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(-) Description

Title :  CRYSTAL STRUCTURE OF GLUCOSYL-3-PHOSPHOGLYCERATE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH MN2+, URIDINE-DIPHOSPHATE-GLUCOSE (UDP-GLC) AND PHOSPHOGLYCERIC ACID (PGA) - GPGS MN2+ UDP-GLC PGA-3
 
Authors :  D. Albesa-Jove, A. Rodrigo-Unzueta, J. O. Cifuente, S. Urresti, N. Com E. Sancho-Vaello, M. E. Guerin
Date :  17 Feb 15  (Deposition) - 15 Jul 15  (Release) - 27 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.64
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Albesa-Jove, F. Mendoza, A. Rodrigo-Unzueta, F. Gomollon-Bel, J. O. Cifuente, S. Urresti, N. Comino, H. Gomez, J. Romero-Garcia, J. M. Lluch, E. Sancho-Vaello, X. Biarnes, A. Planas, P. Merino, L. Masgrau, M. E. Guerin
A Native Ternary Complex Trapped In A Crystal Reveals The Catalytic Mechanism Of A Retaining Glycosyltransferase.
Angew. Chem. Int. Ed. Engl. V. 54 9898 2015
PubMed-ID: 26136334  |  Reference-DOI: 10.1002/ANIE.201504617

(-) Compounds

Molecule 1 - GLUCOSYL-3-PHOSPHOGLYCERATE SYNTHASE
    Chains: A
    EC Number: 2.4.1.266
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: GPGS, RV1208
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS (STRAIN ATCC 25618 / H37RV)
    Organism Taxid: 83332

 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, 7)

Asymmetric Unit (5, 7)
No.NameCountTypeFull Name
13PG1Ligand/Ion3-PHOSPHOGLYCERIC ACID
2CL1Ligand/IonCHLORIDE ION
3EDO3Ligand/Ion1,2-ETHANEDIOL
4MN1Ligand/IonMANGANESE (II) ION
5UPG1Ligand/IonURIDINE-5'-DIPHOSPHATE-GLUCOSE
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
13PG2Ligand/Ion3-PHOSPHOGLYCERIC ACID
2CL-1Ligand/IonCHLORIDE ION
3EDO6Ligand/Ion1,2-ETHANEDIOL
4MN-1Ligand/IonMANGANESE (II) ION
5UPG2Ligand/IonURIDINE-5'-DIPHOSPHATE-GLUCOSE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:136 , HIS A:258 , UPG A:404 , HOH A:508 , HOH A:530binding site for residue MN A 401
2AC2SOFTWAREARG A:242 , LYS A:319binding site for residue CL A 402
3AC3SOFTWAREGLY A:183 , GLY A:184 , ARG A:185 , VAL A:186 , THR A:187 , HIS A:258 , ASN A:260 , UPG A:404 , HOH A:510 , HOH A:560binding site for residue 3PG A 403
4AC4SOFTWAREPRO 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 , LEU A:209 , GLY A:211 , TYR A:229 , GLU A:232 , ARG A:256 , HIS A:258 , ARG A:259 , ARG A:261 , MET A:269 , MN A:401 , 3PG A:403 , HOH A:508 , HOH A:530binding site for residue UPG A 404
5AC5SOFTWAREARG A:101 , HOH A:556binding site for residue EDO A 405
6AC6SOFTWAREALA A:226 , PRO A:227 , THR A:276 , SER A:279 , ARG A:280 , SER A:311 , LEU A:312 , ASP A:314binding site for residue EDO A 406
7AC7SOFTWAREARG A:43 , GLY A:155 , GLY A:157binding site for residue EDO A 407

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Y9X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4Y9X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Y9X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Y9X)

(-) Exons   (0, 0)

(no "Exon" information available for 4Y9X)

(-) 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:280
                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee......hhhhhhhhh....eeeeeee.....hhhhhhhhhhhhh.....eeeeee.....hhhhhhhhh..eeeehhhhh.......hhhhhhhhhhhh....eeee..........hhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhhhhh.........eeeehhhhh.....hhhhhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhhhhhhhhhhhh.........eee...eee.........hhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y9x A  19 ALPLDTTWHRPGWTIGELEAAKAGRTISVVLPALNEEATIESVIDSISPLVDGLVDELIVLDSGSTDDTEIRAIASGARVVSREQALPEVPVRPGKGEALWRSLAATSGDIVVFIDSDLINPHPLFVPWLVGPLLTGEGIQLVKSFYRGGRVTELVARPLLAALRPELGCVLQPLSGEYAASRELLTSLPFAPGYGVEIGLLIDTFDRLGLDAIAQVNLGVRAHRNRPLDELGAMSRQVIATLLSRCGIPDSGVGLTQFLYTRHTWPVSLVDRPPMKVMR 322
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       184       194       204       214       224       234       244       254       264       274       284       294|      312       322
                                                                                                                                                                             166|                                                                                                            294|                   
                                                                                                                                                                              183                                                                                                             303
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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 4Y9X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Y9X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Y9X)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

4y6n 4y6u 4y7f 4y7g