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(-) Description

Title :  CRYSTAL STRUCTURE OF TAGATOSE-1,6-BISPHOSPHATE ALDOLASE FROM STAPHYLOCOCCUS AUREUS
 
Authors :  S. J. Lee, H. S. Kim, D. J. Kim, H. J. Yoon, K. H. Kim, J. Y. Yoon, S. W. Suh
Date :  10 May 10  (Deposition) - 26 Jan 11  (Release) - 26 Jan 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.99
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Beta-Alpha-Barrel, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. J. Lee, H. S. Kim, D. J. Kim, H. J. Yoon, K. H. Kim, J. Y. Yoon, S. W. Suh
Crystal Structures Of Lacd From Staphylococcus Aureus And Lacd. 1 From Streptococcus Pyogenes: Insights Into Substrate Specificity And Virulence Gene Regulation
Febs Lett. V. 585 307 2011
PubMed-ID: 21192932  |  Reference-DOI: 10.1016/J.FEBSLET.2010.12.038

(-) Compounds

Molecule 1 - TAGATOSE 1,6-DIPHOSPHATE ALDOLASE
    Chains: A, B, C, D
    EC Number: 4.1.2.40
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A(+)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: LACD, SACOL2183
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 93062
    Strain: COL
    Synonym: TAGATOSE-BISPHOSPHATE ALDOLASE, D-TAGATOSE-1,6-BISPHOSPHATE ALDOLASE

 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  (1, 16)

Asymmetric Unit (1, 16)
No.NameCountTypeFull Name
1MSE16Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3MYP)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gln A:40 -Thr A:41
2Gln B:40 -Thr B:41

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3MYP)

(-) 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:321
 aligned with LACD_STAAC | Q5HE13 from UniProtKB/Swiss-Prot  Length:326

    Alignment length:321
                                    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 
           LACD_STAAC     4 SNQKIASIEQLSNNEGIISALAFDQRGALKRMMAKHQTEEPTVAQIEQLKVLVAEELTQYASSILLDPEYGLPASDARNKDCGLLLAYEKTGYDVNAKGRLPDCLVEWSAKRLKEQGANAVKFLLYYDVDDAEEINIQKKAYIERIGSECVAEDIPFFLEVLTYDDNIPDNGSVEFAKVKPRKVNEAMKLFSEPRFNVDVLKVEVPVNMKYVEGFAEGEVVYTKEEAAQHFKDQDAATHLPYIYLSAGVSAELFQETLKFAHEAGAKFNGVLCGRATWSGAVQVYIEQGEDAAREWLRTTGFKNIDDLNKVLKDTATSWKQ 324
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh.......eeeeee..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh....eeee...hhhhhhhh.......eee.....................hhhhhhh....eeeeeeee....hhhhhhhhhhhhhhhhhhhhhh...eeeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhh..eeee....hhhhh..........hhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh.....eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3myp A   4 SNQKIASIEQLSNNEGIISALAFDQRGALKRmmAKHQTEEPTVAQIEQLKVLVAEELTQYASSILLDPEYGLPASDARNKDCGLLLAYEKTGYDVNAKGRLPDCLVEWSAKRLKEQGANAVKFLLYYDVDDAEEINIQKKAYIERIGSECVAEDIPFFLEVLTYDDNIPDNGSVEFAKVKPRKVNEAmKLFSEPRFNVDVLKVEVPVNmKYVEGFAEGEVVYTKEEAAQHFKDQDAATHLPYIYLSAGVSAELFQETLKFAHEAGAKFNGVLCGRATWSGAVQVYIEQGEDAAREWLRTTGFKNIDDLNKVLKDTATSWKQ 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 
                                                          35-MSE                                                                                                                                                     191-MSE              212-MSE                                                                                                            
                                                           36-MSE                                                                                                                                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:321
 aligned with LACD_STAAC | Q5HE13 from UniProtKB/Swiss-Prot  Length:326

    Alignment length:321
                                    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 
           LACD_STAAC     4 SNQKIASIEQLSNNEGIISALAFDQRGALKRMMAKHQTEEPTVAQIEQLKVLVAEELTQYASSILLDPEYGLPASDARNKDCGLLLAYEKTGYDVNAKGRLPDCLVEWSAKRLKEQGANAVKFLLYYDVDDAEEINIQKKAYIERIGSECVAEDIPFFLEVLTYDDNIPDNGSVEFAKVKPRKVNEAMKLFSEPRFNVDVLKVEVPVNMKYVEGFAEGEVVYTKEEAAQHFKDQDAATHLPYIYLSAGVSAELFQETLKFAHEAGAKFNGVLCGRATWSGAVQVYIEQGEDAAREWLRTTGFKNIDDLNKVLKDTATSWKQ 324
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh.....eeeeee..hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh.eeee....hhhhhhh.....eeeee.....................hhhhhhh....eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhh..eeee....hhhhh..........hhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhh.....eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3myp B   4 SNQKIASIEQLSNNEGIISALAFDQRGALKRmmAKHQTEEPTVAQIEQLKVLVAEELTQYASSILLDPEYGLPASDARNKDCGLLLAYEKTGYDVNAKGRLPDCLVEWSAKRLKEQGANAVKFLLYYDVDDAEEINIQKKAYIERIGSECVAEDIPFFLEVLTYDDNIPDNGSVEFAKVKPRKVNEAmKLFSEPRFNVDVLKVEVPVNmKYVEGFAEGEVVYTKEEAAQHFKDQDAATHLPYIYLSAGVSAELFQETLKFAHEAGAKFNGVLCGRATWSGAVQVYIEQGEDAAREWLRTTGFKNIDDLNKVLKDTATSWKQ 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 
                                                          35-MSE                                                                                                                                                     191-MSE              212-MSE                                                                                                            
                                                           36-MSE                                                                                                                                                                                                                                                                                            


