex With Shikimate
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SHIKIMATE DEHYDROGENASE
    Chains: A, B, C, D
    EC Number: 1.1.1.25
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)/MAGIC
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AROE, VC_0056
    Organism Scientific: VIBRIO CHOLERAE O1 BIOVAR ELTOR
    Organism Taxid: 243277
    Strain: N16961

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A  D
Biological Unit 2 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1SKM4Ligand/Ion(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLICACID
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1SKM2Ligand/Ion(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLICACID
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1SKM2Ligand/Ion(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLICACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:18 , SER A:20 , ASN A:63 , THR A:65 , LYS A:69 , ASN A:90 , ASP A:106 , GLN A:248 , HOH A:287BINDING SITE FOR RESIDUE SKM A 279
2AC2SOFTWAREVAL B:10 , SER B:18 , SER B:20 , ASN B:63 , THR B:65 , LYS B:69 , ASN B:90 , ASP B:106 , GLN B:248 , HOH B:297BINDING SITE FOR RESIDUE SKM B 279
3AC3SOFTWAREVAL C:10 , SER C:18 , SER C:20 , ASN C:63 , THR C:65 , LYS C:69 , ASN C:90 , ASP C:106 , GLN C:248BINDING SITE FOR RESIDUE SKM C 279
4AC4SOFTWAREVAL D:10 , SER D:18 , SER D:20 , THR D:65 , LYS D:69 , ASN D:90 , ASP D:106 , GLN D:248BINDING SITE FOR RESIDUE SKM D 279

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:41 -D:41
2B:41 -C:41

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Asn A:13 -Pro A:14
2Pro A:14 -Ile A:15
3Val A:66 -Pro A:67
4Val B:66 -Pro B:67
5Asn C:13 -Pro C:14
6Val C:66 -Pro C:67
7Asn D:13 -Pro D:14
8Val D:66 -Pro D:67

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3PGJ)

(-) 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:272
 aligned with AROE_VIBCH | Q9KVT3 from UniProtKB/Swiss-Prot  Length:278

    Alignment length:272
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274  
           AROE_VIBCH     5 IDQYAVFGNPINHSKSPFIHTLFARQTQQSMIYTAQCVPVDGFTEAAKHFFAQGGRGCNVTVPFKEEAYRFADRLTERARLAGAVNTLKKLDDGEILGDNTDGEGLVQDLLAQQVLLKGATILLIGAGGAARGVLKPLLDQQPASITVTNRTFAKAEQLAELVAAYGEVKAQAFEQLKQSYDVIINSTSASLDGELPAIDPVIFSSRSVCYDMMYGKGYTVFNQWARQHGCAQAIDGLGMLVGQAAESFMLWRGLRPGTKQILRELRKNLEG 276
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee......hhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhh.eeeeee...hhhhhhhhh.eehhhhhhhh...eeee.....eeee.hhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhh.eeeee.hhh.....eeee..hhhhhh.....hhhhh....eeee.......hhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pgj A   5 IDQYAVFGNPINHSKSPFIHTLFARQTQQSMIYTAQCVPVDGFTEAAKHFFAQGGRGCNVTVPFKEEAYRFADRLTERARLAGAVNTLKKLDDGEILGDNTDGEGLVQDLLAQQVLLKGATILLIGAGGAARGVLKPLLDQQPASITVTNRTFAKAEQLAELVAAYGEVKAQAFEQLKQSYDVIINSTSASLDGELPAIDPVIFSSRSVCYDMMYGKGYTVFNQWARQHGCAQAIDGLGMLVGQAAESFMLWRGLRPGTKQILRELRKNLEG 276
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274  


Chain B from PDB  Type:PROTEIN  Length:268
 aligned with AROE_VIBCH | Q9KVT3 from UniProtKB/Swiss-Prot  Length:278

    Alignment length:271
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274 
           AROE_VIBCH     5 IDQYAVFGNPINHSKSPFIHTLFARQTQQSMIYTAQCVPVDGFTEAAKHFFAQGGRGCNVTVPFKEEAYRFADRLTERARLAGAVNTLKKLDDGEILGDNTDGEGLVQDLLAQQVLLKGATILLIGAGGAARGVLKPLLDQQPASITVTNRTFAKAEQLAELVAAYGEVKAQAFEQLKQSYDVIINSTSASLDGELPAIDPVIFSSRSVCYDMMYGKGYTVFNQWARQHGCAQAIDGLGMLVGQAAESFMLWRGLRPGTKQILRELRKNLE 275
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.---..hhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhh...eeee...hhhhhhhhh.eehhhhhhhh...eeee.....eeee.hhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhh...eeeee.hhh.....eeee.............hhhhh....eeee.......hhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pgj B   5 IDQYAVFGN---HSKSPFIHTLFARQTQQSMIYTAQCVPVDGFTEAAKHFFAQGGRGCNVTVPFKEEAYRFADRLTERARLAGAVNTLKKLDDGEILGDNTDGEGLVQDLLAQQVLLKGATILLIGAGGAARGVLKPLLDQQPASITVTNRTFAKAEQLAELVAAYGEVKAQAFEQLKQSYDVIINSTSASLDGELPAIDPVIFSSRSVCYDMMYGKGYTVFNQWARQHGCAQAIDGLGMLVGQAAESFMLWRGLRPGTKQILRELRKNLE 275
                                    |-  |     24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274 
                                   13  17                                                                                                                                                                                                                                                                  


Chain C from PDB  Type:PROTEIN  Length:264
 aligned with AROE_VIBCH | Q9KVT3 from UniProtKB/Swiss-Prot  Length:278

