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(-) Description

Title :  DIHYDROXYACETONE PHOSPHATE CARBANION INTERMEDIATE IN TAGATOSE-1,6-BISPHOSPHATE ALDOLASE FROM STREPTOCOCCUS PYOGENES
 
Authors :  C. Lowkam, B. Liotard
Date :  07 Apr 10  (Deposition) - 28 Apr 10  (Release) - 24 Nov 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.92
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Tagatose Aldolase Class I, Beta Barrel, Streptococcus Pyogenes, Schiff Base, Carbanion, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Lowkam, B. Liotard, J. Sygusch
Structure Of A Class I Tagatose-1, 6-Bisphosphate Aldolase: Investigation Into An Apparent Loss Of Stereospecificity.
J. Biol. Chem. V. 285 21143 2010
PubMed-ID: 20427286  |  Reference-DOI: 10.1074/JBC.M109.080358

(-) 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 Plasmid: PKK222
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: LACD.2, LACD2, M5005_SPY1635, SPY_1919
    Organism Scientific: STREPTOCOCCUS PYOGENES SEROTYPE M1
    Organism Taxid: 301447
    Synonym: TAGATOSE-BISPHOSPHATE ALDOLASE 2, D-TAGATOSE-1,6- BISPHOSPHATE ALDOLASE 2

 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, 11)

Asymmetric Unit (2, 11)
No.NameCountTypeFull Name
113P4Ligand/Ion1,3-DIHYDROXYACETONEPHOSPHATE
2CA7Ligand/IonCALCIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
113P2Ligand/Ion1,3-DIHYDROXYACETONEPHOSPHATE
2CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
113P2Ligand/Ion1,3-DIHYDROXYACETONEPHOSPHATE
2CA-1Ligand/IonCALCIUM ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:27 , GLN A:28 , LEU A:68 , LYS A:125 , GLU A:163 , LYS A:205 , SER A:249 , ALA A:250 , LEU A:275 , GLY A:277 , ARG A:278 , HOH A:516BINDING SITE FOR RESIDUE 13P A 3001
02AC2SOFTWAREHOH C:346 , HOH C:352 , HOH C:397 , HOH C:413 , HOH C:414 , HOH C:446 , HOH C:1940BINDING SITE FOR RESIDUE CA A 327
03AC3SOFTWAREHOH A:554 , HOH A:557 , HOH A:558 , HOH A:560 , HOH A:561 , HOH A:1835 , HOH C:379BINDING SITE FOR RESIDUE CA A 328
04AC4SOFTWAREGLU A:238 , THR A:241 , HOH A:1268 , GLU C:83 , GLU C:84BINDING SITE FOR RESIDUE CA A 329
05AC5SOFTWAREASP B:27 , GLN B:28 , LEU B:68 , LYS B:125 , GLU B:163 , LYS B:205 , LEU B:248 , SER B:249 , ALA B:250 , LEU B:275 , GLY B:277 , ARG B:278 , HOH B:1232 , HOH B:1565BINDING SITE FOR RESIDUE 13P B 3002
06AC6SOFTWAREASP B:259 , HOH B:893 , HOH B:1580 , HOH B:2129 , ASP D:259BINDING SITE FOR RESIDUE CA B 327
07AC7SOFTWAREASP C:27 , GLN C:28 , LYS C:125 , GLU C:163 , LYS C:205 , LEU C:248 , SER C:249 , ALA C:250 , LEU C:275 , GLY C:277 , ARG C:278 , HOH C:738 , HOH C:1926BINDING SITE FOR RESIDUE 13P C 3003
08AC8SOFTWAREGLU A:83 , GLU A:84 , GLU C:238 , THR C:241 , HOH C:1277BINDING SITE FOR RESIDUE CA C 327
09AC9SOFTWAREALA C:37 , GLN C:40 , HOH C:495 , HOH C:779 , HOH C:1812BINDING SITE FOR RESIDUE CA C 328
10BC1SOFTWAREALA D:25 , ASP D:27 , GLN D:28 , LEU D:68 , LYS D:125 , GLU D:163 , LYS D:205 , SER D:249 , ALA D:250 , LEU D:275 , GLY D:277 , ARG D:278 , HOH D:924 , HOH D:2410BINDING SITE FOR RESIDUE 13P D 3004
11BC2SOFTWAREGLU D:84 , HOH D:959 , HOH D:1282 , HOH D:1820 , HOH D:2164 , HOH D:2165BINDING SITE FOR RESIDUE CA D 327

