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(-) Description

Title :  THE STRUCTURE OF TREHALOSE SYNTHASE (TRES) OF MYCOBACTERIUM SMEGMATIS
 
Authors :  S. Caner, N. Nguyen, A. Aguda, R. Zhang, Y. T. Pan, S. G. Withers, G. D. Bra
Date :  21 Feb 13  (Deposition) - 17 Jul 13  (Release) - 07 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.84
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Hydrolase, Glycohydrolase, Drug Design, Tuberculosis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Caner, N. Nguyen, A. Aguda, R. Zhang, Y. T. Pan, S. G. Withers, G. D. Brayer
The Structure Of The Mycobacterium Smegmatis Trehalose Synthase Reveals An Unusual Active Site Configuration And Acarbose-Binding Mode.
Glycobiology V. 23 1075 2013
PubMed-ID: 23735230  |  Reference-DOI: 10.1093/GLYCOB/CWT044

(-) Compounds

Molecule 1 - TREHALOSE SYNTHASE/AMYLASE TRES
    Chains: A, B
    EC Number: 3.2.1.1, 5.4.99.16
    Organism Scientific: MYCOBACTERIUM SMEGMATIS
    Organism Taxid: 1772
    Synonym: MALTOSE ALPHA-D-GLUCOSYLTRANSFERASE, MTASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric Unit (3, 11)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2CL7Ligand/IonCHLORIDE ION
3MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG B:228 , ARG B:339 , GLU B:343BINDING SITE FOR RESIDUE CL B1588
02AC2SOFTWAREASN B:340 , HIS B:341 , ARG B:374 , ARG B:375BINDING SITE FOR RESIDUE CL B1589
03AC3SOFTWAREARG A:228 , ARG A:339 , GLU A:343BINDING SITE FOR RESIDUE CL A1587
04AC4SOFTWAREASN A:340 , HIS A:341 , ARG A:374 , ARG A:375 , HOH A:2362BINDING SITE FOR RESIDUE CL A1588
05AC5SOFTWAREASN A:132 , ASP A:200 , TYR A:234 , LEU A:235 , GLU A:237 , HOH A:2142 , HOH A:2255BINDING SITE FOR RESIDUE CA A1589
06AC6SOFTWAREASN B:132 , ASP B:200 , TYR B:234 , LEU B:235 , GLU B:237 , HOH B:2135 , HOH B:2226BINDING SITE FOR RESIDUE CA B1590
07AC7SOFTWAREVAL B:46 , ARG B:47 , PHE B:105 , HOH B:2020BINDING SITE FOR RESIDUE CL B1591
08AC8SOFTWARELEU A:45 , VAL A:46 , ARG A:47 , PHE A:105BINDING SITE FOR RESIDUE CL A1590
09AC9SOFTWAREVAL A:101 , VAL A:108BINDING SITE FOR RESIDUE CL A1591
10BC1SOFTWAREASP A:51 , ASN A:53 , ASP A:55 , ILE A:57 , ASP A:59 , HOH A:2022BINDING SITE FOR RESIDUE MG A1592
11BC2SOFTWAREASP B:51 , ASN B:53 , ASP B:55 , ILE B:57 , ASP B:59 , HOH B:2035BINDING SITE FOR RESIDUE MG B1592

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ZO9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3ZO9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ZO9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ZO9)

(-) Exons   (0, 0)

(no "Exon" information available for 3ZO9)

(-) 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:549
 aligned with TRES_MYCS2 | A0R6E0 from UniProtKB/Swiss-Prot  Length:593

