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(-) Description

Title :  THERMUS THERMOPHILUS AMYLOMALTASE AT PH 5.6
 
Authors :  T. R. M. Barends, T. Kaper, J. J. Bultema, L. Dijkhuizen, J. E. C. Van Der B. W. Dijkstra
Date :  17 Feb 07  (Deposition) - 03 Apr 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta-Alpha-8 Barrel, Succinimide Residue In Main Chain, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. R. Barends, J. B. Bultema, T. Kaper, M. J. Van Der Maarel, L. Dijkhuizen, B. W. Dijkstra
Three-Way Stabilization Of The Covalent Intermediate In Amylomaltase, An Alpha-Amylase-Like Transglycosylase.
J. Biol. Chem. V. 282 17242 2007
PubMed-ID: 17420245  |  Reference-DOI: 10.1074/JBC.M701444200

(-) Compounds

Molecule 1 - 4-ALPHA-GLUCANOTRANSFERASE
    Chains: A
    EC Number: 2.4.1.25
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PCCBMALQ
    Expression System Strain: BL21(DE-3)
    Expression System Taxid: 469008
    Expression System Vector: PLASMID
    Fragment: SEQUENCE DATABASE RESIDUES 21-500
    Gene: MALQ
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274
    Synonym: AMYLOMALTASE, DISPROPORTIONATING ENZYME, D-ENZYME

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MLI1Ligand/IonMALONATE ION
3SUI1Mod. Amino Acid(3-AMINO-2,5-DIOXO-1-PYRROLIDINYL)ACETIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:101 , TRP A:105 , LYS A:109 , HIS A:185 , LYS A:441 , HOH A:546BINDING SITE FOR RESIDUE MLI A 501
2AC2SOFTWAREGLN A:365 , PHE A:366 , ASP A:369 , TRP A:402 , GLU A:410BINDING SITE FOR RESIDUE GOL A 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OWX)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2OWX)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2OWX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2OWX)

(-) Exons   (0, 0)

(no "Exon" information available for 2OWX)

(-) 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:499
 aligned with MALQ_THETH | O87172 from UniProtKB/Swiss-Prot  Length:500

    Alignment length:500
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500
           MALQ_THETH     1 MELPRAFGLLLHPTSLPGPYGVGVLGREARDFLRFLKEAGGRYWQVLPLGPTGYGDSPYQSFSAFAGNPYLIDLRPLAERGYVRLEDPGFPQGRVDYGLLYAWKWPALKEAFRGFKEKASPEEREAFAAFREREAWWLEDYALFMALKGAHGGLPWNRWPLPLRKREEKALREAKSALAEEVAFHAFTQWLFFRQWGALKAEAEALGIRIIGDMPIFVAEDSAEVWAHPEWFHLDEEGRPTVVAGVPPDYFSETGQRWGNPLYRWDVLEREGFSFWIRRLEKALELFHLVRIDHFRGFEAYWEIPASCPTAVEGRWVKAPGEKLFQKIQEVFGEVPVLAEDLGVITPEVEALRDRFGLPGMKVLQFAFDDGMENPFLPHNYPAHGRVVVYTGTHDNDTTLGWYRTATPHEKAFMARYLADWGITFREEEEVPWALMHLGMKSVARLAVYPVQDVLALGSEARMNYPGRPSGNWAWRLLPGELSPEHGARLRAMAEATERL 500
               SCOP domains d2owxa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 2owxA00 A:1-500 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         CATH domains
               Pfam domains ----------Glyco_hydro_77-2owxA01 A:11-497                                                                                                                                                                                                                                                                                                                                                                                                                                                                        --- Pfam domains
         Sec.struct. author .....eeeee.hhhhh.........hhhhhhhhhhhhhh...eee......................hhhhh.hhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.......hhhhhhhhhhh.........eeeee.........eeeeee..hhhhhhhhhhhhhhhhhhhhhhhh.eeee.hhhhh.eeeeee.........eeee.hhhhhhhhhhhhhh...eee......hhhhhhhhhhh...eeee.hhh...-.....hhhhh.....eeee.......hhhhhhhh.hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh...eeeeehhhhh..hhhhh....................hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2owx A   1 MELPRAFGLLLHPTSLPGPYGVGVLGQEARDFLRFLKEAGGRYWQVLPLGPTGYGDSPYQSFSAFAGNPYLIDLRPLAERGYVRLEDPGFPQGRVDYGLLYAWKWPALKEAFRGFKEKASPEEREAFAAFREREAWWLEDYALFMALKGAHGGLPWNRWPLPLRKREEKALREAKSALAEEVAFHAFTQWLFFRQWGALKAEAEALGIRIIGDMPIFVAEDSAEVWAHPEWFHLDEEGRPTVVAGVPPDYFSETGQRWGNPLYRWDVLEREGFSFWIRRLEKALELFHLVRIDHFRGFEAYWEIPASCPTAVEGRWVKAPGEKLFQKIQEVFGEVPVLAEDLGVITPEVEALRDRFGLPGMKVLQFAFDd-MENPFLPHNYPAHGRVVVYTGTHDNDTTLGWYRTATPHEKAFMARYLADWGITFREEEEVPWALMHLGMKSVARLAVYPVQDVLALGSEARMNYPGRPSGNWAWRLLPGELSPEHGARLRAMAEATERL 500
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370 |     380       390       400       410       420       430       440       450       460       470       480       490       500
                                                                                                                                                                                                                                                                                                                                                                                                           370-SUI                                                                                                                              
                                                                                                                                                                                                                                                                                                                                                                                                             372                                                                                                                                