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3MHG)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3MHG)

(-) 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:323
 aligned with LACD2_STRP1 | P63705 from UniProtKB/Swiss-Prot  Length:327

    Alignment length:323
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323   
          LACD2_STRP1     4 TLTENKRKSMEKLSVDGVISALAFDQRGALKRMMAQHQTKEPTVEQIEELKSLVSEELTPFASSILLDPEYGLPASRVRSEEAGLLLAYEKTGYDATTTSRLPDCLDVWSAKRIKEAGAEAVKFLLYYDIDGDQDVNEQKKAYIERIGSECRAEDIPFYLEILTYDEKIADNASPEFAKVKAHKVNEAMKVFSKERFGVDVLKVEVPVNMKFVEGFADGEVLFTKEEAAQAFRDQEASTDLPYIYLSAGVSAKLFQDTLVFAAESGAKFNGVLCGRATWAGSVKVYIEEGPQAAREWLRTEGFKNIDELNKVLDKTASPWTEK 326
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh....eeeeee..hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh.eeee....hhhhhhh.....eeeee.....................hhhhhhhh...eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhh..eeee....hhhhh..........hhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mhg A   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 B from PDB  Type:PROTEIN  Length:323
 aligned with LACD2_STRP1 | P63705 from UniProtKB/Swiss-Prot  Length:327

    Alignment length:323
                                    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   
          LACD2_STRP1     3 ITLTENKRKSMEKLSVDGVISALAFDQRGALKRMMAQHQTKEPTVEQIEELKSLVSEELTPFASSILLDPEYGLPASRVRSEEAGLLLAYEKTGYDATTTSRLPDCLDVWSAKRIKEAGAEAVKFLLYYDIDGDQDVNEQKKAYIERIGSECRAEDIPFYLEILTYDEKIADNASPEFAKVKAHKVNEAMKVFSKERFGVDVLKVEVPVNMKFVEGFADGEVLFTKEEAAQAFRDQEASTDLPYIYLSAGVSAKLFQDTLVFAAESGAKFNGVLCGRATWAGSVKVYIEEGPQAAREWLRTEGFKNIDELNKVLDKTASPWTE 325
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh.....eeeeee..hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.eeee....hhhhhhh.....eeeee.....................hhhhhhhh...eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhh..eeee....hhhhh..........hhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mhg B   2 ITLTENKRKSMEKLSVDGVISALAFDQRGALKRMMAQHQTKEPTVEQIEELKSLVSEELTPFASSILLDPEYGLPASRVRSEEAGLLLAYEKTGYDATTTSRLPDCLDVWSAKRIKEAGAEAVKFLLYYDIDGDQDVNEQKKAYIERIGSECRAEDIPFYLEILTYDEKIADNASPEFAKVKAHKVNEAMKVFSKERFGVDVLKVEVPVNMKFVEGFADGEVLFTKEEAAQAFRDQEASTDLPYIYLSAGVSAKLFQDTLVFAAESGAKFNGVLCGRATWAGSVKVYIEEGPQAAREWLRTEGFKNIDELNKVLDKTASPWTE 324
                                    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:322
 aligned with LACD2_STRP1 | P63705 from UniProtKB/Swiss-Prot  Length:327

    Alignment length:322
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323  
          LACD2_STRP1     4 TLTENKRKSMEKLSVDGVISALAFDQRGALKRMMAQHQTKEPTVEQIEELKSLVSEELTPFASSILLDPEYGLPASRVRSEEAGLLLAYEKTGYDATTTSRLPDCLDVWSAKRIKEAGAEAVKFLLYYDIDGDQDVNEQKKAYIERIGSECRAEDIPFYLEILTYDEKIADNASPEFAKVKAHKVNEAMKVFSKERFGVDVLKVEVPVNMKFVEGFADGEVLFTKEEAAQAFRDQEASTDLPYIYLSAGVSAKLFQDTLVFAAESGAKFNGVLCGRATWAGSVKVYIEEGPQAAREWLRTEGFKNIDELNKVLDKTASPWTE 325
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh.....eeeeee..hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh.eeee....hhhhhhh.....eeeee.....................hhhhhhhh...eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhh..eeee....hhhhh..........hhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mhg C   3 TLTENKRKSMEKLSVDGVISALAFDQRGALKRMMAQHQTKEPTVEQIEELKSLVSEELTPFASSILLDPEYGLPASRVRSEEAGLLLAYEKTGYDATTTSRLPDCLDVWSAKRIKEAGAEAVKFLLYYDIDGDQDVNEQKKAYIERIGSECRAEDIPFYLEILTYDEKIADNASPEFAKVKAHKVNEAMKVFSKERFGVDVLKVEVPVNMKFVEGFADGEVLFTKEEAAQAFRDQEASTDLPYIYLSAGVSAKLFQDTLVFAAESGAKFNGVLCGRATWAGSVKVYIEEGPQAAREWLRTEGFKNIDELNKVLDKTASPWTE 324
                                    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:324
 aligned with LACD2_STRP1 | P63705 from UniProtKB/Swiss-Prot  Length:327