    Alignment length:558
                                    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       518       528       538       548       558       568       578        
           TRES_MYCS2    29 LPTDTNWFKHAVFYEVLVRAFYDSNADGIGDLRGLTEKLDYIKWLGVDCLWLPPFYDSPLRDGGYDIRDFYKVLPEFGTVDDFVTLLDAAHRRGIRIITDLVMNHTSDQHEWFQESRHNPDGPYGDFYVWSDTSDRYPDARIIFVDTEESNWTFDPVRRQFYWHRFFSHQPDLNYDNPAVQEAMLDVLRFWLDLGIDGFRLDAVPYLFEREGTNCENLPETHAFLKRCRKAIDDEYPGRVLLAEANQWPADVVAYFGDPDTGGDECHMAFHFPLMPRIFMAVRRESRFPISEILAQTPPIPDTAQWGIFLRNHDELTLEMVTDEERDYMYAEYAKDPRMKANVGIRRRLAPLLENDRNQIELFTALLLSLPGSPVLYYGDEIGMGDIIWLGDRDSVRTPMQWTPDRNAGFSKATPGRLYLPPNQDAVYGYHSVNVEAQLDSSSSLLNWTRNMLAVRSRHDAFAVGTFRELGGSNPSVLAYIREVTRQQGDGGAKTDAVLCVNNLSRFPQPIELNLQQWAGYIPVEMTGYVEFPSIGQLPYLLTLPGHGFYWFQLREPD 586
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhh.eee.hhhhhh........hhhhhhhhhhhhhhhh..eeee...ee...........eeeee.hhhhhhhhhhhhhhhhhhh..eeeeeee.......hhhhhhhhhh..........ee....................eee......eee.............hhhhhhhhhhhhhhhhhhh..eeeee.hhhh..........hhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhh.....eee..hhhhhhhhhhhhh.hhhhhhhhhh........eeee.......................hhhhhhhhhhh.....hhhhhh..hhhhhhhhhhhhhhh..eeeee.........hhhhh.hhhhh.......hhhhhh...hhhhh...............hhhhhhh...hhhhhhhhhhhhhhhhhhhhhheeee.......eeeeeeee.---------.eeeeeeee.....eeeee.hhhhh..eeee..............eeeee....eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3zo9 A  29 LPTDTNWFKHAVFYEVLVRAFYDSNADGIGDLRGLTEKLDYIKWLGVDCLWLPPFYDSPLRDGGYDIRDFYKVLPEFGTVDDFVTLLDAAHRRGIRIITDLVMNHTSDQHEWFQESRHNPDGPYGDFYVWSDTSDRYPDARIIFVDTEESNWTFDPVRRQFYWHRFFSHQPDLNYDNPAVQEAMLDVLRFWLDLGIDGFRLDAVPYLFEREGTNCENLPETHAFLKRCRKAIDDEYPGRVLLAEANQWPADVVAYFGDPDTGGDECHMAFHFPLMPRIFMAVRRESRFPISEILAQTPPIPDTAQWGIFLRNHDELTLEMVTDEERDYMYAEYAKDPRMKANVGIRRRLAPLLENDRNQIELFTALLLSLPGSPVLYYGDEIGMGDIIWLGDRDSVRTPMQWTPDRNAGFSKATPGRLYLPPNQDAVYGYHSVNVEAQLDSSSSLLNWTRNMLAVRSRHDAFAVGTFRELGGSNPSVLAYIREVT---------TDAVLCVNNLSRFPQPIELNLQQWAGYIPVEMTGYVEFPSIGQLPYLLTLPGHGFYWFQLREPD 586
                                    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    |    -    |  528       538       548       558       568       578        
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              513       523                                                               


Chain B from PDB  Type:PROTEIN  Length:571
 aligned with TRES_MYCS2 | A0R6E0 from UniProtKB/Swiss-Prot  Length:593

