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(-) Description

Title :  CRYSTAL STRUCTURE OF MANNOSYL-3-PHOSPHOGLYCERATE SYNTHASE FROM RUBROBACTER XYLANOPHILUS
 
Authors :  S. Macedo-Ribeiro, P. J. B. Pereira, N. Empadinhas, M. S. Da Costa
Date :  01 Nov 09  (Deposition) - 03 Nov 10  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,C
Keywords :  Gt-A Type Glycosyltransferase, Gt-81, Mannosyl-3-Phosphoglycerate Synthase, Rubrobacter Xylanophilus, Gdp-Mannose, Glycosyltransferase, 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, C
    EC Number: 2.4.1.217
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET30A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: 266117
    Organism Scientific: SYNTHETIC CONSTRUCT, RUBROBACTER XYLANOPHILUS
    Organism Taxid: 32630, 49319
    Strain: DSM 9941

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
15GP2Ligand/IonGUANOSINE-5'-MONOPHOSPHATE
2CL3Ligand/IonCHLORIDE ION
3MG3Ligand/IonMAGNESIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO 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 , TYR A:227 , MG A:340 , HOH A:386BINDING SITE FOR RESIDUE 5GP A 336
2AC2SOFTWAREARG A:273 , LEU A:322BINDING SITE FOR RESIDUE CL A 337
3AC3SOFTWAREARG A:273 , ARG A:277 , HOH A:383BINDING SITE FOR RESIDUE CL A 338
4AC4SOFTWAREGLN A:299 , ASP A:302 , HOH A:349 , HOH A:393 , HOH A:394 , HOH C:390BINDING SITE FOR RESIDUE MG A 339
5AC5SOFTWAREASP A:137 , 5GP A:336BINDING SITE FOR RESIDUE MG A 340
6AC6SOFTWAREPRO C:49 , SER C:50 , ARG C:51 , VAL C:53 , VAL C:80 , ALA C:82 , GLU C:102 , GLY C:114 , LYS C:115 , ALA C:118 , ASP C:135 , ALA C:136 , ASP C:137 , TYR C:227 , MG C:338BINDING SITE FOR RESIDUE 5GP C 336
7AC7SOFTWAREASP C:137 , 5GP C:336BINDING SITE FOR RESIDUE MG C 338

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3KIA)

(-) 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:313
 aligned with B7SY86_9ACTN | B7SY86 from UniProtKB/TrEMBL  Length:335

    Alignment length:320
                                    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       333
         B7SY86_9ACTN    14 AAEWFRQRSYDYGQFPPEDLARRKRELGLTVSAVLPSRNVADTVGGIIDEIHALNERAPLIDQILVVDADSEDGTAGVAASHGAEVYSENELMSGYGDAHGKGDAMWRALSVTRGDLVLYIDADTRDFRPQLAYGVLGPVLEVPGVRFVKAAYRRPFRKGESIEEDGGGRVTELTAKPLFNLFYPELAGFVQPLAGEFVADRELFCSIPFLTGYAVETGIMIDVLKKVGLGAMAQVDLGERQNRHQHLRDLSRMSYAVVRAVARRLRQEGRLQQLREPGLPESFFQLSDYLHAVATPEGLKLQEYVEELVERPPINEVLR 333
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhheee.hhhhhhhhhhhhhhhh..eeeeeee.....hhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhh..eeee....hhhhh..hhhhhhhhhhhhhh...eeee.........hhhhhhhhhhhhhh....eeeeeee..-------.....hhhhhhhhhhhhhhhhhhhhhh.......eeeehhhhh...ee...hhhhhhhhhhhhhhh...eeeeeeee......hhhhhhhhhhhhhhhhhhhhhhh...........hhhhh...eeeeeeee..eeeeeeee....ee.hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kia A  14 AAEWFRQRSYDYGQFPPEDLARRKRELGLTVSAVLPSRNVADTVGGIIDEIHALNERAPLIDQILVVDADSEDGTAGVAASHGAEVYSENELMSGYGDAHGKGDAMWRALSVTRGDLVLYIDADTRDFRPQLAYGVLGPVLEVPGVRFVKAAYRRP-------EEDGGGRVTELTAKPLFNLFYPELAGFVQPLAGEFVADRELFCSIPFLTGYAVETGIMIDVLKKVGLGAMAQVDLGERQNRHQHLRDLSRMSYAVVRAVARRLRQEGRLQQLREPGLPESFFQLSDYLHAVATPEGLKLQEYVEELVERPPINEVLR 333
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163     |   -   |   183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333
                                                                                                                                                                                     169     177                                                                                                                                                            