Chain C from PDB  Type:PROTEIN  Length:321
 aligned with LACD_STAAC | Q5HE13 from UniProtKB/Swiss-Prot  Length:326

    Alignment length:321
                                    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 
           LACD_STAAC     4 SNQKIASIEQLSNNEGIISALAFDQRGALKRMMAKHQTEEPTVAQIEQLKVLVAEELTQYASSILLDPEYGLPASDARNKDCGLLLAYEKTGYDVNAKGRLPDCLVEWSAKRLKEQGANAVKFLLYYDVDDAEEINIQKKAYIERIGSECVAEDIPFFLEVLTYDDNIPDNGSVEFAKVKPRKVNEAMKLFSEPRFNVDVLKVEVPVNMKYVEGFAEGEVVYTKEEAAQHFKDQDAATHLPYIYLSAGVSAELFQETLKFAHEAGAKFNGVLCGRATWSGAVQVYIEQGEDAAREWLRTTGFKNIDDLNKVLKDTATSWKQ 324
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh........eeeee...hhhhhhhhh.......hhhhhhhhhhhhhhhhh....eeee....hhhhhhhh....eeeee.....................hhhhhhh....eeeeeeee....hhhhhhhhhhhhhhhhhhhhhh...eeeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhh..eeee....hhhhh..........hhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3myp C   4 SNQKIASIEQLSNNEGIISALAFDQRGALKRmmAKHQTEEPTVAQIEQLKVLVAEELTQYASSILLDPEYGLPASDARNKDCGLLLAYEKTGYDVNAKGRLPDCLVEWSAKRLKEQGANAVKFLLYYDVDDAEEINIQKKAYIERIGSECVAEDIPFFLEVLTYDDNIPDNGSVEFAKVKPRKVNEAmKLFSEPRFNVDVLKVEVPVNmKYVEGFAEGEVVYTKEEAAQHFKDQDAATHLPYIYLSAGVSAELFQETLKFAHEAGAKFNGVLCGRATWSGAVQVYIEQGEDAAREWLRTTGFKNIDDLNKVLKDTATSWKQ 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 
                                                          35-MSE                                                                                                                                                     191-MSE              212-MSE                                                                                                            
                                                           36-MSE                                                                                                                                                                                                                                                                                            


Chain D from PDB  Type:PROTEIN  Length:321
 aligned with LACD_STAAC | Q5HE13 from UniProtKB/Swiss-Prot  Length:326

    Alignment length:321
                                    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 
           LACD_STAAC     4 SNQKIASIEQLSNNEGIISALAFDQRGALKRMMAKHQTEEPTVAQIEQLKVLVAEELTQYASSILLDPEYGLPASDARNKDCGLLLAYEKTGYDVNAKGRLPDCLVEWSAKRLKEQGANAVKFLLYYDVDDAEEINIQKKAYIERIGSECVAEDIPFFLEVLTYDDNIPDNGSVEFAKVKPRKVNEAMKLFSEPRFNVDVLKVEVPVNMKYVEGFAEGEVVYTKEEAAQHFKDQDAATHLPYIYLSAGVSAELFQETLKFAHEAGAKFNGVLCGRATWSGAVQVYIEQGEDAAREWLRTTGFKNIDDLNKVLKDTATSWKQ 324
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------DeoC-3mypD01 D:21-283                                                                                                                                                                                                                                                  ----------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------DeoC-3mypD02 D:21-283                                                                                                                                                                                                                                                  ----------------------------------------- Pfam domains (2)
           Pfam domains (3) -----------------DeoC-3mypD03 D:21-283                                                                                                                                                                                                                                                  ----------------------------------------- Pfam domains (3)
           Pfam domains (4) -----------------DeoC-3mypD04 D:21-283                                                                                                                                                                                                                                                  ----------------------------------------- Pfam domains (4)
         Sec.struct. author hhhhhhhhhh.......eeeee...hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.eeee....hhhhhhh.....eeeee.....................hhhhhhhh...eeeeeeee....hhhhhhhhhhhhhhhhhhhhhh...eeeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhh..eeee....hhhhh..........hhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhh.....eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3myp D   4 SNQKIASIEQLSNNEGIISALAFDQRGALKRmmAKHQTEEPTVAQIEQLKVLVAEELTQYASSILLDPEYGLPASDARNKDCGLLLAYEKTGYDVNAKGRLPDCLVEWSAKRLKEQGANAVKFLLYYDVDDAEEINIQKKAYIERIGSECVAEDIPFFLEVLTYDDNIPDNGSVEFAKVKPRKVNEAmKLFSEPRFNVDVLKVEVPVNmKYVEGFAEGEVVYTKEEAAQHFKDQDAATHLPYIYLSAGVSAELFQETLKFAHEAGAKFNGVLCGRATWSGAVQVYIEQGEDAAREWLRTTGFKNIDDLNKVLKDTATSWKQ 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 
                                                          35-MSE                                                                                                                                                     191-MSE              212-MSE                                                                                                            
                                                           36-MSE
   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 3MYP)

(-) CATH Domains  (0, 0)

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

(-) 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   (LACD_STAAC | Q5HE13)
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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 Related Entries

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3myo THE SAME PROTEIN FROM STREPTOCOCCUS PYOGENES