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(-) Description

Title :  STRUCTURE OF TENEBRIO MOLITOR LARVAL ALPHA-AMYLASE IN COMPLEX WITH RAGI BIFUNCTIONAL INHIBITOR
 
Authors :  F. X. Gomis-Rueth, S. Strobl, R. Glockshuber
Date :  13 Jan 98  (Deposition) - 02 Mar 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha-Amylase, Carbohydrate Metabolism, Alpha-1, 4-Glucan-4- Glucanohydrolase, Hydrolase Bifunctional Alpha- Amylase/Trypsin Inhibitor, Complex (Enzyme/ Inhibitor), Hydrolase/Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Strobl, K. Maskos, G. Wiegand, R. Huber, F. X. Gomis-Ruth, R. Glockshuber
A Novel Strategy For Inhibition Of Alpha-Amylases: Yellow Meal Worm Alpha-Amylase In Complex With The Ragi Bifunctional Inhibitor At 2. 5 A Resolution.
Structure V. 6 911 1998
PubMed-ID: 9687373  |  Reference-DOI: 10.1016/S0969-2126(98)00092-6
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (ALPHA-AMYLASE)
    Chains: A
    EC Number: 3.2.1.1
    Organism Common: YELLOW MEALWORM
    Organism Scientific: TENEBRIO MOLITOR
    Organism Taxid: 7067
    Tissue: LARVAE
 
Molecule 2 - PROTEIN (RAGI BIFUNCTIONAL INHIBITOR)
    Chains: B
    Organ: SEED
    Organism Common: FINGER MILLET
    Organism Scientific: ELEUSINE CORACANA
    Organism Taxid: 4511

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2CL1Ligand/IonCHLORIDE ION
3PCA1Mod. Amino AcidPYROGLUTAMIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:183 , LEU A:243 , ASN A:285 , ARG A:321 , HOH A:1067BINDING SITE FOR RESIDUE CL A 1002
2AC2SOFTWAREASN A:98 , ARG A:146 , ASP A:155 , HIS A:189 , HOH A:1049 , HOH A:5011BINDING SITE FOR RESIDUE CA A 1001

(-) SS Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1A:28 -A:84
2A:134 -A:148
3A:354 -A:360
4A:425 -A:437
5B:506 -B:555
6B:520 -B:544
7B:529 -B:585
8B:545 -B:603
9B:557 -B:614

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Val A:123 -Pro A:124

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_IAAT_ELECO_001 *T28AIAAT_ELECO  ---  ---BT528A
2UniProtVAR_IAAT_ELECO_002 *P70SIAAT_ELECO  ---  ---BS570S
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CEREAL_TRYP_AMYL_INHPS00426 Cereal trypsin/alpha-amylase inhibitors family signature.IAAT_ELECO6-29  1B:506-529

(-) Exons   (0, 0)

(no "Exon" information available for 1TMQ)

(-) 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:471
 aligned with AMY_TENMO | P56634 from UniProtKB/Swiss-Prot  Length:471