Chain A from PDB  Type:PROTEIN  Length:313
 aligned with Q1ATN7_RUBXD | Q1ATN7 from UniProtKB/TrEMBL  Length:335

    Alignment length:320
                                    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       333
         Q1ATN7_RUBXD    14 AADWFRQRSYEYGQFPPERLARRKRELGLAVSAVLPSRNVAETVGGIIDEIHALNERAPLIDQVLVVDADSEDGTAGIAASRGAEVYSENELMSGYGDAHGKGDAMWRALSVARGDLVLYVDADTRDFRPQLAYGVLGPILEVPEVRFVKAAYRRPFRKGESIEEDGGGRVTELTAKPLFNLFYPELTGFVQPLAGEFVADRELFCSIPFLTGYAVETGIMIDVLKKVGLGAMAQVDLGERQNRHQHLRDLSRMSYAVVRAVARRLRQEGRLQQVREPGLPESFFQFSDYLHAVATPEGLKLQEYVEELVERPPINEVLR 333
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhheee.hhhhhhhhhhhhhhhh..eeeeeee.....hhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhh..eeee....hhhhh..hhhhhhhhhhhhhh...eeee.........hhhhhhhhhhhhhh....eeeeeee..-------.....hhhhhhhhhhhhhhhhhhhhhh.......eeeehhhhh...ee...hhhhhhhhhhhhhhh...eeeeeeee......hhhhhhhhhhhhhhhhhhhhhhh...........hhhhh...eeeeeeee..eeeeeeee....ee.hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kia A  14 AAEWFRQRSYDYGQFPPEDLARRKRELGLTVSAVLPSRNVADTVGGIIDEIHALNERAPLIDQILVVDADSEDGTAGVAASHGAEVYSENELMSGYGDAHGKGDAMWRALSVTRGDLVLYIDADTRDFRPQLAYGVLGPVLEVPGVRFVKAAYRRP-------EEDGGGRVTELTAKPLFNLFYPELAGFVQPLAGEFVADRELFCSIPFLTGYAVETGIMIDVLKKVGLGAMAQVDLGERQNRHQHLRDLSRMSYAVVRAVARRLRQEGRLQQLREPGLPESFFQLSDYLHAVATPEGLKLQEYVEELVERPPINEVLR 333
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163     |   -   |   183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333
                                                                                                                                                                                     169     177                                                                                                                                                            


Chain C from PDB  Type:PROTEIN  Length:308
 aligned with B7SY86_9ACTN | B7SY86 from UniProtKB/TrEMBL  Length:335

    Alignment length:325
                                    18        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       328     
         B7SY86_9ACTN     9 LGPASAAEWFRQRSYDYGQFPPEDLARRKRELGLTVSAVLPSRNVADTVGGIIDEIHALNERAPLIDQILVVDADSEDGTAGVAASHGAEVYSENELMSGYGDAHGKGDAMWRALSVTRGDLVLYIDADTRDFRPQLAYGVLGPVLEVPGVRFVKAAYRRPFRKGESIEEDGGGRVTELTAKPLFNLFYPELAGFVQPLAGEFVADRELFCSIPFLTGYAVETGIMIDVLKKVGLGAMAQVDLGERQNRHQHLRDLSRMSYAVVRAVARRLRQEGRLQQLREPGLPESFFQLSDYLHAVATPEGLKLQEYVEELVERPPINEVLR 333
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------Glycos_transf_2-3kiaC01 C:45-149                                                                         ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------Glycos_transf_2-3kiaC02 C:45-149                                                                         ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ....hhhhhhhhheee.hhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhh..eeee....hhhhh..hhhhhhhhhhh......eeee.........hhhhhhhhhhhhhh....eeeeeee..--------....hhhhhhhhhhhhhhhhhhhh.........eeeehhhhhhh.ee...hhhhhhhhhhhhhhh...eeeeeeee....--hhhhhhhhhhhhhhhhhhhhhhh......-------......eeeeeeee..eeeeeeee....ee.hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kia C   9 LGPASAAEWFRQRSYDYGQFPPEDLARRKRELGLTVSAVLPSRNVADTVGGIIDEIHALNERAPLIDQILVVDADSEDGTAGVAASHGAEVYSENELMSGYGDAHGKGDAMWRALSVTRGDLVLYIDADTRDFRPQLAYGVLGPVLEVPGVRFVKAAYRRP--------EDGGGRVTELTAKPLFNLFYPELAGFVQPLAGEFVADRELFCSIPFLTGYAVETGIMIDVLKKVGLGAMAQVDLGERQNR--HLRDLSRMSYAVVRAVARRLRQEGRLQQL-------SFFQLSDYLHAVATPEGLKLQEYVEELVERPPINEVLR 333
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168|      178       188       198       208       218       228       238       248        |- |     268       278       288       298       308       318       328     
                                                                                                                                                                                          169      178                                                                            257  |                         288     296                                     
                                                                                                                                                                                                                                                                                     260                                                                         


