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(-) Description

Title :  CRYSTAL STRUCTURE OF GLUCOSYL-3-PHOSPHOGLYCERATE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH MN2+, URIDINE-DIPHOSPHATE (UDP) AND PHOSPHOGLYCERIC ACID (PGA)
 
Authors :  D. Albesa-Jove, S. Urresti, M. Van Der Woerd, M. E. Guerin
Date :  20 Jan 12  (Deposition) - 06 Jun 12  (Release) - 09 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.98
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Urresti, D. Albesa-Jove, F. Schaeffer, H. T. Pham, D. Kaur, P. Gest, M. J. Van Der Woerd, A. Carreras-Gonzalez, S. Lopez-Fernandez, P. M. Alzari, P. J. Brennan, M. Jackson, M. E. Guerin
Mechanistic Insights Into The Retaining Glucosyl-3-Phosphoglycerate Synthase From Mycobacteria.
J. Biol. Chem. V. 287 24649 2012
PubMed-ID: 22637481  |  Reference-DOI: 10.1074/JBC.M112.368191

(-) Compounds

Molecule 1 - GLUCOSYL-3-PHOSPHOGLYCERATE SYNTHASE (GPGS)
    Chains: A
    EC Number: 2.4.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A-GPGS
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: GPGS, MT1246, RV1208
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 83332
    Strain: H37RV

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 6)

Asymmetric Unit (5, 6)
No.NameCountTypeFull Name
13PG1Ligand/Ion3-PHOSPHOGLYCERIC ACID
2GOL1Ligand/IonGLYCEROL
3MN1Ligand/IonMANGANESE (II) ION
4PO42Ligand/IonPHOSPHATE ION
5UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 1 (4, 10)
No.NameCountTypeFull Name
13PG2Ligand/Ion3-PHOSPHOGLYCERIC ACID
2GOL2Ligand/IonGLYCEROL
3MN-1Ligand/IonMANGANESE (II) ION
4PO44Ligand/IonPHOSPHATE ION
5UDP2Ligand/IonURIDINE-5'-DIPHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO 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:259 , ARG A:261 , MN A:402 , HOH A:548 , HOH A:693 , HOH A:697 , HOH A:713BINDING SITE FOR RESIDUE UDP A 401
2AC2SOFTWAREASP A:136 , HIS A:258 , UDP A:401 , HOH A:501 , HOH A:713BINDING SITE FOR RESIDUE MN A 402
3AC3SOFTWAREGLY A:184 , ARG A:185 , VAL A:186 , THR A:187 , ASN A:260 , HOH A:713BINDING SITE FOR RESIDUE 3PG A 403
4AC4SOFTWAREGLN A:159 , GLU A:218 , LEU A:219 , ARG A:242BINDING SITE FOR RESIDUE PO4 A 404
5AC5SOFTWAREARG A:97 , VAL A:98 , HOH A:674BINDING SITE FOR RESIDUE GOL A 405
6AC6SOFTWARETHR A:25 , TRP A:26 , HIS A:27BINDING SITE FOR RESIDUE PO4 A 406

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4DEC)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4DEC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4DEC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4DEC)

(-) Exons   (0, 0)

(no "Exon" information available for 4DEC)

(-) 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:284
 aligned with GPGS_MYCTO | P9WMW8 from UniProtKB/Swiss-Prot  Length:324