    Alignment length:571
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586 
           TRES_MYCS2    17 HPNAEDFGHARTLPTDTNWFKHAVFYEVLVRAFYDSNADGIGDLRGLTEKLDYIKWLGVDCLWLPPFYDSPLRDGGYDIRDFYKVLPEFGTVDDFVTLLDAAHRRGIRIITDLVMNHTSDQHEWFQESRHNPDGPYGDFYVWSDTSDRYPDARIIFVDTEESNWTFDPVRRQFYWHRFFSHQPDLNYDNPAVQEAMLDVLRFWLDLGIDGFRLDAVPYLFEREGTNCENLPETHAFLKRCRKAIDDEYPGRVLLAEANQWPADVVAYFGDPDTGGDECHMAFHFPLMPRIFMAVRRESRFPISEILAQTPPIPDTAQWGIFLRNHDELTLEMVTDEERDYMYAEYAKDPRMKANVGIRRRLAPLLENDRNQIELFTALLLSLPGSPVLYYGDEIGMGDIIWLGDRDSVRTPMQWTPDRNAGFSKATPGRLYLPPNQDAVYGYHSVNVEAQLDSSSSLLNWTRNMLAVRSRHDAFAVGTFRELGGSNPSVLAYIREVTRQQGDGGAKTDAVLCVNNLSRFPQPIELNLQQWAGYIPVEMTGYVEFPSIGQLPYLLTLPGHGFYWFQLREPDP 587
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh..........hhhhhh.eee.hhhhhh........hhhhhhhhhhhhhhhh..eeee...ee...........eeeee.hhhhhhhhhhhhhhhhhhh..eeeeeee.......hhhhhhhhhh..........ee....................eee......eee.............hhhhhhhhhhhhhhhhhhh..eeeee.hhhh..........hhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhh.....eee..hhhhhhhhhhhhh.hhhhhhhhhhh.......eeeee......................hhhhhhhhhhh.....hhhhhh..hhhhhhhhhhhhhhh..eeeee.hhhhh...hhhhh.hhhhh.......hhhhhh...hhhhh...............hhhhhhh...hhhhhhhhhhhhhhhhhhhhhh..ee.......eeeeee.........hhhhheeeeeee.....eeeee.hhhhh..eeee..............eeeee....eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zo9 B  17 HPNAEDFGHARTLPTDTNWFKHAVFYEVLVRAFYDSNADGIGDLRGLTEKLDYIKWLGVDCLWLPPFYDSPLRDGGYDIRDFYKVLPEFGTVDDFVTLLDAAHRRGIRIITDLVMNHTSDQHEWFQESRHNPDGPYGDFYVWSDTSDRYPDARIIFVDTEESNWTFDPVRRQFYWHRFFSHQPDLNYDNPAVQEAMLDVLRFWLDLGIDGFRLDAVPYLFEREGTNCENLPETHAFLKRCRKAIDDEYPGRVLLAEANQWPADVVAYFGDPDTGGDECHMAFHFPLMPRIFMAVRRESRFPISEILAQTPPIPDTAQWGIFLRNHDELTLEMVTDEERDYMYAEYAKDPRMKANVGIRRRLAPLLENDRNQIELFTALLLSLPGSPVLYYGDEIGMGDIIWLGDRDSVRTPMQWTPDRNAGFSKATPGRLYLPPNQDAVYGYHSVNVEAQLDSSSSLLNWTRNMLAVRSRHDAFAVGTFRELGGSNPSVLAYIREVTRQQGDGGAKTDAVLCVNNLSRFPQPIELNLQQWAGYIPVEMTGYVEFPSIGQLPYLLTLPGHGFYWFQLREPDP 587
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586
   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 3ZO9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ZO9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ZO9)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (TRES_MYCS2 | A0R6E0)
molecular function
    GO:0004556    alpha-amylase activity    Catalysis of the endohydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides containing three or more alpha-(1->4)-linked D-glucose units.
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    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:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0047471    maltose alpha-D-glucosyltransferase activity    Catalysis of the reaction: maltose = trehalose.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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.
    GO:0000023    maltose metabolic process    The chemical reactions and pathways involving the disaccharide maltose (4-O-alpha-D-glucopyranosyl-D-glucopyranose), an intermediate in the catabolism of glycogen and starch.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0000272    polysaccharide catabolic process    The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
    GO:0005991    trehalose metabolic process    The chemical reactions and pathways involving trehalose, a disaccharide isomeric with sucrose and obtained from certain lichens and fungi.

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 Related Entries

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        TRES_MYCS2 | A0R6E0: 3zoa 5jy7

(-) Related Entries Specified in the PDB File

3zoa NOVEL ACTIVE SITE AND INHIBITION SITES IDENTIFIED IN TREHALOSE SYNTHASE