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(-) Description

Title :  TAGATOSE-1,6-BISPHOSPHATE ALDOLASE FROM STREPTOCOCCUS PYOGENES IN COMPLEX WITH FBP
 
Authors :  C. Lowkam
Date :  03 Dec 15  (Deposition) - 28 Dec 16  (Release) - 28 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.72
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Covalent Intermediate, Acidic Ph, Substrate, Aldolase, Class I, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Lowkam, B. Liotard, J. Sygusch
Non-Stereospecific Substrate Cleavage By Tagatose-Bisphosphate Class I Aldolase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TAGATOSE 1,6-DIPHOSPHATE ALDOLASE 2
    Chains: A, B, C, D
    EC Number: 4.1.2.40
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: LACD2, LACD.2, SPY_1919, M5005_SPY1635
    Organism Scientific: STREPTOCOCCUS PYOGENES SEROTYPE M1
    Organism Taxid: 301447
    Synonym: D-TAGATOSE-1,6-BISPHOSPHATE ALDOLASE 2,TAGATOSE-BISPHOSPHATE ALDOLASE 2

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric Unit (4, 9)
No.NameCountTypeFull Name
113P2Ligand/Ion1,3-DIHYDROXYACETONEPHOSPHATE
2CA5Ligand/IonCALCIUM ION
3CL1Ligand/IonCHLORIDE ION
4P6F1Ligand/Ion1,6-DI-O-PHOSPHONO-D-FRUCTOSE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
113P1Ligand/Ion1,3-DIHYDROXYACETONEPHOSPHATE
2CA-1Ligand/IonCALCIUM ION
3CL-1Ligand/IonCHLORIDE ION
4P6F1Ligand/Ion1,6-DI-O-PHOSPHONO-D-FRUCTOSE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
113P1Ligand/Ion1,3-DIHYDROXYACETONEPHOSPHATE
2CA-1Ligand/IonCALCIUM ION
3CL-1Ligand/IonCHLORIDE ION
4P6F-1Ligand/Ion1,6-DI-O-PHOSPHONO-D-FRUCTOSE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:27 , GLN A:28 , ARG A:29 , GLY A:30 , ALA A:31 , LEU A:68 , THR A:94 , LEU A:127 , GLU A:163 , SER A:249 , ALA A:250 , LEU A:275 , CYS A:276 , GLY A:277 , ARG A:278 , CL A:3003 , HOH A:3108 , HOH A:3111 , HOH A:3115 , HOH A:3147 , HOH A:3236 , HOH A:3272 , HOH A:3274 , HOH A:3310binding site for residue P6F A 3001
2AC2SOFTWAREARG A:29 , GLY A:30 , ALA A:31 , THR A:94 , P6F A:3001binding site for residue CL A 3003
3AC3SOFTWAREHOH A:3277 , HOH A:3298 , HOH A:3341 , HOH A:3454 , HOH B:646 , HOH B:834 , HOH B:853binding site for residue CA A 3004
4AC4SOFTWAREGLU A:238 , THR A:241 , HOH A:3263 , GLU B:83 , GLU B:84binding site for residue CA A 3005
5AC5SOFTWAREHOH A:3296 , HOH A:3465 , HOH A:3494 , HOH B:635 , HOH B:668 , HOH B:686 , HOH B:833binding site for residue CA B 402
6AC6SOFTWAREGLU A:83 , GLU A:84 , GLU B:238 , THR B:241 , HOH B:651binding site for residue CA B 403
7AC7SOFTWAREASP C:259 , ASP D:259 , HOH D:465 , HOH D:585binding site for residue CA C 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5F4S)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Ala B:250 -Gly B:251
2Glu B:324 -Lys B:325
3Gln D:40 -Thr D:41

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5F4S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5F4S)

(-) Exons   (0, 0)

(no "Exon" information available for 5F4S)

(-) 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:324
                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhh.....eeeeee..hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh.eeee....hhhhhh......eeeee.....................hhhhhhhh....eeeeeee....hhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhh..eeee....hhhhh..........hhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5f4s A   2 ITLTENKRKSMEKLSVDGVISALAFDQRGALKRMMAQHQTKEPTVEQIEELKSLVSEELTPFASSILLDPEYGLPASRVRSEEAGLLLAYEKTGYDATTTSRLPDCLDVWSAKRIKEAGAEAVKFLLYYDIDGDQDVNEQKKAYIERIGSECRAEDIPFYLEILTYDEKIADNASPEFAKVKAHKVNEAMKVFSKERFGVDVLKVEVPVNMKFVEGFADGEVLFTKEEAAQAFRDQEASTDLPYIYLSAGVSAKLFQDTLVFAAESGAKFNGVLCGRATWAGSVKVYIEEGPQAAREWLRTEGFKNIDELNKVLDKTASPWTEK 325
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321    


