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(-) Description

Title :  ACARBOSE COMPLEX OF CHIMAERIC AMYLASE FROM B. AMYLOLIQUEFACIENS AND B. LICHENIFORMIS AT 1.93A
 
Authors :  A. M. Brzozowski, D. M. Lawson, J. P. Turkenburg, H. Bisgaard-Frantzen, A. Svendsen, T. V. Borchert, Z. Dauter, K. S. Wilson, G. J. Davies
Date :  27 Jun 00  (Deposition) - 21 Jun 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.93
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Amylase, Family 13, Acarbose, Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. M. Brzozowski, D. M. Lawson, J. P. Turkenburg, H. Bisgaard-Frantzen, A. Svendsen, T. V. Borchert, Z. Dauter, K. S. Wilson, G. J. Davies
Structural Analysis Of A Chimeric Bacterial Alpha-Amylase. High Resolution Analysis Of Native And Ligand Complexes
Biochemistry V. 39 9099 2000
PubMed-ID: 10924103  |  Reference-DOI: 10.1021/BI0000317

(-) Compounds

Molecule 1 - ALPHA-AMYLASE
    Chains: A
    EC Number: 3.2.1.1
    Engineered: YES
    Expression System: BACILLUS AMYLOLIQUEFACIENS
    Expression System Taxid: 1390
    Organism Scientific: BACILLUS AMYLOLIQUEFACIENS
    Organism Taxid: 1390
    Other Details: CHIMAERIC STRUCTURE CONSISTING OF RESIDUES 1 - 300 OF B. AMYLOLIQUEFACIENS AND RESIDUES 301 - 483 OF B. LICHENIFORMIS IN COMPLEX WITH ACARBOSE
    Other Details - Source: SYNTHETIC GENE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 15)

Asymmetric/Biological Unit (5, 15)
No.NameCountTypeFull Name
1ACI3Ligand/Ion6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4-ENE-1,2,3-TRIOL
2CA4Ligand/IonCALCIUM ION
3GLC4Ligand/IonALPHA-D-GLUCOSE
4GLD3Ligand/Ion4,6-DIDEOXYGLUCOSE
5NA1Ligand/IonSODIUM ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:106 , ALA A:107 , TRP A:136 , TYR A:198 , GLD A:802 , ACI A:804 , HOH A:2664 , HOH A:2665 , HOH A:2666BINDING SITE FOR RESIDUE GLC A 803
02AC2SOFTWARELEU A:47 , LYS A:68 , HIS A:316 , GLD A:802 , HOH A:2080 , HOH A:2659 , HOH A:2660 , HOH A:2661BINDING SITE FOR RESIDUE ACI A 801
03AC3SOFTWARELYS A:68 , GLY A:106 , ALA A:107 , TRP A:136 , ACI A:801 , GLC A:803 , HOH A:2080 , HOH A:2662 , HOH A:2663BINDING SITE FOR RESIDUE GLD A 802
04AC4SOFTWAREASP A:162 , TYR A:198 , GLC A:803 , GLD A:805 , HOH A:2667 , HOH A:2668 , HOH A:2670 , HOH A:2671BINDING SITE FOR RESIDUE ACI A 804
05AC5SOFTWAREMET A:197 , TYR A:198 , ACI A:804 , GLC A:806 , HOH A:2339 , HOH A:2675BINDING SITE FOR RESIDUE GLD A 805
06AC6SOFTWARETRP A:11 , TYR A:54 , MET A:197 , ASP A:328 , SER A:334 , GLD A:805 , ACI A:807 , GLD A:808 , HOH A:2098 , HOH A:2482 , HOH A:2674 , HOH A:2675 , HOH A:2676BINDING SITE FOR RESIDUE GLC A 806
07AC7SOFTWARETYR A:54 , HIS A:103 , ARG A:229 , ASP A:231 , GLU A:261 , HIS A:327 , ASP A:328 , GLC A:806 , GLD A:808BINDING SITE FOR RESIDUE ACI A 807
08AC8SOFTWAREALA A:232 , HIS A:235 , GLU A:261 , GLC A:806 , ACI A:807 , GLC A:809 , HOH A:2403 , HOH A:2677BINDING SITE FOR RESIDUE GLD A 808
09AC9SOFTWAREGLU A:189 , LYS A:234 , LEU A:335 , GLD A:808 , GLC A:810BINDING SITE FOR RESIDUE GLC A 809
10BC1SOFTWAREGLC A:809 , HOH A:2405 , HOH A:2679 , HOH A:2680BINDING SITE FOR RESIDUE GLC A 810
11BC2SOFTWAREASN A:102 , ASP A:194 , ASP A:200 , HIS A:235 , HOH A:2341BINDING SITE FOR RESIDUE CA A 501
12BC3SOFTWAREASP A:159 , ALA A:181 , ASP A:183 , ASP A:202 , ASP A:204 , HOH A:2342BINDING SITE FOR RESIDUE CA A 502
13BC4SOFTWAREASN A:444 , GLU A:447 , HOH A:2592 , HOH A:2593 , HOH A:2609 , HOH A:2613 , HOH A:2657BINDING SITE FOR RESIDUE CA A 503
14BC5SOFTWAREGLY A:300 , TYR A:302 , HIS A:406 , ASP A:407 , ASP A:430 , HOH A:2450BINDING SITE FOR RESIDUE CA A 504
15BC6SOFTWAREASP A:159 , ASP A:183 , ASP A:194 , ASP A:200 , VAL A:201BINDING SITE FOR RESIDUE NA A 505