Chain C from PDB  Type:PROTEIN  Length:308
 aligned with Q1ATN7_RUBXD | Q1ATN7 from UniProtKB/TrEMBL  Length:335

    Alignment length:325
                                    18        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       328     
         Q1ATN7_RUBXD     9 LGPTSAADWFRQRSYEYGQFPPERLARRKRELGLAVSAVLPSRNVAETVGGIIDEIHALNERAPLIDQVLVVDADSEDGTAGIAASRGAEVYSENELMSGYGDAHGKGDAMWRALSVARGDLVLYVDADTRDFRPQLAYGVLGPILEVPEVRFVKAAYRRPFRKGESIEEDGGGRVTELTAKPLFNLFYPELTGFVQPLAGEFVADRELFCSIPFLTGYAVETGIMIDVLKKVGLGAMAQVDLGERQNRHQHLRDLSRMSYAVVRAVARRLRQEGRLQQVREPGLPESFFQFSDYLHAVATPEGLKLQEYVEELVERPPINEVLR 333
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------Glycos_transf_2-3kiaC01 C:45-149                                                                         ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------Glycos_transf_2-3kiaC02 C:45-149                                                                         ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ....hhhhhhhhheee.hhhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhh..eeee....hhhhh..hhhhhhhhhhh......eeee.........hhhhhhhhhhhhhh....eeeeeee..--------....hhhhhhhhhhhhhhhhhhhh.........eeeehhhhhhh.ee...hhhhhhhhhhhhhhh...eeeeeeee....--hhhhhhhhhhhhhhhhhhhhhhh......-------......eeeeeeee..eeeeeeee....ee.hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kia C   9 LGPASAAEWFRQRSYDYGQFPPEDLARRKRELGLTVSAVLPSRNVADTVGGIIDEIHALNERAPLIDQILVVDADSEDGTAGVAASHGAEVYSENELMSGYGDAHGKGDAMWRALSVTRGDLVLYIDADTRDFRPQLAYGVLGPVLEVPGVRFVKAAYRRP--------EDGGGRVTELTAKPLFNLFYPELAGFVQPLAGEFVADRELFCSIPFLTGYAVETGIMIDVLKKVGLGAMAQVDLGERQNR--HLRDLSRMSYAVVRAVARRLRQEGRLQQL-------SFFQLSDYLHAVATPEGLKLQEYVEELVERPPINEVLR 333
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168|      178       188       198       208       218       228       238       248        |- |     268       278       288       298       308       318       328     
                                                                                                                                                                                          169      178                                                                            257  |                         288     296                                     
                                                                                                                                                                                                                                                                                     260
   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 3KIA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (3, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,C   (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,C   (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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 Related Entries

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

UniProtKB/Swiss-Prot
        B7SY86_9ACTN | B7SY86: 3f1y 3o3p
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(-) Related Entries Specified in the PDB File

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3e26 CRYSTAL STRUCTURE OF HOMOLOGOUS GLUCOSYLTRANSFERASE FROM M. TUBERCULOSIS
3f1y CRYSTAL STRUCTURE OF APO-ENZYME