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(-) Description

Title :  CRYSTAL STRUCTURE OF R. XYLANOPHILUS MPGS IN COMPLEX WITH GDP-MANNOSE
 
Authors :  S. Macedo-Ribeiro, P. J. B. Pereira, N. Empadinhas, M. S. Da Costa
Date :  25 Jul 10  (Deposition) - 03 Nov 10  (Release) - 21 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.53
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Gta, Gt-81 Family, Dinucleotide-Binding Fold, Glucosyltransferase, Mannosylglycerate Biosynthesis, Gdp-Mannose, Gdp-Glucose, Mpgs, Gpgs, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Empadinhas, P. J. B. Pereira, L. Albuquerque, J. Costa, B. Sa-Moura A. T. Marques, S. Macedo-Ribeiro, M. S. Da Costa
Functional And Structural Characterization Of A Novel Mannosyl-3-Phosphoglycerate Synthase From Rubrobacter Xylanophilus Reveals Its Dual Substrate Specificity
Mol. Microbiol. V. 79 76 2011
PubMed-ID: 21166895  |  Reference-DOI: 10.1111/J.1365-2958.2010.07432.X

(-) Compounds

Molecule 1 - MANNOSYL-3-PHOSPHOGLYCERATE SYNTHASE
    Chains: A, B
    EC Number: 2.4.1.217
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET30A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: RUBROBACTER XYLANOPHILUS
    Organism Taxid: 49319
    Strain: DSM 9941 / NBRC 16129

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric/Biological Unit (4, 6)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2GDD1Ligand/IonGUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE
3GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
4MG2Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:273 , LEU A:322BINDING SITE FOR RESIDUE CL A 336
2AC2SOFTWAREARG A:273 , ARG A:277 , ARG A:280BINDING SITE FOR RESIDUE CL A 337
3AC3SOFTWAREGLN A:299 , ASP A:302 , HOH A:390 , HOH A:391 , HOH B:365 , HOH B:373BINDING SITE FOR RESIDUE MG A 338
4AC4SOFTWAREASP A:137 , ASN A:256 , GDD A:340BINDING SITE FOR RESIDUE MG A 339
5AC5SOFTWAREPRO A:49 , SER A:50 , ARG A:51 , VAL A:53 , VAL A:80 , ALA A:82 , GLU A:102 , GLY A:114 , LYS A:115 , ALA A:118 , ASP A:135 , ALA A:136 , ASP A:137 , LEU A:207 , GLY A:209 , TYR A:227 , GLU A:230 , ASN A:256 , GLN A:259 , MET A:267 , MG A:339 , HOH A:350 , HOH A:396BINDING SITE FOR RESIDUE GDD A 340
6AC6SOFTWAREPRO B:49 , SER B:50 , ARG B:51 , VAL B:53 , VAL B:80 , ALA B:82 , GLU B:102 , GLY B:114 , LYS B:115 , ALA B:118 , ALA B:136 , ASP B:137 , TYR B:227 , GLN B:259 , HOH B:357 , HOH B:387BINDING SITE FOR RESIDUE GDP B 336

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3O3P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3O3P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3O3P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3O3P)

(-) Exons   (0, 0)

(no "Exon" information available for 3O3P)

(-) Sequences/Alignments

Asymmetric/Biological 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:318
 aligned with B7SY86_9ACTN | B7SY86 from UniProtKB/TrEMBL  Length:335

    Alignment length:325
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329     
         B7SY86_9ACTN    10 GPASAAEWFRQRSYDYGQFPPEDLARRKRELGLTVSAVLPSRNVADTVGGIIDEIHALNERAPLIDQILVVDADSEDGTAGVAASHGAEVYSENELMSGYGDAHGKGDAMWRALSVTRGDLVLYIDADTRDFRPQLAYGVLGPVLEVPGVRFVKAAYRRPFRKGESIEEDGGGRVTELTAKPLFNLFYPELAGFVQPLAGEFVADRELFCSIPFLTGYAVETGIMIDVLKKVGLGAMAQVDLGERQNRHQHLRDLSRMSYAVVRAVARRLRQEGRLQQLREPGLPESFFQLSDYLHAVATPEGLKLQEYVEELVERPPINEVLRV 334
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhheee.hhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhh..eeee....hhhhh..hhhhhhhhhhh......eeee.........hhhhhhhhhhhhhh....eeeeeee..-------.....hhhhhhhhhhhhhhhhhhhh.........eeeehhhhh...ee...hhhhhhhhhhhhhhh...eeeeeeee......hhhhhhhhhhhhhhhhhhhhhhh...........hhhhh...eeeeeeee..eeeeeeee....ee.hhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o3p A  10 GPASAAEWFRQRSYDYGQFPPEDLARRKRELGLTVSAVLPSRNVADTVGGIIDEIHALNERAPLIDQILVVDADSEDGTAGVAASHGAEVYSENELMSGYGDAHGKGDAMWRALSVTRGDLVLYIDADTRDFRPQLAYGVLGPVLEVPGVRFVKAAYRRP-------EEDGGGRVTELTAKPLFNLFYPELAGFVQPLAGEFVADRELFCSIPFLTGYAVETGIMIDVLKKVGLGAMAQVDLGERQNRHQHLRDLSRMSYAVVRAVARRLRQEGRLQQLREPGLPESFFQLSDYLHAVATPEGLKLQEYVEELVERPPINEVLRV 334
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329     
                                                                                                                                                                                         169     177                                                                                                                                                             


