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(-) Description

Title :  CRYSTAL STRUCTURE OF 4-O-BETA-D-MANNOSYL-D-GLUCOSE PHOSPHORYLASE MGP COMPLEXED WITH MAN+GLC
 
Authors :  S. Nakae, S. Ito, M. Higa, T. Senoura, J. Wasaki, A. Hijikata, M. Shionyu T. Shirai
Date :  08 May 13  (Deposition) - 04 Sep 13  (Release) - 20 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  5-Bladed Beta Propeller Fold, Phosphorylase, Mannan Biodegradation, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Nakae, S. Ito, M. Higa, T. Senoura, J. Wasaki, A. Hijikata, M. Shionyu, S. Ito, T. Shirai
Structure Of Novel Enzyme In Mannan Biodegradation Process 4-O-Beta-D-Mannosyl-D-Glucose Phosphorylase Mgp
J. Mol. Biol. V. 425 4468 2013
PubMed-ID: 23954514  |  Reference-DOI: 10.1016/J.JMB.2013.08.002

(-) Compounds

Molecule 1 - 4-O-BETA-D-MANNOSYL-D-GLUCOSE PHOSPHORYLASE
    Chains: A, B
    EC Number: 2.4.1.281
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-23A(+)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BF0772
    Organism Scientific: BACTEROIDES FRAGILIS
    Organism Taxid: 272559
    Strain: NCTC 9343
    Synonym: MGP, MANNOSYLGLUCOSE PHOSPHORYLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1BGC2Ligand/IonBETA-D-GLUCOSE
2BMA2Ligand/IonBETA-D-MANNOSE
3PO44Ligand/IonPHOSPHATE ION
Biological Unit 1 (3, 24)
No.NameCountTypeFull Name
1BGC6Ligand/IonBETA-D-GLUCOSE
2BMA6Ligand/IonBETA-D-MANNOSE
3PO412Ligand/IonPHOSPHATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:191 , ASN A:192 , ARG A:209 , LYS A:254 , HIS A:273 , TYR A:284 , BMA A:404BINDING SITE FOR RESIDUE PO4 A 401
2AC2SOFTWAREVAL A:311 , GLY A:312 , ARG A:315 , HOH A:534 , HOH A:556 , HOH A:886 , HOH A:921 , HOH A:933 , HOH A:1120BINDING SITE FOR RESIDUE PO4 A 402
3AC3SOFTWAREARG A:88 , ARG A:94 , TYR A:130 , ARG A:191 , PHE A:214 , BMA A:404 , HOH A:601 , HOH A:615 , HOH A:885 , HOH A:928 , HOH A:936 , HOH A:937BINDING SITE FOR RESIDUE BGC A 403
4AC4SOFTWAREASN A:73 , ARG A:88 , ASP A:131 , ARG A:191 , TYR A:284 , VAL A:319 , PHE A:324 , ASP A:344 , PO4 A:401 , BGC A:403 , HOH A:606BINDING SITE FOR RESIDUE BMA A 404
5AC5SOFTWAREARG B:191 , ASN B:192 , ARG B:209 , LYS B:254 , HIS B:273 , TYR B:284 , BMA B:404BINDING SITE FOR RESIDUE PO4 B 401
6AC6SOFTWAREVAL B:311 , GLY B:312 , ARG B:315 , HOH B:563 , HOH B:592 , HOH B:754 , HOH B:857 , HOH B:908BINDING SITE FOR RESIDUE PO4 B 402
7AC7SOFTWAREARG B:88 , ARG B:94 , TYR B:130 , ARG B:191 , PHE B:214 , BMA B:404 , HOH B:612 , HOH B:723 , HOH B:777 , HOH B:836 , HOH B:896 , HOH B:935BINDING SITE FOR RESIDUE BGC B 403
8AC8SOFTWAREASN B:73 , ARG B:88 , ASP B:131 , ARG B:191 , TYR B:284 , VAL B:319 , PHE B:324 , ASP B:344 , PO4 B:401 , BGC B:403 , HOH B:581BINDING SITE FOR RESIDUE BMA B 404

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3WAT)

(-) 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:389
 aligned with MGP_BACFN | Q5LH68 from UniProtKB/Swiss-Prot  Length:390

