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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SHIKIMATE 5-DEHYDROGENASE (AROE) FROM HELICOBACTER PYLORI
 
Authors :  W. C. Cheng, S. C. Lin, W. C. Wang
Date :  04 Nov 10  (Deposition) - 09 Nov 11  (Release) - 09 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.57
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Shikimate Dehydrogenase, Shikimate Pathway, Helicobacter Pylori, Oxidoreductase, Alpha/Beta Domain, Rossmann Fold (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. C. Cheng, S. C. Lin, W. C. Wang
Crystal Structure Of The Shikimate 5-Dehydrogenase (Aroe) From Helicobacter Pylori
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SHIKIMATE DEHYDROGENASE
    Chains: A, B
    EC Number: 1.1.1.25
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AROE, HP_1249
    Organism Common: CAMPYLOBACTER PYLORI
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 85962
    Strain: 26695

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3PHG)

(-) Sites  (0, 0)

(no "Site" information available for 3PHG)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Asn A:11 -Pro A:12
2Leu A:66 -Pro A:67
3Asn B:11 -Pro B:12
4Leu B:66 -Pro B:67

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3PHG)

(-) 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:258
 aligned with AROE_HELPY | P56119 from UniProtKB/Swiss-Prot  Length:263

    Alignment length:263
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260   
           AROE_HELPY     1 MKLKSFGVFGNPIKHSKSPLIHNACFLTFQKELRFLGHYHPILLPLESHIKSEFLHLGLSGANVTLPFKERAFQVCDKIKGIALECGAVNTLVLENDELVGYNTDALGFYLSLKQKNYQNALILGAGGSAKALACELKKQGLQVSVLNRSSRGLDFFQRLGCDCFMEPPKSAFDLIINATSASLHNELPLNKEVLKGYFKEGKLAYDLAYGFLTPFLSLAKELKTPFQDGKDMLIYQAALSFEKFSASQIPYSKAFEVMRSVF 263
               SCOP domains d3phga1 A:1-104 automated matches                                                                       d3phga2 A:   105-263 automated matches                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee......hhhhhhhhhhhhhhhhhh.eeeeeeee.....hhhhhhhhh.eeeeee...hhhhhhhhh.ee..hhhhhh...eeeee..eeeee.hhhhhhhhhh.---..eeeee..hhhhhhhhhhhhhh..eeeee.....hhhhhhhhh.eee.........eeee...hhhhh....hhhhhhhhhhhh.eeee...--.hhhhhhhhhh...ee.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3phg A   1 MKLKSFGVFGNPIKHSKSPLIHNACFLTFQKELRFLGHYHPILLPLESHIKSEFLHLGLSGANVTLPFKERAFQVCDKIKGIALECGAVNTLVLENDELVGYNTDALGFYLSLK---YQNALILGAGGSAKALACELKKQGLQVSVLNRSSRGLDFFQRLGCDCFMEPPKSAFDLIINATSASLHNELPLNKEVLKGYFKEGKLAYDLAY--LTPFLSLAKELKTPFQDGKDMLIYQAALSFEKFSASQIPYSKAFEVMRSVF 263
                                    10        20        30        40        50        60        70        80        90       100       110   |   120       130       140       150       160       170       180       190       200       210  |    220       230       240       250       260   
                                                                                                                                           114 118                                                                                         210  |                                                  
                                                                                                                                                                                                                                              213                                                  


Chain B from PDB  Type:PROTEIN  Length:255
 aligned with AROE_HELPY | P56119 from UniProtKB/Swiss-Prot  Length:263

    Alignment length:263
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260   
           AROE_HELPY     1 MKLKSFGVFGNPIKHSKSPLIHNACFLTFQKELRFLGHYHPILLPLESHIKSEFLHLGLSGANVTLPFKERAFQVCDKIKGIALECGAVNTLVLENDELVGYNTDALGFYLSLKQKNYQNALILGAGGSAKALACELKKQGLQVSVLNRSSRGLDFFQRLGCDCFMEPPKSAFDLIINATSASLHNELPLNKEVLKGYFKEGKLAYDLAYGFLTPFLSLAKELKTPFQDGKDMLIYQAALSFEKFSASQIPYSKAFEVMRSVF 263
               SCOP domains d3phgb1 B:1-104 automated matches                                                                       d3phgb2 B:   105-263 automated matches                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee......hhhhhhhhhhhhhhhhhheeeeeeeee.....hhhhhhhhh.eeeeee...hhhhhhhhh.ee..hhhhhh...eeeee..eeeee.hhhhhhhhhh.---..eeeee..hhhhhhhhhhhhhh..eeeee-----hhhhhhhh..ee..........eeee..hhhhhh....hhhhhhhhhh...eeee......hhhhhhhhhh...ee.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3phg B   1 MKLKSFGVFGNPIKHSKSPLIHNACFLTFQKELRFLGHYHPILLPLESHIKSEFLHLGLSGANVTLPFKERAFQVCDKIKGIALECGAVNTLVLENDELVGYNTDALGFYLSLK---YQNALILGAGGSAKALACELKKQGLQVSVL-----GLDFFQRLGCDCFMEPPKSAFDLIINATSASLHNELPLNKEVLKGYFKEGKLAYDLAYGFLTPFLSLAKELKTPFQDGKDMLIYQAALSFEKFSASQIPYSKAFEVMRSVF 263
                                    10        20        30        40        50        60        70        80        90       100       110   |   120       130       140      |  -  |    160       170       180       190       200       210       220       230       240       250       260   
                                                                                                                                           114 118                          147   153
   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  (2, 4)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (AROE_HELPY | P56119)
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: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: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.

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  Cis Peptide Bonds
    Asn A:11 - Pro A:12   [ RasMol ]  
    Asn B:11 - Pro B:12   [ RasMol ]  
    Leu A:66 - Pro A:67   [ RasMol ]  
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  AROE_HELPY | P56119
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  1.1.1.25
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 Related Entries

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

UniProtKB/Swiss-Prot
        AROE_HELPY | P56119: 3phh 3phi 3phj 4foo 4fos 4fpx 4fq8 4fr5 4fsh

(-) Related Entries Specified in the PDB File

3phh THE SAME PROTEIN COMPLEXED WITH SHIKIMATE
3phi THE SAME PROTEIN COMPLEXED WITH SHIKIMATE AND NADPH
3phj THE SAME PROTEIN COMPLEXED WITH 3-DEHYDROSHIKIMATE