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1E3Z)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Trp A:184 -Glu A:185

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1E3Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1E3Z)

(-) Exons   (0, 0)

(no "Exon" information available for 1E3Z)

(-) 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:483
 aligned with AMY_BACAM | P00692 from UniProtKB/Swiss-Prot  Length:514

    Alignment length:483
                                    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       391       401       411       421       431       441       451       461       471       481       491       501       511   
            AMY_BACAM    32 VNGTLMQYFEWYTPNDGQHWKRLQNDAEHLSDIGITAVWIPPAYKGLSQSDNGYGPYDLYDLGEFQQKGTVRTKYGTKSELQDAIGSLHSRNVQVYGDVVLNHKAGADATEDVTAVEVNPANRNQETSEEYQIKAWTDFRFPGRGNTYSDFKWHWYHFDGADWDESRKISRIFKFRGEGKAWDWEVSSENGNYDYLMYADVDYDHPDVVAETKKWGIWYANELSLDGFRIDAAKHIKFSFLRDWVQAVRQATGKEMFTVAEYWQNNAGKLENYLNKTSFNQSVFDVPLHFNLQAASSQGGGYDMRRLLDGTVVSRHPEKAVTFVENHDTQPGQSLESTVQTWFKPLAYAFILTRESGYPQVFYGDMYGTKGTSPKEIPSLKDNIEPILKARKEYAYGPQHDYIDHPDVIGWTREGDSSAAKSGLAALITDGPGGSKRMYAGLKNAGETWYDITGNRSDTVKIGSDGWGEFHVNDGSVSIYVQK 514
               SCOP domains d1e3za2 A:1-393 Bacterial alpha-amylase                                                                                                                                                                                                                                                                                                                                                                  d1e3za1 A:394-483 Bacterial alpha-Amylase                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1e3zA03 A:397-483 Golgi alpha-mannosidase II                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..........hhhhhhhhhhhhhhhhh..eeee....................................hhhhhhhhhhhhhhh..eeeeee.........eeeeeeeee.............eeeeeeee...............hhh................eee.............................hhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhh.......hhhhhhhhhhhhhh....hhhhh........hhh..eee................hhhhhhhhhhhhhhh...eeeeehhhhhh...........hhhhhhhhhhhhhhh....eeee.....eeeeee..........eeeeee....eeeeee.hhhhh...eee...............eeeeee....eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e3z A   1 VNGTLMQYFEWYTPNDGQHWKRLQNDAEHLSDIGITAVWIPPAYKGLSQSDNGYGPYDLYDLGEFQQKGTVRTKYGTKSELQDAIGSLHSRNVQVYGDVVLNHKAGADATEDVTAVEVNPANRNQETSEEYQIKAWTDFRFPGRGNTYSDFKWHWYHFDGADWDESRKISRIFKFRGEGKAWDWEVSSENGNYDYLMYADVDYDHPDVVAETKKWGIWYANELSLDGFRIDAAKHIKFSFLRDWVQAVRQATGKEMFTVAEYWQNNAGKLENYLNKTSFNQSVFDVPLHFNLQAASSQGGGYDMRKLLNGTVVSKHPLKSVTFVDNHDTQPGQSLESTVQTWFKPLAYAFILTRESGYPQVFYGDMYGTKGDSQREIPALKHKIEPILKARKQYAYGAQHDYFDHHDIVGWTREGDSSVANSGLAALITDGPGGAKRMYVGRQNAGETWHDITGNRSEPVVINSEGWGEFHVNGGSVSIYVQR 483
                                    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   


Chain A from PDB  Type:PROTEIN  Length:483
 aligned with AMY_BACLI | P06278 from UniProtKB/Swiss-Prot  Length:512