    Alignment length:389
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381         
            MGP_BACFN     2 SLFNDKVAKLLAGHEALLMRKNEPVEEGNGVITRYRYPVLTAAHTPVFWRYDLNEETNPFLMERIGMNATLNAGAIKWDGKYLMLVRVEGADRKSFFAVAESPNGIDNFRFWEYPVTLPEDVVPATNVYDMRLTAHEDGWIYGIFCAERHDDNAPIGDLSSATATAGIARTKDLKNWERLPDLKTKSQQRNVVLHPEFVDGKYALYTRPQDGFIDTGSGGGIGWALIDDITHAEVGEEKIIDKRYYHTIKEVKNGEGPHPIKTPQGWLHLAHGVRNCAAGLRYVLYMYMTSLDDPTRLIASPAGYFMAPVGEERIGDVSNVLFSNGWIADDDGKVFIYYASSDTRMHVATSTIERLVDYCLHTPQDGFSSSASVEILKNLIERNLRLMK 390
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh............ee......hhhhhhhhhhh...............eeeeeeeeeeee..eeeeeeeeee....eeeeeeee.......ee...............eeeeeeeee.....eeeeeeeeee...........eeeeeeeeee.....eeee.......ee...ee........eeeee.ee..........eeeeeee.hhhhh.....eeeee.........eeee....eee..eeeeeeeeeeee..eeeeeeeeeee.......eee.........hhhhhh......eeeeeeee....eeeeeeee...eeeeeeeehhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wat A   2 SLFNDKVAKLLAGHEALLMRKNEPVEEGNGVITRYRYPVLTAAHTPVFWRYDLNEETNPFLMERIGMNATLNAGAIKWDGKYLMLVRVEGADRKSFFAVAESPNGIDNFRFWEYPVTLPEDVVPATNVYDMRLTAHEDGWIYGIFCAERHDDNAPIGDLSSATATAGIARTKDLKNWERLPDLKTKSQQRNVVLHPEFVDGKYALYTRPQDGFIDTGSGGGIGWALIDDITHAEVGEEKIIDKRYYHTIKEVKNGEGPHPIKTPQGWLHLAHGVRNCAAGLRYVLYMYMTSLDDPTRLIASPAGYFMAPVGEERIGDVSNVLFSNGWIADDDGKVFIYYASSDTRMHVATSTIERLVDYCLHTPQDGFSSSASVEILKNLIERNLRLMK 390
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381         


Chain B from PDB  Type:PROTEIN  Length:389
 aligned with MGP_BACFN | Q5LH68 from UniProtKB/Swiss-Prot  Length:390

    Alignment length:389
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381         
            MGP_BACFN     2 SLFNDKVAKLLAGHEALLMRKNEPVEEGNGVITRYRYPVLTAAHTPVFWRYDLNEETNPFLMERIGMNATLNAGAIKWDGKYLMLVRVEGADRKSFFAVAESPNGIDNFRFWEYPVTLPEDVVPATNVYDMRLTAHEDGWIYGIFCAERHDDNAPIGDLSSATATAGIARTKDLKNWERLPDLKTKSQQRNVVLHPEFVDGKYALYTRPQDGFIDTGSGGGIGWALIDDITHAEVGEEKIIDKRYYHTIKEVKNGEGPHPIKTPQGWLHLAHGVRNCAAGLRYVLYMYMTSLDDPTRLIASPAGYFMAPVGEERIGDVSNVLFSNGWIADDDGKVFIYYASSDTRMHVATSTIERLVDYCLHTPQDGFSSSASVEILKNLIERNLRLMK 390
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh............ee......hhhhhhhhhhh...............eeeeeeeeeeee..eeeeeeeeee....eeeeeeee.......ee...............eeeeeeeee.....eeeeeeeeee...........eeeeeeeeee.....eee........ee...ee........eeeee.ee..........eeeeeee.hhhhh.....eeeee.........eeee....eee..eeeeeeeeeeee..eeeeeeeeeee.......eee.........hhhhhh......eeeeeeee....eeeeeeee...eeeeeeeehhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wat B   2 SLFNDKVAKLLAGHEALLMRKNEPVEEGNGVITRYRYPVLTAAHTPVFWRYDLNEETNPFLMERIGMNATLNAGAIKWDGKYLMLVRVEGADRKSFFAVAESPNGIDNFRFWEYPVTLPEDVVPATNVYDMRLTAHEDGWIYGIFCAERHDDNAPIGDLSSATATAGIARTKDLKNWERLPDLKTKSQQRNVVLHPEFVDGKYALYTRPQDGFIDTGSGGGIGWALIDDITHAEVGEEKIIDKRYYHTIKEVKNGEGPHPIKTPQGWLHLAHGVRNCAAGLRYVLYMYMTSLDDPTRLIASPAGYFMAPVGEERIGDVSNVLFSNGWIADDDGKVFIYYASSDTRMHVATSTIERLVDYCLHTPQDGFSSSASVEILKNLIERNLRLMK 390
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381
   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 3WAT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (MGP_BACFN | Q5LH68)
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.
    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:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0071555    cell wall organization    A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MGP_BACFN | Q5LH68: 3was 3wau 4kmi

(-) Related Entries Specified in the PDB File

3was 3wau 4kmi