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(-) Description

Title :  CRYSTAL STRUCTURE OF M. TUBERCULOSIS GLUCOSYL-3-PHOSPHOGLYCERATE SYNTHASE
 
Authors :  P. J. B. Pereira, N. Empadinhas, M. S. Costa, S. Macedo-Ribeiro
Date :  05 Aug 08  (Deposition) - 02 Dec 08  (Release) - 09 Dec 08  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Glucosyltransferase, Mycobacterial, Gt81 Udp-Glucose, 3- Phosphoglycerate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. J. B. Pereira, N. Empadinhas, L. Albuquerque, B. Sa-Moura, M. S. Da Costa, S. Macedo-Ribeiro
Mycobacterium Tuberculosis Glucosyl-3-Phosphoglycerate Synthase: Structure Of A Key Enzyme In Methylglucose Lipopolysaccharide Biosynthesis
Plos One V. 3 E3748 2008
PubMed-ID: 19015727  |  Reference-DOI: 10.1371/JOURNAL.PONE.0003748
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUTATIVE UNCHARACTERIZED PROTEIN
    Chains: A
    EC Number: 2.4.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET30A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MT1246, RV1208
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Synonym: GLUCOSYL-3-PHOSPHOGLYCERATE SYNTHASE, GPGS

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
13PG1Ligand/Ion3-PHOSPHOGLYCERIC ACID
2MG1Ligand/IonMAGNESIUM ION
3UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
13PG2Ligand/Ion3-PHOSPHOGLYCERIC ACID
2MG-1Ligand/IonMAGNESIUM ION
3UDP2Ligand/IonURIDINE-5'-DIPHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:134 , ASP A:136 , UDP A:339BINDING SITE FOR RESIDUE MG A 338
2AC2SOFTWAREPRO A:50 , ALA A:51 , LEU A:52 , GLU A:54 , SER A:81 , GLY A:113 , LYS A:114 , ASP A:134 , SER A:135 , ASP A:136 , TYR A:229 , ARG A:261 , MET A:269 , MG A:338 , 3PG A:340 , HOH A:345 , HOH A:371BINDING SITE FOR RESIDUE UDP A 339
3AC3SOFTWAREARG A:185 , VAL A:186 , THR A:187 , UDP A:339BINDING SITE FOR RESIDUE 3PG A 340

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3E25)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Tyr A:303 -Thr A:304

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3E25)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3E25)

(-) Exons   (0, 0)

(no "Exon" information available for 3E25)

(-) 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:270
 aligned with GPGS_MYCTO | P9WMW8 from UniProtKB/Swiss-Prot  Length:324

    Alignment length:300
                                    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
           GPGS_MYCTO    24 TTWHRPGWTIGELEAAKAGRTISVVLPALNEEATIESVIDSISPLVDGLVDELIVLDSGSTDDTEIRAIASGARVVSREQALPEVPVRPGKGEALWRSLAATSGDIVVFIDSDLINPHPLFVPWLVGPLLTGEGIQLVKSFYRRPLQVSDVTSGVCATGGGRVTELVARPLLAALRPELGCVLQPLSGEYAASRELLTSLPFAPGYGVEIGLLIDTFDRLGLDAIAQVNLGVRAHRNRPLDELGAMSRQVIATLLSRCGIPDSGVGLTQFLPGGPDDSDYTRHTWPVSLVDRPPMKVMRP 323
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee.....hhhhhhhhh....eeeeeee.....hhhhhhhhhhhhh.....eeeeee.....hhhhhhhhh..eeeehhhhh.......hhhhhhhhhhhhh...eeee..........hhhhhhhhhhhhh....eeeee..------------------hhhhhhhhhhhhhhhhhhh.........eeeehhhhhhh...hhhhhhhhhhhhhhhhhh...eeeee....---...hhhhhhhhhhhhhhhhhhh.........ee.---------...ee.........hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3e25 A  24 TTWHRPGWTIGELEAAKAGRTISVVLPALNEEATIESVIDSISPLVDGLVDELIVLDSGSTDDTEIRAIASGARVVSREQALPEVPVRPGKGEALWRSLAATSGDIVVFIDSDLINPHPLFVPWLVGPLLTGEGIQLVKSFYR------------------RVTELVARPLLAALRPELGCVLQPLSGEYAASRELLTSLPFAPGYGVEIGLLIDTFDRLGLDAIAQVNLGVR---NRPLDELGAMSRQVIATLLSRCGIPDSGVGLTQF---------YTRHTWPVSLVDRPPMKVMRP 323
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163  |      -         - |     193       203       213       223       233       243       253  |   |263       273       283       293       303       313       323
                                                                                                                                                                        166                185                                                                    256 260                              293       303                    