    Alignment length:304
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318    
           GPGS_MYCTO    19 ALPLDTTWHRPGWTIGELEAAKAGRTISVVLPALNEEATIESVIDSISPLVDGLVDELIVLDSGSTDDTEIRAIASGARVVSREQALPEVPVRPGKGEALWRSLAATSGDIVVFIDSDLINPHPLFVPWLVGPLLTGEGIQLVKSFYRRPLQVSDVTSGVCATGGGRVTELVARPLLAALRPELGCVLQPLSGEYAASRELLTSLPFAPGYGVEIGLLIDTFDRLGLDAIAQVNLGVRAHRNRPLDELGAMSRQVIATLLSRCGIPDSGVGLTQFLPGGPDDSDYTRHTWPVSLVDRPPMKVMR 322
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee......hhhhhhhhhh...eeeeeee.....hhhhhhhhhhhhh.....eeeeee.....hhhhhhhhh..eeeehhhhh.......hhhhhhhhhhhh....eeee..........hhhhhhhhhhhhh....eeeeeee----------------.hhhhhhhhhhhhhhhhhhhhhh.......eeeehhhhh.....hhhhhhhhhhhhhhhhhh...eeeeeeee......hhhhhhhhhhhhhhhhhhhh.........eeeee.----..eeeee.........hhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dec A  19 ALPLDTTWHRPGWTIGELEAAKAGRTISVVLPALNEEATIESVIDSISPLVDGLVDELIVLDSGSTDDTEIRAIASGARVVSREQALPEVPVRPGKGEALWRSLAATSGDIVVFIDSDLINPHPLFVPWLVGPLLTGEGIQLVKSFYR----------------GGRVTELVARPLLAALRPELGCVLQPLSGEYAASRELLTSLPFAPGYGVEIGLLIDTFDRLGLDAIAQVNLGVRAHRNRPLDELGAMSRQVIATLLSRCGIPDSGVGLTQFLPG----SDYTRHTWPVSLVDRPPMKVMR 322
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       | -         -    |  188       198       208       218       228       238       248       258       268       278       288       | -  |    308       318    
                                                                                                                                                                             166              183                                                                                                              296  301                     


Chain A from PDB  Type:PROTEIN  Length:284
 aligned with GPGS_MYCTU | P9WMW9 from UniProtKB/Swiss-Prot  Length:324

    Alignment length:304
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318    
           GPGS_MYCTU    19 ALPLDTTWHRPGWTIGELEAAKAGRTISVVLPALNEEATIESVIDSISPLVDGLVDELIVLDSGSTDDTEIRAIASGARVVSREQALPEVPVRPGKGEALWRSLAATSGDIVVFIDSDLINPHPLFVPWLVGPLLTGEGIQLVKSFYRRPLQVSDVTSGVCATGGGRVTELVARPLLAALRPELGCVLQPLSGEYAASRELLTSLPFAPGYGVEIGLLIDTFDRLGLDAIAQVNLGVRAHRNRPLDELGAMSRQVIATLLSRCGIPDSGVGLTQFLPGGPDDSDYTRHTWPVSLVDRPPMKVMR 322
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee......hhhhhhhhhh...eeeeeee.....hhhhhhhhhhhhh.....eeeeee.....hhhhhhhhh..eeeehhhhh.......hhhhhhhhhhhh....eeee..........hhhhhhhhhhhhh....eeeeeee----------------.hhhhhhhhhhhhhhhhhhhhhh.......eeeehhhhh.....hhhhhhhhhhhhhhhhhh...eeeeeeee......hhhhhhhhhhhhhhhhhhhh.........eeeee.----..eeeee.........hhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dec A  19 ALPLDTTWHRPGWTIGELEAAKAGRTISVVLPALNEEATIESVIDSISPLVDGLVDELIVLDSGSTDDTEIRAIASGARVVSREQALPEVPVRPGKGEALWRSLAATSGDIVVFIDSDLINPHPLFVPWLVGPLLTGEGIQLVKSFYR----------------GGRVTELVARPLLAALRPELGCVLQPLSGEYAASRELLTSLPFAPGYGVEIGLLIDTFDRLGLDAIAQVNLGVRAHRNRPLDELGAMSRQVIATLLSRCGIPDSGVGLTQFLPG----SDYTRHTWPVSLVDRPPMKVMR 322
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       | -         -    |  188       198       208       218       228       238       248       258       268       278       288       | -  |    308       318    
                                                                                                                                                                             166              183                                                                                                              296  301
   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 4DEC)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4DEC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4DEC)

(-) Gene Ontology  (8, 11)

Asymmetric Unit(hide GO term definitions)
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).

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.

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  4dec
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 Related Entries

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

UniProtKB/Swiss-Prot
        GPGS_MYCTO | P9WMW8: 3e25 3e26 4ddz 4de7
        GPGS_MYCTU | P9WMW9: 3e25 3e26 4ddz 4de7 4y6n 4y6u 4y7f 4y7g 4y9x 5jqq 5jqx 5jt0 5juc

(-) Related Entries Specified in the PDB File

4ddz 4de7