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(-) Description

Title :  THERMUS THERMOPHILUS FAMILY GH57 BRANCHING ENZYME: CRYSTAL STRUCTURE, MECHANISM OF ACTION AND PRODUCTS FORMED
 
Authors :  T. Pijning, B. W. Dijkstra
Date :  28 Sep 10  (Deposition) - 20 Oct 10  (Release) - 27 Oct 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym./Biol. Unit :  A
Keywords :  Glycoside Hydrolase Gh57, Glycogen Branching, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Palomo-Reixach, T. Pijning, T. Booiman, J. Dobruchowska, J. Van Der Vlist, S. Kralj, A. Planas, K. Loos, J. P. Kamerling, B. W. Dijkstra, M. J. E. C. Van Der Maarel, L. Dijkhuizen, H. Leemhuis
Thermus Thermophilus Glycosyl Hydrolase Family 57 Branching Enzyme: Crystal Structure, Mechanism Of Action And Products Formed
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TT1467 PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: BRANCHING ENZYME
    Gene: TTHHB8IM
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:501 , PRO A:508 , HOH A:667 , HOH A:736 , HOH A:778 , HOH A:980 , HOH A:1072 , HOH A:1093 , HOH A:1146BINDING SITE FOR RESIDUE GOL A 521

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3P0B)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Trp A:21 -Pro A:22
2Glu A:198 -Gly A:199

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3P0B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3P0B)

(-) Exons   (0, 0)

(no "Exon" information available for 3P0B)

(-) 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:511
 aligned with BE_THET8 | Q5SH28 from UniProtKB/Swiss-Prot  Length:520

    Alignment length:519
                              1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
                              |      8        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       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508         
             BE_THET8     - --MARFALVLHAHLPYVRAHGMWPFGEETLYEAMAETYLPLIRVLERLRAEGVEAPFTLGITPILAEQLADARIKEGFWAYAKDRLERAQGDYQRYRGTALEASARHQVAFWELTLDHFQRLSGDLVAAFRKAEEGGQVELITSNATHGYSPLLGYDEALWAQIKTGVSTYRRHFAKDPTGFWLPEMAYRPKGPWKPPVEGPPEGVRPGVDELLMRAGIRYTFVDAHLVQGGEPLSPYGEAALGPVESQEATYHVHELESGLRVLARNPETTLQVWSADYGYPGEGLYREFHRKDPLSGLHHWRVTHRKADLAEKAPYDPEAAFAKTEEHARHFVGLLERLAGRHPEGVILSPYDAELFGHWWYEGVAWLEAVLRLLAQNPKVRPVTAREAVQGPAVRTALPEGSWGRGGDHRVWLNEKTLDYWEKVYRAEGAMREAARRGVLPEGVLRQAMRELLLLEASDWPFLMETGQAEAYARERYEEHARAFFHLLKGASPEELRALEERDNPFPEADPRLYLF 517
               SCOP domains d3p0ba1 A:-1-412 automated matches                                                                                                                                                                                                                                                                                                                                                                                            d3p0ba2 A:413-517 automated matches                                                                       SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh..eeeeee.....hhhhh.hhhhhhhhhhhhhhhhhhhhh.....eehhhhh....eee.........eee.hhhhhhhhh...eeee.hhhhhh.....--------....hhhhhheee.....eeee.hhhhhhhhhh...hhhhh.........................hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhh.....hhhhhhhhhhhhhh....eee.hhhhhh...eee........hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh......hhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p0b A  -1 SHMARFALVLHAHLPYVRAHGMWPFGEETLYEAMAETYLPLIRVLERLRAEGVEAPFTLGITPILAEQLADARIKEGFWAYAKDRLERAQGDYQRYRGTALEASARHQVAFWELTLDHFQRLSGDLVAAFRKAEEGGQVELITSNATHGYSPLLGYDEALWAQIKTGVSTYRRHFAKDPTGFWLPEMAYRPKGPWKPPVEGPPEGVRPGVDELLMRAGIRYTFVDAHLVQGGEPLS--------PVESQEATYHVHELESGLRVLARNPETTLQVWSADYGYPGEGLYREFHRKDPLSGLHHWRVTHRKADLAEKAPYDPEAAFAKTEEHARHFVGLLERLAGRHPEGVILSPYDAELFGHWWYEGVAWLEAVLRLLAQNPKVRPVTAREAVQGPAVRTALPEGSWGRGGDHRVWLNEKTLDYWEKVYRAEGAMREAARRGVLPEGVLRQAMRELLLLEASDWPFLMETGQAEAYARERYEEHARAFFHLLKGASPEELRALEERDNPFPEADPRLYLF 517
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228     |   -    |  248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508         
                                                                                                                                                                                                                                                                     234      243
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3P0B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3P0B)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (BE_THET8 | Q5SH28)
molecular function
    GO:0003844    1,4-alpha-glucan branching enzyme activity    Catalysis of the transfer of a segment of a (1->4)-alpha-D-glucan chain to a primary hydroxyl group in a similar glucan chain.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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).
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:0005978    glycogen biosynthetic process    The chemical reactions and pathways resulting in the formation of glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues.
    GO:0005977    glycogen metabolic process    The chemical reactions and pathways involving glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues in alpha-(1->4) glycosidic linkage, joined together by alpha-(1->6) glycosidic linkages.

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 Related Entries

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

UniProtKB/Swiss-Prot
        BE_THET8 | Q5SH28: 1ufa

(-) Related Entries Specified in the PDB File

1ufa CRYSTAL STRUCTURE OF TT1467 FROM THERMUS THERMOPHILUS HB8