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(-) Description

Title :  CRYSTAL STRUCTURE OF SHIKIMATE DEHYDROGENASE (AROE) Y210S MUTANT FROM HELICOBACTER PYLORI IN COMPLEX WITH SHIKIMATE
 
Authors :  W. C. Cheng, T. J. Chen, W. C. Wang
Date :  26 Jun 12  (Deposition) - 26 Dec 12  (Release) - 26 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A (1x),B (1x)
Keywords :  Dehydrogenase, Nadp Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  

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: 469008
    Expression System Vector Type: PLASMID
    Gene: AROE, HP_1249
    Mutation: YES
    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
Biological Unit 3 (1x): A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1SKM2Ligand/Ion(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLICACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SKM1Ligand/Ion(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLICACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1SKM1Ligand/Ion(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLICACID
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1SKM1Ligand/Ion(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLICACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:16 , SER A:18 , ASN A:63 , THR A:65 , LYS A:69 , ASN A:90 , ASP A:105 , GLN A:237 , HOH A:620 , HOH A:671BINDING SITE FOR RESIDUE SKM A 500
2AC2SOFTWARESER B:16 , SER B:18 , ASN B:63 , VAL B:64 , THR B:65 , LYS B:69 , ASN B:90 , ASP B:105 , GLN B:237 , HOH B:610 , HOH B:649BINDING SITE FOR RESIDUE SKM B 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4FR5)

(-) 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 4FR5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4FR5)

(-) Exons   (0, 0)

(no "Exon" information available for 4FR5)

(-) 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:263
                                                                                                                                                                                                                                                                                                       
               SCOP domains d4fr5a1 A:1-104 automated matches                                                                       d4fr5a2 A:105-263 automated matches                                                                                                                             SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee......hhhhhhhhhhhhhhhhhh.eeeeeeee.....hhhhhhhhh...eeee...hhhhhhhhh.ee..hhhhhh...eeeee..eeeee.hhhhhhhhhh......eeeee..hhhhhhhhhhhhhh..eeeee.....hhhhhhhhh.eee.........eeee...hhhhh....hhhhhhhhhhh..eeee......hhhhhhhhhh...ee.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fr5 A   1 MKLKSFGVFGNPIKHSKSPLIHNACFLTFQKELRFLGHYHPILLPLESHIKSEFLHLGLSGANVTLPFKERAFQVCDKIKGIALECGAVNTLVLENDELVGYNTDALGFYLSLKQKNYQNALILGAGGSAKALACELKKQGLQVSVLNRSSRGLDFFQRLGCDCFMEPPKSAFDLIINATSASLHNELPLNKEVLKGYFKEGKLAYDLASGFLTPFLSLAKELKTPFQDGKDMLIYQAALSFEKFSASQIPYSKAFEVMRSVF 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   


Chain B from PDB  Type:PROTEIN  Length:263
                                                                                                                                                                                                                                                                                                       
               SCOP domains d4fr5b1 B:1-104 automated matches                                                                       d4fr5b2 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...eeee....eeee.hhhhhhhhhh......eeeee..hhhhhhhhhhhhhh..eeeee.....hhhhhhhhh.eee.........eeee...hhhhh....hhhhhhhhhhhh.eeee......hhhhhhhhhhh..ee.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fr5 B   1 MKLKSFGVFGNPIKHSKSPLIHNACFLTFQKELRFLGHYHPILLPLESHIKSEFLHLGLSGANVTLPFKERAFQVCDKIKGIALECGAVNTLVLENDELVGYNTDALGFYLSLKQKNYQNALILGAGGSAKALACELKKQGLQVSVLNRSSRGLDFFQRLGCDCFMEPPKSAFDLIINATSASLHNELPLNKEVLKGYFKEGKLAYDLASGFLTPFLSLAKELKTPFQDGKDMLIYQAALSFEKFSASQIPYSKAFEVMRSVF 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
   Legend:   → Mismatch (orange background)
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  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 4FR5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4FR5)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)

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  4fr5
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  AROE_HELPY | P56119
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

3phg CRYSTAL STRUCTURE OF THE SHIKIMATE 5-DEHYDROGENASE (AROE) FROM HELICOBACTER PYLORI
3phh SHIKIMATE 5-DEHYDROGENASE (AROE) FROM HELICOBACTER PYLORI IN COMPLEX WITH SHIKIMATE
3phi SHIKIMATE 5-DEHYDROGENASE (AROE) FROM HELICOBACTER PYLORI IN COMPLEX WITH SHIKIMATE AND NADPH
3phj SHIKIMATE 5-DEHYDROGENASE (AROE) FROM HELICOBACTER PYLORI IN COMPLEX WITH 3-DEHYDROSHIKIMATE
4foo
4fos
4fpx
4fq8