Chain A from PDB  Type:PROTEIN  Length:318
 aligned with Q1ATN7_RUBXD | Q1ATN7 from UniProtKB/TrEMBL  Length:335

    Alignment length:325
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329     
         Q1ATN7_RUBXD    10 GPTSAADWFRQRSYEYGQFPPERLARRKRELGLAVSAVLPSRNVAETVGGIIDEIHALNERAPLIDQVLVVDADSEDGTAGIAASRGAEVYSENELMSGYGDAHGKGDAMWRALSVARGDLVLYVDADTRDFRPQLAYGVLGPILEVPEVRFVKAAYRRPFRKGESIEEDGGGRVTELTAKPLFNLFYPELTGFVQPLAGEFVADRELFCSIPFLTGYAVETGIMIDVLKKVGLGAMAQVDLGERQNRHQHLRDLSRMSYAVVRAVARRLRQEGRLQQVREPGLPESFFQFSDYLHAVATPEGLKLQEYVEELVERPPINEVLRV 334
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhheee.hhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhh..eeee....hhhhh..hhhhhhhhhhh......eeee.........hhhhhhhhhhhhhh....eeeeeee..-------.....hhhhhhhhhhhhhhhhhhhh.........eeeehhhhh...ee...hhhhhhhhhhhhhhh...eeeeeeee......hhhhhhhhhhhhhhhhhhhhhhh...........hhhhh...eeeeeeee..eeeeeeee....ee.hhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3o3p A  10 GPASAAEWFRQRSYDYGQFPPEDLARRKRELGLTVSAVLPSRNVADTVGGIIDEIHALNERAPLIDQILVVDADSEDGTAGVAASHGAEVYSENELMSGYGDAHGKGDAMWRALSVTRGDLVLYIDADTRDFRPQLAYGVLGPVLEVPGVRFVKAAYRRP-------EEDGGGRVTELTAKPLFNLFYPELAGFVQPLAGEFVADRELFCSIPFLTGYAVETGIMIDVLKKVGLGAMAQVDLGERQNRHQHLRDLSRMSYAVVRAVARRLRQEGRLQQLREPGLPESFFQLSDYLHAVATPEGLKLQEYVEELVERPPINEVLRV 334
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329     
                                                                                                                                                                                         169     177                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:317
 aligned with B7SY86_9ACTN | B7SY86 from UniProtKB/TrEMBL  Length:335