Chain A from PDB  Type:PROTEIN  Length:270
 aligned with GPGS_MYCTU | P9WMW9 from UniProtKB/Swiss-Prot  Length:324

    Alignment length:300
                                    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
           GPGS_MYCTU    24 TTWHRPGWTIGELEAAKAGRTISVVLPALNEEATIESVIDSISPLVDGLVDELIVLDSGSTDDTEIRAIASGARVVSREQALPEVPVRPGKGEALWRSLAATSGDIVVFIDSDLINPHPLFVPWLVGPLLTGEGIQLVKSFYRRPLQVSDVTSGVCATGGGRVTELVARPLLAALRPELGCVLQPLSGEYAASRELLTSLPFAPGYGVEIGLLIDTFDRLGLDAIAQVNLGVRAHRNRPLDELGAMSRQVIATLLSRCGIPDSGVGLTQFLPGGPDDSDYTRHTWPVSLVDRPPMKVMRP 323
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee.....hhhhhhhhh....eeeeeee.....hhhhhhhhhhhhh.....eeeeee.....hhhhhhhhh..eeeehhhhh.......hhhhhhhhhhhhh...eeee..........hhhhhhhhhhhhh....eeeee..------------------hhhhhhhhhhhhhhhhhhh.........eeeehhhhhhh...hhhhhhhhhhhhhhhhhh...eeeee....---...hhhhhhhhhhhhhhhhhhh.........ee.---------...ee.........hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3e25 A  24 TTWHRPGWTIGELEAAKAGRTISVVLPALNEEATIESVIDSISPLVDGLVDELIVLDSGSTDDTEIRAIASGARVVSREQALPEVPVRPGKGEALWRSLAATSGDIVVFIDSDLINPHPLFVPWLVGPLLTGEGIQLVKSFYR------------------RVTELVARPLLAALRPELGCVLQPLSGEYAASRELLTSLPFAPGYGVEIGLLIDTFDRLGLDAIAQVNLGVR---NRPLDELGAMSRQVIATLLSRCGIPDSGVGLTQF---------YTRHTWPVSLVDRPPMKVMRP 323
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163  |      -         - |     193       203       213       223       233       243       253  |   |263       273       283       293       303       313       323
                                                                                                                                                                        166                185                                                                    256 260                              293       303
   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 3E25)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3E25)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3E25)

(-) Gene Ontology  (8, 11)

Asymmetric Unit(hide GO term definitions)
Chain A   (GPGS_MYCTU | P9WMW9)
molecular function
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
    GO:0016758    transferase activity, transferring hexosyl groups    Catalysis of the transfer of a hexosyl group from one compound (donor) to another (acceptor).
biological process
    GO:0006011    UDP-glucose metabolic process    The chemical reactions and pathways involving UDP-glucose, uridinediphosphoglucose, a substance composed of glucose in glycosidic linkage with uridine diphosphate.
    GO:0040007    growth    The increase in size or mass of an entire organism, a part of an organism or a cell.

Chain A   (GPGS_MYCTO | P9WMW8)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).

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 Related Entries

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

UniProtKB/Swiss-Prot
        GPGS_MYCTO | P9WMW8: 3e26 4ddz 4de7 4dec
        GPGS_MYCTU | P9WMW9: 3e26 4ddz 4de7 4dec 4y6n 4y6u 4y7f 4y7g 4y9x 5jqq 5jqx 5jt0 5juc

(-) Related Entries Specified in the PDB File

3e26 THE SAME PROTEIN, APO FORM