    Alignment length:324
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323    
          LACD2_STRP1     4 TLTENKRKSMEKLSVDGVISALAFDQRGALKRMMAQHQTKEPTVEQIEELKSLVSEELTPFASSILLDPEYGLPASRVRSEEAGLLLAYEKTGYDATTTSRLPDCLDVWSAKRIKEAGAEAVKFLLYYDIDGDQDVNEQKKAYIERIGSECRAEDIPFYLEILTYDEKIADNASPEFAKVKAHKVNEAMKVFSKERFGVDVLKVEVPVNMKFVEGFADGEVLFTKEEAAQAFRDQEASTDLPYIYLSAGVSAKLFQDTLVFAAESGAKFNGVLCGRATWAGSVKVYIEEGPQAAREWLRTEGFKNIDELNKVLDKTASPWTEKM 327
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ------------------DeoC-3mhgD01 D:21-283                                                                                                                                                                                                                                                  ------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------------------DeoC-3mhgD02 D:21-283                                                                                                                                                                                                                                                  ------------------------------------------- Pfam domains (2)
           Pfam domains (3) ------------------DeoC-3mhgD03 D:21-283                                                                                                                                                                                                                                                  ------------------------------------------- Pfam domains (3)
           Pfam domains (4) ------------------DeoC-3mhgD04 D:21-283                                                                                                                                                                                                                                                  ------------------------------------------- Pfam domains (4)
         Sec.struct. author ..hhhhhhhhhhh.....eeeeee..hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh.eeee....hhhhhhh.....eeeee.....................hhhhhhhh...eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhh..eeee....hhhhh..........hhhhhhhhhhhhhh.....eee.....hhhhhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3mhg D   3 TLTENKRKSMEKLSVDGVISALAFDQRGALKRMMAQHQTKEPTVEQIEELKSLVSEELTPFASSILLDPEYGLPASRVRSEEAGLLLAYEKTGYDATTTSRLPDCLDVWSAKRIKEAGAEAVKFLLYYDIDGDQDVNEQKKAYIERIGSECRAEDIPFYLEILTYDEKIADNASPEFAKVKAHKVNEAMKVFSKERFGVDVLKVEVPVNMKFVEGFADGEVLFTKEEAAQAFRDQEASTDLPYIYLSAGVSAKLFQDTLVFAAESGAKFNGVLCGRATWAGSVKVYIEEGPQAAREWLRTEGFKNIDELNKVLDKTASPWTEKM 326
                                    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
   Legend:   → Mismatch (orange background)
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  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 3MHG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (LACD2_STRP1 | P63705)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0009024    tagatose-6-phosphate kinase activity    Catalysis of the reaction: ATP + D-tagatose 6-phosphate = ADP + D-tagatose 1,6-bisphosphate.
    GO:0009025    tagatose-bisphosphate aldolase activity    Catalysis of the reaction: D-tagatose 1,6-diphosphate = D-glyceraldehyde 3-phosphate + glycerone phosphate.
biological process
    GO:2001059    D-tagatose 6-phosphate catabolic process    The chemical reactions and pathways resulting in the breakdown of a D-tagatose 6-phosphate.
    GO:0019512    lactose catabolic process via tagatose-6-phosphate    The chemical reactions and pathways resulting in the breakdown of lactose, via the intermediate tagatose-6-phosphate.
    GO:0005988    lactose metabolic process    The chemical reactions and pathways involving lactose, the disaccharide galactopyranosyl-glucose.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.

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  3mhg
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  LACD2_STRP1 | P63705
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 Related Entries

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

UniProtKB/Swiss-Prot
        LACD2_STRP1 | P63705: 3jrk 3mhf 5f2g 5f2i 5f2l 5f2m 5f4s 5f4w 5ff7

(-) Related Entries Specified in the PDB File

3mhf