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(-) Description

Title :  2.4 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF SHIKIMATE 5-DEHYDROGENASE (AROE) FROM VIBRIO CHOLERAE O1 BIOVAR ELTOR STR. N16961 IN COMPLEX WITH SHIKIMATE AND NADPH
 
Authors :  A. S. Halavaty, S. H. Light, G. Minasov, L. Shuvalova, L. Papazisi, W. F. Center For Structural Genomics Of Infectious Diseases (Csgi
Date :  10 Jun 11  (Deposition) - 27 Jul 11  (Release) - 10 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Shikimate, Alpha/Beta Domain, Rossmann Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. S. Halavaty, S. H. Light, G. Minasov, L. Shuvalova, L. Papazisi, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
2. 4 Angstrom Resolution Crystal Structure Of Shikimate 5-Dehydrogenase (Aroe) From Vibrio Cholerae O1 Biovar Eltor Str. N16961 In Complex With Shikimate And Nadph
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SHIKIMATE 5-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/MAGIC
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AROE, VC_0056
    Organism Scientific: VIBRIO CHOLERAE O1 BIOVAR EL TOR
    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  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
2SKM2Ligand/Ion(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLICACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
2SKM-1Ligand/Ion(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLICACID
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
2SKM2Ligand/Ion(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLICACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:131 , GLY A:132 , GLY A:133 , ALA A:134 , ASN A:154 , ARG A:155 , THR A:156 , LYS A:159 , SER A:191 , THR A:192 , SER A:193 , ALA A:194 , MET A:218BINDING SITE FOR RESIDUE NDP A 279
2AC2SOFTWAREALA B:131 , GLY B:132 , GLY B:133 , ALA B:134 , ASN B:154 , ARG B:155 , THR B:156 , LYS B:159 , SER B:191 , THR B:192 , SER B:193 , GLU B:199 , PRO B:201 , MET B:218 , TYR B:219 , HOH B:282 , HOH B:291 , HOH B:292BINDING SITE FOR RESIDUE NDP B 279
3AC3SOFTWARESER 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:299BINDING SITE FOR RESIDUE SKM B 280
4AC4SOFTWARESER C:18 , SER C:20 , THR C:65 , LYS C:69 , ASN C:90 , ASP C:106 , GLN C:248BINDING SITE FOR RESIDUE SKM C 279

(-) SS Bonds  (2, 2)

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

(-) Cis Peptide Bonds  (6, 6)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3SEF)

(-) 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:268
 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..---.hhhhhhhhhhhhh...eeeeeee..-.hhhhhhhhhhhh...eeee...hhhhhhhhh.eehhhhhhhh...eeee.....eeee.hhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhh.eeeehhhhh.....eeee..hhhhhh.....hhhhh....eeee.......hhhhhhhhh....eee.hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sef A   5 IDQYAVFGNP---SKSPFIHTLFARQTQQSMIYTAQCVP-DGFTEAAKHFFAQGGRGCNVTVPFKEEAYRFADRLTERARLAGAVNTLKKLDDGEILGDNTDGEGLVQDLLAQQVLLKGATILLIGAGGAARGVLKPLLDQQPASITVTNRTFAKAEQLAELVAAYGEVKAQAFEQLKQSYDVIINSTSASLDGELPAIDPVIFSSRSVCYDMMYGKGYTVFNQWARQHGCAQAIDGLGMLVGQAAESFMLWRGLRPGTKQILRELRKNLEG 276
                                    14   |    24        34        |-|       54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274  
                                    14  18                       43 |                                                                                                                                                                                                                                       
                                                                   45                                                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:269
 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 .eeeeee..---..hhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhh..eeee...hhhhhhhhh.eehhhhhhhh...eeee.....eeee.hhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhh.eee.hhhhh.....eeee..hhhhhh.....hhhhh....eeee.......hhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sef B   5 IDQYAVFGN---HSKSPFIHTLFARQTQQSMIYTAQCVPVDGFTEAAKHFFAQGGRGCNVTVPFKEEAYRFADRLTERARLAGAVNTLKKLDDGEILGDNTDGEGLVQDLLAQQVLLKGATILLIGAGGAARGVLKPLLDQQPASITVTNRTFAKAEQLAELVAAYGEVKAQAFEQLKQSYDVIINSTSASLDGELPAIDPVIFSSRSVCYDMMYGKGYTVFNQWARQHGCAQAIDGLGMLVGQAAESFMLWRGLRPGTKQILRELRKNLEG 276
                                    |-  |     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:244
 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....hhhhhhhhhhh....eeee...hhhhhhhhh.eehhhhhhhh...eee.-.....eee.hhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhh....eeeee..hhhhhhhhhhhh.....eee.hhhhh.....eeee...--------..hhhhh....eeee....------------------..hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sef C   5 IDQYAVFGNPINHSKSPFIHTLFARQTQQSMIYTAQCVPVDGFTEAAKHFFAQGGRGCNVTVPFKEEAYRFADRLTERARLAGAVNTLKK-DDGEILGDNTDGEGLVQDLLAQQVLLKGATILLIGAGGAARGVLKPLLDQQPASITVTNRTFAKAEQLAELVAAYGEVKAQAFEQLKQSYDVIINSTS--------AIDPVIFSSRSVCYDMMYG------------------IDGLGMLVGQAAESFMLWRGLRPGTKQILRELRKNLE 275
                                    14        24        34        44        54        64        74        84        94 |     104       114       124       134       144       154       164       174       184        |-       204       214     |   -         -    |  244       254       264       274 
                                                                                                                    94 |                                                                                              193      202               220                239                                    
                                                                                                                      96                                                                                                                                                                                   


Chain D 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......hhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhh.eeeeee...hhhhhhhhh.eehhhhhhhh...eeee.....eeee.hhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhh.eeeee.........eeee.............hhhhh....eeee.......hhhhhhhhhh...eee.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sef D   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
   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 3SEF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3SEF)

(-) 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: 3pgj

(-) 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
3pgj 2.49 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF SHIKIMATE 5- DEHYDROGENASE (AROE) FROM VIBRIO CHOLERAE O1 BIOVAR ELTOR STR. N16961 IN COMPLEX WITH SHIKIMATE