    Alignment length:271
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274 
           AROE_VIBCH     5 IDQYAVFGNPINHSKSPFIHTLFARQTQQSMIYTAQCVPVDGFTEAAKHFFAQGGRGCNVTVPFKEEAYRFADRLTERARLAGAVNTLKKLDDGEILGDNTDGEGLVQDLLAQQVLLKGATILLIGAGGAARGVLKPLLDQQPASITVTNRTFAKAEQLAELVAAYGEVKAQAFEQLKQSYDVIINSTSASLDGELPAIDPVIFSSRSVCYDMMYGKGYTVFNQWARQHGCAQAIDGLGMLVGQAAESFMLWRGLRPGTKQILRELRKNLE 275
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee......hhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhh...eeee...hhhhhhhhh.eehhhhhhhh...eeee.....eeee.hhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhh....eeeee.......eeeeee...-------...hhh.eeeeeeeee.......hhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pgj C   5 IDQYAVFGNPINHSKSPFIHTLFARQTQQSMIYTAQCVPVDGFTEAAKHFFAQGGRGCNVTVPFKEEAYRFADRLTERARLAGAVNTLKKLDDGEILGDNTDGEGLVQDLLAQQVLLKGATILLIGAGGAARGVLKPLLDQQPASITVTNRTFAKAEQLAELVAAYGEVKAQAFEQLKQSYDVIINSTS-------PAIDPVIFSSRSVCYDMMYGKGYTVFNQWARQHGCAQAIDGLGMLVGQAAESFMLWRGLRPGTKQILRELRKNLE 275
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184        |-      |204       214       224       234       244       254       264       274 
                                                                                                                                                                                                                      193     201                                                                          


Chain D from PDB  Type:PROTEIN  Length:271
 aligned with AROE_VIBCH | Q9KVT3 from UniProtKB/Swiss-Prot  Length:278

    Alignment length:271
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274 
           AROE_VIBCH     5 IDQYAVFGNPINHSKSPFIHTLFARQTQQSMIYTAQCVPVDGFTEAAKHFFAQGGRGCNVTVPFKEEAYRFADRLTERARLAGAVNTLKKLDDGEILGDNTDGEGLVQDLLAQQVLLKGATILLIGAGGAARGVLKPLLDQQPASITVTNRTFAKAEQLAELVAAYGEVKAQAFEQLKQSYDVIINSTSASLDGELPAIDPVIFSSRSVCYDMMYGKGYTVFNQWARQHGCAQAIDGLGMLVGQAAESFMLWRGLRPGTKQILRELRKNLE 275
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----Shikimate_dh_N-3pgjD05 D:10-92                                                     ---------------------Shikimate_DH-3pgjD01 D:114-218                                                                           --------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----Shikimate_dh_N-3pgjD06 D:10-92                                                     ---------------------Shikimate_DH-3pgjD02 D:114-218                                                                           --------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) -----Shikimate_dh_N-3pgjD07 D:10-92                                                     ---------------------Shikimate_DH-3pgjD03 D:114-218                                                                           --------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) -----Shikimate_dh_N-3pgjD08 D:10-92                                                     ---------------------Shikimate_DH-3pgjD04 D:114-218                                                                           --------------------------------------------------------- Pfam domains (4)
         Sec.struct. author .eeeeeee......hhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhh.eeeeee...hhhhhhhhh.eehhhhhhhh...eeee.....eeee.hhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhh.eeeee.hhh.....eeee..hhhhhh.....hhhhh....eeee.......hhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pgj D   5 IDQYAVFGNPINHSKSPFIHTLFARQTQQSMIYTAQCVPVDGFTEAAKHFFAQGGRGCNVTVPFKEEAYRFADRLTERARLAGAVNTLKKLDDGEILGDNTDGEGLVQDLLAQQVLLKGATILLIGAGGAARGVLKPLLDQQPASITVTNRTFAKAEQLAELVAAYGEVKAQAFEQLKQSYDVIINSTSASLDGELPAIDPVIFSSRSVCYDMMYGKGYTVFNQWARQHGCAQAIDGLGMLVGQAAESFMLWRGLRPGTKQILRELRKNLE 275
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274
   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 3PGJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 8)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)
(-)
Clan: no clan defined [family: Shikimate_dh_N] (15)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (AROE_VIBCH | Q9KVT3)
molecular function
    GO:0050661    NADP binding    Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0004764    shikimate 3-dehydrogenase (NADP+) activity    Catalysis of the reaction: shikimate + NADP+ = 3-dehydroshikimate + NADPH + H+.
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:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
    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:0009423    chorismate biosynthetic process    The chemical reactions and pathways resulting in the formation of the unsymmetrical ether derived from phosphoenolpyruvate and 5-phosphoshikimic acid formed as an intermediate in the biosynthesis of aromatic amino acids and many other compounds.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0019632    shikimate metabolic process    The chemical reactions and pathways involving shikimate, (3R,4S,5R)--3,4,5-trihydroxycyclohex-1-ene-1-carboxylate, the anion of shikimic acid. It is an important intermediate in the biosynthesis of aromatic amino acids.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

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 Related Entries

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

UniProtKB/Swiss-Prot
        AROE_VIBCH | Q9KVT3: 3sef

(-) Related Entries Specified in the PDB File

3o8q 1.45 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF SHIKIMATE 5- DEHYDROGENASE (AROE) FROM VIBRIO CHOLERAE RELATED ID: IDP90792 RELATED DB: TARGETDB