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(-) Description

Title :  CRYSTAL STRUCTURE OF SHIKIMATE DEHYDROGENASE (AROE) CLINICAL VARIANT V2356 FROM HELICOBACTER PYLORI IN COMPLEX WITH SHIKIMATE
 
Authors :  W. C. Cheng, T. J. Chen, W. C. Wang
Date :  27 Jun 12  (Deposition) - 30 Jan 13  (Release) - 30 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Dehydrogenase, Nadp Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. C. Cheng, T. J. Chen, W. C. Wang
Crystal Structure Of Shikimate Dehydrogenase (Aroe) Clinica Variant V2356 From Helicobacter Pylori In Complex With Shikimate
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: 469008
    Expression System Vector Type: PLASMID
    Gene: AROE, HP_1249
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 85962
    Strain: HELICOBACTER PYLORI 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  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1SKM1Ligand/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 (0, 0)
No.NameCountTypeFull Name
1SKM-1Ligand/Ion(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLICACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:16 , SER A:18 , ASN A:63 , VAL A:64 , THR A:65 , LYS A:69 , ASN A:90 , ASP A:105 , TYR A:210 , GLN A:237BINDING SITE FOR RESIDUE SKM A 500

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (7, 7)

Asymmetric Unit
No.Residues
1Asn A:11 -Pro A:12
2Leu A:66 -Pro A:67
3Leu A:113 -Lys A:114
4Leu A:184 -Asn A:185
5Asn B:11 -Pro B:12
6Leu B:66 -Pro B:67
7Gly B:127 -Gly B:128

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4FSH)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4FSH)

(-) 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:260
                                                                                                                                                                                                                                                                                                    
               SCOP domains d4fsha1 A:1-104 automated matches                                                                       d4fsha2 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.hhhhhhhhh.......eeeee..hhhhhhhhhhhhhh..eeeee......hhhhhhh..eee.........ee...........hhhhhhhhhh.............hhhhhhhhhh......hhhhhhhhhhhhhhhhh....hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fsh A   1 MKLKSFGVFGNPIKHSKSPLIHNACFLTFQKKLGFLGHYRPILLPLESHIKNEFLHLGLSGANVTLPFKERAFQVCDKIKGIALECASINTLVLENDELVGYNTDALGFYLSLKHQNYQNALILGSGGSAKALACGLKKQGLKVSVLNRSPRGLDFFQRLGCDCFMEPPKSAFDLIINATSASLNPLNKEVLKGYFKEAKLAYDLAYGFLTPFLALAKELKIPFQDGKDMLIYQASLSFEKFSASQIPYSKAFEVMRSVF 263
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180    || 193       203       213       223       233       243       253       263
                                                                                                                                                                                                                  185|                                                                          
                                                                                                                                                                                                                   189                                                                          


Chain B from PDB  Type:PROTEIN  Length:263
                                                                                                                                                                                                                                                                                                       
               SCOP domains d4fshb1 B:1-104 automated matches                                                                       d4fshb2 B:105-263 automated matches                                                                                                                             SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.......hhhhhhhhhhhhhhhhhh.eeeeeee......hhhhhhhhh...eeee...hhhhhhhh..ee..hhhhhh...eeeee..eeeee.hhhhhhhhh.......eeeee...hhhhhhhhhhhhh..eeeee......hhhhhhhh.eee.........eeee..hhhhhh....hhhhhhhhhhh..eeee......hhhhhhhhhh...ee.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fsh B   1 MKLKSFGVFGNPIKHSKSPLIHNACFLTFQKKLGFLGHYRPILLPLESHIKNEFLHLGLSGANVTLPFKERAFQVCDKIKGIALECASINTLVLENDELVGYNTDALGFYLSLKHQNYQNALILGSGGSAKALACGLKKQGLKVSVLNRSPRGLDFFQRLGCDCFMEPPKSAFDLIINATSASLNNELPLNKEVLKGYFKEAKLAYDLAYGFLTPFLALAKELKIPFQDGKDMLIYQASLSFEKFSASQIPYSKAFEVMRSVF 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 4FSH)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)

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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: 3phg 3phh 3phi 3phj 4foo 4fos 4fpx 4fq8 4fr5

(-) 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