    Alignment length:471
                                    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 
            AMY_TENMO     1 QKDANFASGRNSIVHLFEWKWNDIADECERFLQPQGFGGVQISPPNEYLVADGRPWWERYQPVSYIINTRSGDESAFTDMTRRCNDAGVRIYVDAVINHMTGMNGVGTSGSSADHDGMNYPAVPYGSGDFHSPCEVNNYQDADNVRNCELVGLRDLNQGSDYVRGVLIDYMNHMIDLGVAGFRVDAAKHMSPGDLSVIFSGLKNLNTDYGFADGARPFIYQEVIDLGGEAISKNEYTGFGCVLEFQFGVSLGNAFQGGNQLKNLANWGPEWGLLEGLDAVVFVDNHDNQRTGGSQILTYKNPKPYKMAIAFMLAHPYGTTRIMSSFDFTDNDQGPPQDGSGNLISPGINDDNTCSNGYVCEHRWRQVYGMVGFRNAVEGTQVENWWSNDDNQIAFSRGSQGFVAFTNGGDLNQNLNTGLPAGTYCDVISGELSGGSCTGKSVTVGDNGSADISLGSAEDDGVLAIHVNAKL 471
               SCOP domains d1tmqa2 A:1-378 Animal alpha-amylase                                                                                                                                                                                                                                                                                                                                                      d1tmqa1 A:379-471 Animal alpha-amylase                                                        SCOP domains
               CATH domains -1tmqA01 A:2-379 Glycosidases                                                                                                                                                                                                                                                                                                                                                              1tmqA02 A:380-471 Golgi alpha-mannosidase II                                                 CATH domains
               Pfam domains ------------------Alpha-amylase-1tmqA02 A:19-324                                                                                                                                                                                                                                                                                    ------------------------------------------------------------Alpha-amylase_C-1tmqA01 A:385-470                                                     - Pfam domains
         Sec.struct. author ............eeee....hhhhhhhhhh........eee..............hhhhh.............hhhhhhhhhhhhh...eeeeee...............................hhh............hhhhhh.............hhhhhhhhhhhhhhhh....eeee..hhh..hhhhhhhhhh.....hhh........eeee...........hhh.........hhhhhhhhhhhh....hhhhhh..hhh....hhh.........hhhh.......hhhhhhhhhhhhhhhh......eeee......................eee...eee.....hhh.hhhhhhhhhhhh...............eeeee....eeeeee....eeeeee.....eeee...............eeee....eeeeee.......eeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tmq A   1 xKDANFASGRNSIVHLFEWKWNDIADECERFLQPQGFGGVQISPPNEYLVADGRPWWERYQPVSYIINTRSGDESAFTDMTRRCNDAGVRIYVDAVINHMTGMNGVGTSGSSADHDGMNYPAVPYGSGDFHSPCEVNNYQDADNVRNCELVGLRDLNQGSDYVRGVLIDYMNHMIDLGVAGFRVDAAKHMSPGDLSVIFSGLKNLNTDYGFADGARPFIYQEVIDLGGEAISKNEYTGFGCVLEFQFGVSLGNAFQGGNQLKNLANWGPEWGLLEGLDAVVFVDNHDNQRTGGSQILTYKNPKPYKMAIAFMLAHPYGTTRIMSSFDFTDNDQGPPQDGSGNLISPGINDDNTCSNGYVCEHRWRQVYGMVGFRNAVEGTQVENWWSNDDNQIAFSRGSQGFVAFTNGGDLNQNLNTGLPAGTYCDVISGELSGGSCTGKSVTVGDNGSADISLGSAEDDGVLAIHVNAKL 471
                            |       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 
                            |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
                            1-PCA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:117
 aligned with IAAT_ELECO | P01087 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:117
                                    10        20        30        40        50        60        70        80        90       100       110       
           IAAT_ELECO     1 SVGTSCIPGMAIPHNPLDSCRWYVSTRTCGVGPRLATQEMKARCCRQLEAIPAYCRCEAVRILMDGVVTPSGQHEGRLLQDLPGCPRQVQRAFAPKLVTEVECNLATIHGGPFCLSL 117
               SCOP domains d1tmqb_ B: Trypsin/alpha-amylase inhibitor RBI                                                                        SCOP domains
               CATH domains 1tmqB00 B:501-617 Bifunctional Trypsin/Alpha-Amylase Inhibitor                                                        CATH domains
               Pfam domains -----Tryp_alpha_amyl-1tmqB01 B:506-613                                                                           ---- Pfam domains
         Sec.struct. author .hhhh............hhhhhhhhhhhh.......hhhhhhhhhhhhh...hhhhhhhhhhhhh.....................hhhhhhhhhhhh................... Sec.struct. author
                 SAPs(SNPs) ---------------------------A-----------------------------------------S----------------------------------------------- SAPs(SNPs)
                    PROSITE -----CEREAL_TRYP_AMYL_INH    ---------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 1tmq B 501 SVGTSCIPGMAIPHNPLDSCRWYVSTRTCGVGPRLATQEMKARCCRQLEAIPAYCRCEAVRILMDGVVTSSGQHEGRLLQDLPGCPRQVQRAFAPKLVTEVECNLATIHGGPFCLSL 617
                                   510       520       530       540       550       560       570       580       590       600       610
   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  (3, 3)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Clan: GHD (106)
(-)
Clan: Glyco_hydro_tim (488)
(-)
Clan: Prolamin (17)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (AMY_TENMO | P56634)
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: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:0043169    cation binding    Interacting selectively and non-covalently with cations, charged atoms or groups of atoms with a net positive charge.
    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: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.

Chain B   (IAAT_ELECO | P01087)
molecular function
    GO:0015066    alpha-amylase inhibitor activity    Stops, prevents or reduces the activity of alpha-amylase.
    GO:0030414    peptidase inhibitor activity    Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
    GO:0004867    serine-type endopeptidase inhibitor activity    Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme.
biological process
    GO:0010951    negative regulation of endopeptidase activity    Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
    GO:0010466    negative regulation of peptidase activity    Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
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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 Related Entries

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

UniProtKB/Swiss-Prot
        AMY_TENMO | P56634: 1clv 1jae 1viw
        IAAT_ELECO | P01087: 1b1u 1bip

(-) Related Entries Specified in the PDB File

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