    Alignment length:483
                                                                                                                                                                                                             209                                                                                                                                                                                                                                                                                                               
                                                                                                                                                                                                          208  |                                                                                                                                                                                                                                                                                                               
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201      |209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509   
            AMY_BACLI    32 LNGTLMQYFEWYMPNDGQHWKRLQNDSAYLAEHGITAVWIPPAYKGTSQADVGYGAYDLYDLGEFHQKGTVRTKYGTKGELQSAIKSLHSRDINVYGDVVINHKGGADATEDVTAVEVDPADRNRVISGEHRIKAWTHFHFPGRGSTYSDFKWHWYHFDGTDWDESRKLNRIYKFQG--KAWDWEVSNENGNYDYLMYADIDYDHPDVAAEIKRWGTWYANELQLDGFRLDAVKHIKFSFLRDWVNHVREKTGKEMFTVAEYWQNDLGALENYLNKTNFNHSVFDVPLHYQFHAASTQGGGYDMRKLLNSTVVSKHPLKAVTFVDNHDTQPGQSLESTVQTWFKPLAYAFILTRESGYPQVFYGDMYGTKGDSQREIPALKHKIEPILKARKQYAYGAQHDYFDHHDIVGWTREGDSSVANSGLAALITDGPGGAKRMYVGRQNAGETWHDITGNRSEPVVINSEGWGEFHVNGGSVSIYVQR 512
               SCOP domains d1e3za2 A:1-393 Bacterial alpha-amylase                                                                                                                                                                                                                                                                                                                                                                  d1e3za1 A:394-483 Bacterial alpha-Amylase                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1e3zA03 A:397-483 Golgi alpha-mannosidase II                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..........hhhhhhhhhhhhhhhhh..eeee....................................hhhhhhhhhhhhhhh..eeeeee.........eeeeeeeee.............eeeeeeee...............hhh................eee.............................hhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhh.......hhhhhhhhhhhhhh....hhhhh........hhh..eee................hhhhhhhhhhhhhhh...eeeeehhhhhh...........hhhhhhhhhhhhhhh....eeee.....eeeeee..........eeeeee....eeeeee.hhhhh...eee...............eeeeee....eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e3z A   1 VNGTLMQYFEWYTPNDGQHWKRLQNDAEHLSDIGITAVWIPPAYKGLSQSDNGYGPYDLYDLGEFQQKGTVRTKYGTKSELQDAIGSLHSRNVQVYGDVVLNHKAGADATEDVTAVEVNPANRNQETSEEYQIKAWTDFRFPGRGNTYSDFKWHWYHFDGADWDESRKISRIFKFRGEGKAWDWEVSSENGNYDYLMYADVDYDHPDVVAETKKWGIWYANELSLDGFRIDAAKHIKFSFLRDWVQAVRQATGKEMFTVAEYWQNNAGKLENYLNKTSFNQSVFDVPLHFNLQAASSQGGGYDMRKLLNGTVVSKHPLKSVTFVDNHDTQPGQSLESTVQTWFKPLAYAFILTRESGYPQVFYGDMYGTKGDSQREIPALKHKIEPILKARKQYAYGAQHDYFDHHDIVGWTREGDSSVANSGLAALITDGPGGAKRMYVGRQNAGETWHDITGNRSEPVVINSEGWGEFHVNGGSVSIYVQR 483
                                    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
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1E3Z)

(-) Gene Ontology  (10, 20)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (AMY_BACAM | P00692)
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:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
    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: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.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Chain A   (AMY_BACLI | P06278)
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:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
    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: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.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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  AMY_BACLI | P06278
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 Related Entries

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

UniProtKB/Swiss-Prot
        AMY_BACAM | P00692: 1e3x 1e40 1e43 3bh4
        AMY_BACLI | P06278: 1bli 1bpl 1e3x 1e40 1e43 1ob0 1vjs

(-) Related Entries Specified in the PDB File

1bli BACILLUS LICHENIFORMIS ALPHA-AMYLASE
1bpl GLYCOSYLTRANSFERASE
1e3x NATIVE STRUCTURE OF CHIMAERIC AMYLASE FROM B. AMYLOLIQUEFACIENS AND B. LICHENIFORMIS AT 1.92A
1e40 TRIS/MALTOTRIOSE COMPLEX OF CHIMAERIC AMYLASE FROM B. AMYLOLIQUEFACIENS AND B. LICHENIFORMIS AT 2.2A
1e43 NATIVE STRUCTURE OF CHIMAERIC AMYLASE FROM B. AMYLOLIQUEFACIENS AND B. LICHENIFORMIS AT 1.7A
1vjs STRUCTURE OF ALPHA-AMYLASE PRECURSOR