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(-) Description

Title :  CRYSTAL STRUCTURE OF DEOXYRIBOSE-PHOSPHATE ALDOLASE FROM COLWELLIA PSYCHRERYTHRAEA (HEXAGONAL FORM)
 
Authors :  O. H. Weiergraeber, M. Dick, J. Pietruszka
Date :  22 Jun 15  (Deposition) - 03 Feb 16  (Release) - 03 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Dera, Tim Barrel, Psychrophilic, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Dick, O. H. Weiergraber, T. Classen, C. Bisterfeld, J. Bramski, H. Gohlke, J. Pietruszka
Trading Off Stability Against Activity In Extremophilic Aldolases.
Sci Rep V. 6 17908 2016
PubMed-ID: 26783049  |  Reference-DOI: 10.1038/SREP17908

(-) Compounds

Molecule 1 - DEOXYRIBOSE-PHOSPHATE ALDOLASE
    Chains: A, B, C, D
    EC Number: 4.1.2.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET21A
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: DEOC, CPS_1972
    Organism Scientific: COLWELLIA PSYCHRERYTHRAEA (STRAIN 34H / ATCC BAA-681)
    Organism Taxid: 167879

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2UNL4Ligand/IonUNKNOWN LIGAND
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2UNL2Ligand/IonUNKNOWN LIGAND
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2UNL2Ligand/IonUNKNOWN LIGAND

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:132 , ASN D:132binding site for residue GOL A 302
2AC2SOFTWARELYS A:126 , ASP A:163 , ALA A:194 , HOH A:441binding site for residue GOL A 303
3AC3SOFTWARELYS B:126 , GLY B:161 , ALA B:162 , ASP B:163 , ASN B:192 , ALA B:194 , HOH B:435binding site for residue GOL B 302
4AC4SOFTWARELYS D:126 , GLY D:161 , ASP D:163 , ASN D:192binding site for residue GOL D 302
5AC5SOFTWAREASP B:102 , VAL B:137 , ILE B:138 , ILE B:139 , ILE B:165 , THR B:167 , SER B:168 , LYS B:198 , ALA B:200binding site for residue LYS B 166
6AC6SOFTWAREASP C:102 , VAL C:137 , ILE C:138 , ILE C:139 , ILE C:165 , THR C:167 , SER C:168 , LYS C:198 , ALA C:200binding site for residue LYS C 166
7AC7SOFTWAREASP D:102 , VAL D:137 , ILE D:138 , ILE D:139 , ILE D:165 , THR D:167 , SER D:168 , LYS D:198 , ALA D:200binding site for residue LYS D 166

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5C5Y)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Phe A:76 -Pro A:77
2Phe B:76 -Pro B:77
3Phe C:76 -Pro C:77
4Phe D:76 -Pro D:77

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5C5Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5C5Y)

(-) Exons   (0, 0)

(no "Exon" information available for 5C5Y)

(-) 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:247
                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh.eeee......hhhhhhhhhhhhee..ee..eee.hhhhhhhhhhhhhhh.....eeeeee.......hhhhhhhhhhhhhhhh..eeeee.hhhhhhh..hhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhhhhhhhh..eee..........hhhhhhhhhhhhhhhh...eee......hhhhhhhhhhhhhhhhh..........eee.hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5c5y A   2 SDIKAVAQRALSLMDLTSLTNTETDQEIIDLCRQAKSPAGETAAICIFPRFIPVAKKALKAQQTPHIKIATVTNFPQGNDDLDIALAETRAAVAYGADEVDLVFPYRALIQGNETIGFDMVKVCKQACSGNAKLKVIIETGELKSEELIRKASEIAINAGADFIKTSTGKVAINATPEAAKVMLTVIKNKNTAVGFKPAGGVRNADDAAIYLDLADNILGNEWADANHFRFGASSLLISLLDTLGHK 248
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       


Chain B from PDB  Type:PROTEIN  Length:246
                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhheeee......hhhhhhhhhhhhee..ee..eee.hhhhhhhhhhhhhhh.....eeeeee.......hhhhhhhhhhhhhhhh..eeeee.hhhhhhh..hhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhhhh...eee..........hhhhhhhhhhhhhhhh...eee......hhhhhhhhhhhhhhhhh..........eee.hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5c5y B   3 DIKAVAQRALSLMDLTSLTNTETDQEIIDLCRQAKSPAGETAAICIFPRFIPVAKKALKAQQTPHIKIATVTNFPQGNDDLDIALAETRAAVAYGADEVDLVFPYRALIQGNETIGFDMVKVCKQACSGNAKLKVIIETGELKSEELIRKASEIAINAGADFIKTSTGKVAINATPEAAKVMLTVIKNKNTAVGFKPAGGVRNADDAAIYLDLADNILGNEWADANHFRFGASSLLISLLDTLGHK 248
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242      


Chain C from PDB  Type:PROTEIN  Length:246
                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhheeee......hhhhhhhhhhhhee..ee..eee.hhhhhhhhhhhhhhh.....eeeeee.......hhhhhhhhhhhhhhhh..eeeee.hhhhhhh..hhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhhhh...eee..........hhhhhhhhhhhhhhhh...eee......hhhhhhhhhhhhhhhhh..........eee.hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5c5y C   2 SDIKAVAQRALSLMDLTSLTNTETDQEIIDLCRQAKSPAGETAAICIFPRFIPVAKKALKAQQTPHIKIATVTNFPQGNDDLDIALAETRAAVAYGADEVDLVFPYRALIQGNETIGFDMVKVCKQACSGNAKLKVIIETGELKSEELIRKASEIAINAGADFIKTSTGKVAINATPEAAKVMLTVIKNKNTAVGFKPAGGVRNADDAAIYLDLADNILGNEWADANHFRFGASSLLISLLDTLGH 247
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241      


Chain D from PDB  Type:PROTEIN  Length:247
                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhheeee......hhhhhhhhhhhhee..ee..eee.hhhhhhhhhhhhhhh.....eeeeee.......hhhhhhhhhhhhhhhh..eeeee.hhhhhhh..hhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhhhh...eee..........hhhhhhhhhhhhhhhh...eee......hhhhhhhhhhhhhhhhh..........eee.hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5c5y D   2 SDIKAVAQRALSLMDLTSLTNTETDQEIIDLCRQAKSPAGETAAICIFPRFIPVAKKALKAQQTPHIKIATVTNFPQGNDDLDIALAETRAAVAYGADEVDLVFPYRALIQGNETIGFDMVKVCKQACSGNAKLKVIIETGELKSEELIRKASEIAINAGADFIKTSTGKVAINATPEAAKVMLTVIKNKNTAVGFKPAGGVRNADDAAIYLDLADNILGNEWADANHFRFGASSLLISLLDTLGHK 248
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241
   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 5C5Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5C5Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5C5Y)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)

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