    Alignment length:324
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329    
         B7SY86_9ACTN    10 GPASAAEWFRQRSYDYGQFPPEDLARRKRELGLTVSAVLPSRNVADTVGGIIDEIHALNERAPLIDQILVVDADSEDGTAGVAASHGAEVYSENELMSGYGDAHGKGDAMWRALSVTRGDLVLYIDADTRDFRPQLAYGVLGPVLEVPGVRFVKAAYRRPFRKGESIEEDGGGRVTELTAKPLFNLFYPELAGFVQPLAGEFVADRELFCSIPFLTGYAVETGIMIDVLKKVGLGAMAQVDLGERQNRHQHLRDLSRMSYAVVRAVARRLRQEGRLQQLREPGLPESFFQLSDYLHAVATPEGLKLQEYVEELVERPPINEVLR 333
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -----------------------------------Glycos_transf_2-3o3pB01 B:45-149                                                                         ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------Glycos_transf_2-3o3pB02 B:45-149                                                                         ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ...hhhhhhhhheee.hhhhhhhhhhhhhhh...eeeeeee.....hhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhh..eeee....hhhhh..hhhhhhhhhhhhh....eeee.........hhhhhhhhhhhhhh....eeeeeee..-------.....hhhhhhhhhhhhhhhhhhhh.........eeeehhhhh...ee...hhhhhhhhhhhhhhh...eeeeeeee......hhhhhhhhhhhhhhhhhhhhhhh...................eeeeeeee..eeeeeeee....ee.hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3o3p B  10 GPASAAEWFRQRSYDYGQFPPEDLARRKRELGLTVSAVLPSRNVADTVGGIIDEIHALNERAPLIDQILVVDADSEDGTAGVAASHGAEVYSENELMSGYGDAHGKGDAMWRALSVTRGDLVLYIDADTRDFRPQLAYGVLGPVLEVPGVRFVKAAYRRP-------EEDGGGRVTELTAKPLFNLFYPELAGFVQPLAGEFVADRELFCSIPFLTGYAVETGIMIDVLKKVGLGAMAQVDLGERQNRHQHLRDLSRMSYAVVRAVARRLRQEGRLQQLREPGLPESFFQLSDYLHAVATPEGLKLQEYVEELVERPPINEVLR 333
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329    
                                                                                                                                                                                         169     177                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:317
 aligned with Q1ATN7_RUBXD | Q1ATN7 from UniProtKB/TrEMBL  Length:335

    Alignment length:324
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329    
         Q1ATN7_RUBXD    10 GPTSAADWFRQRSYEYGQFPPERLARRKRELGLAVSAVLPSRNVAETVGGIIDEIHALNERAPLIDQVLVVDADSEDGTAGIAASRGAEVYSENELMSGYGDAHGKGDAMWRALSVARGDLVLYVDADTRDFRPQLAYGVLGPILEVPEVRFVKAAYRRPFRKGESIEEDGGGRVTELTAKPLFNLFYPELTGFVQPLAGEFVADRELFCSIPFLTGYAVETGIMIDVLKKVGLGAMAQVDLGERQNRHQHLRDLSRMSYAVVRAVARRLRQEGRLQQVREPGLPESFFQFSDYLHAVATPEGLKLQEYVEELVERPPINEVLR 333
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -----------------------------------Glycos_transf_2-3o3pB01 B:45-149                                                                         ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------Glycos_transf_2-3o3pB02 B:45-149                                                                         ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ...hhhhhhhhheee.hhhhhhhhhhhhhhh...eeeeeee.....hhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhh..eeee....hhhhh..hhhhhhhhhhhhh....eeee.........hhhhhhhhhhhhhh....eeeeeee..-------.....hhhhhhhhhhhhhhhhhhhh.........eeeehhhhh...ee...hhhhhhhhhhhhhhh...eeeeeeee......hhhhhhhhhhhhhhhhhhhhhhh...................eeeeeeee..eeeeeeee....ee.hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3o3p B  10 GPASAAEWFRQRSYDYGQFPPEDLARRKRELGLTVSAVLPSRNVADTVGGIIDEIHALNERAPLIDQILVVDADSEDGTAGVAASHGAEVYSENELMSGYGDAHGKGDAMWRALSVTRGDLVLYIDADTRDFRPQLAYGVLGPVLEVPGVRFVKAAYRRP-------EEDGGGRVTELTAKPLFNLFYPELAGFVQPLAGEFVADRELFCSIPFLTGYAVETGIMIDVLKKVGLGAMAQVDLGERQNRHQHLRDLSRMSYAVVRAVARRLRQEGRLQQLREPGLPESFFQLSDYLHAVATPEGLKLQEYVEELVERPPINEVLR 333
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329    
                                                                                                                                                                                         169     177
   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 3O3P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3O3P)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: GT-A (172)

(-) Gene Ontology  (3, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q1ATN7_RUBXD | Q1ATN7)
molecular function
    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.

Chain A,B   (B7SY86_9ACTN | B7SY86)
molecular function
    GO:0050504    mannosyl-3-phosphoglycerate synthase activity    Catalysis of the reaction: 3-phospho-D-glycerate + GDP-alpha-D-mannose = 2-(alpha-D-mannosyl)-3-phosphoglycerate + GDP + H(+).
    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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  2.4.1.217
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 Related Entries

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

UniProtKB/Swiss-Prot
        B7SY86_9ACTN | B7SY86: 3f1y 3kia
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        Q1ATN7_RUBXD | Q1ATN7: 3f1y 3kia

(-) Related Entries Specified in the PDB File

3e26 HOMOLOGOUS M. TUBERCULOSIS ENZYME
3f1y APO ENZYME
3kia GDP COMPLEX