Chain B from PDB  Type:PROTEIN  Length:325
                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh....eeeeee...hhhhhhhhh......hhhhhhhhhhhhhhhhhhhh.eeee....hhhhhhh.....eeeee.....................hhhhhhhh...eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhh..eeee....hhhhh..........hhhhhhhhhhhhhh.....eee.....hhhhhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f4s B   2 ITLTENKRKSMEKLSVDGVISALAFDQRGALKRMMAQHQTKEPTVEQIEELKSLVSEELTPFASSILLDPEYGLPASRVRSEEAGLLLAYEKTGYDATTTSRLPDCLDVWSAKRIKEAGAEAVKFLLYYDIDGDQDVNEQKKAYIERIGSECRAEDIPFYLEILTYDEKIADNASPEFAKVKAHKVNEAMKVFSKERFGVDVLKVEVPVNMKFVEGFADGEVLFTKEEAAQAFRDQEASTDLPYIYLSAGVSAKLFQDTLVFAAESGAKFNGVLCGRATWAGSVKVYIEEGPQAAREWLRTEGFKNIDELNKVLDKTASPWTEKM 326
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321     


Chain C from PDB  Type:PROTEIN  Length:323
                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh.....eeeeee..hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.eeee....hhhhhhh.....eeeee.....................hhhhhhhh...eeeeeeee....hhhhhhhhhhhhhhhhhhhhhh...eeeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhh..eeee....hhhhh..........hhhhhhhhhhhhhhh....eee.....hhhhhhhhhhhhhhhh....eeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f4s C   3 TLTENKRKSMEKLSVDGVISALAFDQRGALKRMMAQHQTKEPTVEQIEELKSLVSEELTPFASSILLDPEYGLPASRVRSEEAGLLLAYEKTGYDATTTSRLPDCLDVWSAKRIKEAGAEAVKFLLYYDIDGDQDVNEQKKAYIERIGSECRAEDIPFYLEILTYDEKIADNASPEFAKVKAHKVNEAMKVFSKERFGVDVLKVEVPVNMKFVEGFADGEVLFTKEEAAQAFRDQEASTDLPYIYLSAGVSAKLFQDTLVFAAESGAKFNGVLCGRATWAGSVKVYIEEGPQAAREWLRTEGFKNIDELNKVLDKTASPWTEK 325
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322   


Chain D from PDB  Type:PROTEIN  Length:326
                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh....eeeeee..hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.eeee....hhhhhhh.....eeeee.....................hhhhhhhh...eeeeeeee....hhhhhhhhhhhhhhhhhhhhhh...eeeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhh..eeee....hhhhh..........hhhhhhhhhhhhhh.....eee.....hhhhhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f4s D   1 TITLTENKRKSMEKLSVDGVISALAFDQRGALKRMMAQHQTKEPTVEQIEELKSLVSEELTPFASSILLDPEYGLPASRVRSEEAGLLLAYEKTGYDATTTSRLPDCLDVWSAKRIKEAGAEAVKFLLYYDIDGDQDVNEQKKAYIERIGSECRAEDIPFYLEILTYDEKIADNASPEFAKVKAHKVNEAMKVFSKERFGVDVLKVEVPVNMKFVEGFADGEVLFTKEEAAQAFRDQEASTDLPYIYLSAGVSAKLFQDTLVFAAESGAKFNGVLCGRATWAGSVKVYIEEGPQAAREWLRTEGFKNIDELNKVLDKTASPWTEKM 326
                                    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       270       280       290       300       310       320
   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  (0, 0)

(no "SCOP Domain" information available for 5F4S)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5F4S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5F4S)

(-) Gene Ontology  (8, 8)

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 Related Entries

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        LACD2_STRP1 | P63705: 3jrk 3mhf 3mhg 5f2g 5f2i 5f2l 5f2m 5f4w 5ff7

(-) Related Entries Specified in the PDB File

5f2g 5f2i 5f2j 5f2l 5f2m 5f4w 5f4x