Chain A from PDB  Type:PROTEIN  Length:499
 aligned with Q72J82_THET2 | Q72J82 from UniProtKB/TrEMBL  Length:500

    Alignment length:500
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500
         Q72J82_THET2     1 MELPRAFGLLLHPTSLPGPYGVGVLGQEARDFLRFLKEAGGRYWQVLPLGPTGYGDSPYQSFSAFAGNPYLIDLRPLAERGYVRLEDPGFPQGRVDYGLLYAWKWPALKEAFRGFKEKASPEEREAFAAFREREAWWLEDYALFMALKGAHGGLPWNRWPLPLRKREEKALREAKSALAEEVAFHAFTQWLFFRQWGALKAEAEALGIRIIGDMPIFVAEDSAEVWAHPEWFHLDEEGRPTVVAGVPPDYFSETGQRWGNPLYRWDVLEREGFSFWIRRLEKALELFHLVRIDHFRGFEAYWEIPASCPTAVEGRWVKAPGEKLFQKIQEVFGEVPVLAEDLGVITPEVEALRDRFGLPGMKVLQFAFDDGMENPFLPHNYPAHGRVVVYTGTHDNDTTLGWYRTATPHEKAFMARYLADWGITFREEEEVPWALMHLGMKSVARLAVYPVQDVLALGSEARMNYPGRPSGNWAWRLLPGELSPEHGARLRAMAEATERL 500
               SCOP domains d2owxa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 2owxA00 A:1-500 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         CATH domains
               Pfam domains ----------Glyco_hydro_77-2owxA01 A:11-497                                                                                                                                                                                                                                                                                                                                                                                                                                                                        --- Pfam domains
         Sec.struct. author .....eeeee.hhhhh.........hhhhhhhhhhhhhh...eee......................hhhhh.hhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.......hhhhhhhhhhh.........eeeee.........eeeeee..hhhhhhhhhhhhhhhhhhhhhhhh.eeee.hhhhh.eeeeee.........eeee.hhhhhhhhhhhhhh...eee......hhhhhhhhhhh...eeee.hhh...-.....hhhhh.....eeee.......hhhhhhhh.hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh...eeeeehhhhh..hhhhh....................hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2owx A   1 MELPRAFGLLLHPTSLPGPYGVGVLGQEARDFLRFLKEAGGRYWQVLPLGPTGYGDSPYQSFSAFAGNPYLIDLRPLAERGYVRLEDPGFPQGRVDYGLLYAWKWPALKEAFRGFKEKASPEEREAFAAFREREAWWLEDYALFMALKGAHGGLPWNRWPLPLRKREEKALREAKSALAEEVAFHAFTQWLFFRQWGALKAEAEALGIRIIGDMPIFVAEDSAEVWAHPEWFHLDEEGRPTVVAGVPPDYFSETGQRWGNPLYRWDVLEREGFSFWIRRLEKALELFHLVRIDHFRGFEAYWEIPASCPTAVEGRWVKAPGEKLFQKIQEVFGEVPVLAEDLGVITPEVEALRDRFGLPGMKVLQFAFDd-MENPFLPHNYPAHGRVVVYTGTHDNDTTLGWYRTATPHEKAFMARYLADWGITFREEEEVPWALMHLGMKSVARLAVYPVQDVLALGSEARMNYPGRPSGNWAWRLLPGELSPEHGARLRAMAEATERL 500
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370 |     380       390       400       410       420       430       440       450       460       470       480       490       500
                                                                                                                                                                                                                                                                                                                                                                                                           370-SUI                                                                                                                              
                                                                                                                                                                                                                                                                                                                                                                                                             372
   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  (1, 1)

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

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Glyco_hydro_tim (488)

(-) Gene Ontology  (6, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MALQ_THETH | O87172)
molecular function
    GO:0004134    4-alpha-glucanotransferase activity    Catalysis of the transfer of a segment of a (1->4)-alpha-D-glucan to a new 4-position in an acceptor, which may be glucose or (1->4)-alpha-D-glucan.
    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: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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain A   (Q72J82_THET2 | Q72J82)
molecular function
    GO:0004134    4-alpha-glucanotransferase activity    Catalysis of the transfer of a segment of a (1->4)-alpha-D-glucan to a new 4-position in an acceptor, which may be glucose or (1->4)-alpha-D-glucan.
    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: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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  Q72J82_THET2 | Q72J82
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  2.4.1.25
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 Related Entries

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

UniProtKB/Swiss-Prot
        MALQ_THETH | O87172: 1cwy 1esw 1fp8 1fp9 2owc 2oww 5jiw
        Q72J82_THET2 | Q72J82: 2owc 2oww

(-) Related Entries Specified in the PDB File

1esw 1owc 2oww