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(-) Description

Title :  STRUCTURE OF PORCINE PANCREATIC ALPHA-AMYLASE
 
Authors :  C. Bompard-Gilles, F. Payan
Date :  14 Oct 96  (Deposition) - 24 Dec 97  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Pancreatic Alpha-Amylase, Porcine, Lectin-Like Inhibitor, Complex (Hydrolase-Inhibitor), Complex (Hydrolase-Inhibitor) Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Bompard-Gilles, P. Rousseau, P. Rouge, F. Payan
Substrate Mimicry In The Active Center Of A Mammalian Alpha-Amylase: Structural Analysis Of An Enzyme-Inhibitor Complex.
Structure V. 4 1441 1996
PubMed-ID: 8994970  |  Reference-DOI: 10.1016/S0969-2126(96)00151-7
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PORCINE PANCREATIC ALPHA-AMYLASE
    Chains: A
    EC Number: 3.2.1.1
    Organ: PANCREAS
    Organism Common: PIG
    Organism Scientific: SUS SCROFA
    Organism Taxid: 9823
    Synonym: PPA
 
Molecule 2 - BEAN LECTIN-LIKE INHIBITOR
    Chains: B
    Organ: SEED
    Organism Scientific: PHASEOLUS VULGARIS
    Organism Taxid: 3885

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric Unit (4, 10)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
2CL1Ligand/IonCHLORIDE ION
3NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
4PCA1Mod. Amino AcidPYROGLUTAMIC ACID
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3NAG10Ligand/IonN-ACETYL-D-GLUCOSAMINE
4PCA2Mod. Amino AcidPYROGLUTAMIC ACID

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER B:54 , GLU B:170 , NAG B:511BINDING SITE FOR RESIDUE NAG B 510
2AC2SOFTWAREPHE B:11 , ASN B:12 , SER B:25 , ASP B:173 , TRP B:174 , NAG B:510 , HOH B:520 , HOH B:541BINDING SITE FOR RESIDUE NAG B 511
3AC3SOFTWAREARG B:136 , NAG B:509BINDING SITE FOR RESIDUE NAG B 508
4AC4SOFTWAREASP B:63 , ASN B:65 , ARG B:136 , SER B:199 , NAG B:508BINDING SITE FOR RESIDUE NAG B 509
5AC5SOFTWAREASN B:140 , THR B:143BINDING SITE FOR RESIDUE NAG B 512
6AC6SOFTWAREASN A:100 , ARG A:158 , ASP A:167 , HIS A:201 , HOH A:518 , HOH A:525 , HOH A:537BINDING SITE FOR RESIDUE CA A 500
7AC7SOFTWAREARG A:195 , ASN A:298 , ARG A:337 , HOH A:523BINDING SITE FOR RESIDUE CL A 498
8AC8SOFTWAREGLU A:149 , GLU B:101 , ASP B:112 , ASP B:117 , HOH B:540 , HOH B:545BINDING SITE FOR RESIDUE CA B 497
9AC9SOFTWARESER B:33 , SER B:36 , SER B:189 , HOH B:554 , HOH B:555 , HOH B:556BINDING SITE FOR RESIDUE CA B 499

(-) SS Bonds  (5, 5)

Asymmetric Unit
No.Residues
1A:28 -A:86
2A:70 -A:115
3A:141 -A:160
4A:378 -A:384
5A:450 -A:462

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asn A:53 -Pro A:54
2Val A:129 -Pro A:130

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LECTIN_LEGUME_BETAPS00307 Legume lectins beta-chain signature.LEA1_PHAVU121-127  1B:98-104
2LECTIN_LEGUME_ALPHAPS00308 Legume lectins alpha-chain signature.LEA1_PHAVU194-203  1B:171-180
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LECTIN_LEGUME_BETAPS00307 Legume lectins beta-chain signature.LEA1_PHAVU121-127  2B:98-104
2LECTIN_LEGUME_ALPHAPS00308 Legume lectins alpha-chain signature.LEA1_PHAVU194-203  2B:171-180

(-) Exons   (0, 0)

(no "Exon" information available for 1DHK)

(-) 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:496
 aligned with AMYP_PIG | P00690 from UniProtKB/Swiss-Prot  Length:511

    Alignment length:496
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505      
             AMYP_PIG    16 QYAPQTQSGRTSIVHLFEWRWVDIALECERYLGPKGFGGVQVSPPNENIVVTNPSRPWWERYQPVSYKLCTRSGNENEFRDMVTRCNNVGVRIYVDAVINHMCGSGAAAGTGTTCGSYCNPGNREFPAVPYSAWDFNDGKCKTASGGIESYNDPYQVRDCQLVGLLDLALEKDYVRSMIADYLNKLIDIGVAGFRIDASKHMWPGDIKAVLDKLHNLNTNWFPAGSRPFIFQEVIDLGGEAIQSSEYFGNGRVTEFKYGAKLGTVVRKWSGEKMSYLKNWGEGWGFMPSDRALVFVDNHDNQRGHGAGGASILTFWDARLYKVAVGFMLAHPYGFTRVMSSYRWARNFVNGQDVNDWIGPPNNNGVIKEVTINADTTCGNDWVCEHRWRQIRNMVWFRNVVDGQPFANWWANGSNQVAFGRGNRGFIVFNNDDWQLSSTLQTGLPGGTYCDVISGDKVGNSCTGIKVYVSSDGTAQFSISNSAEDPFIAIHAESKL 511
               SCOP domains d1dhka2 A:1-403 Animal alpha-amylase                                                                                                                                                                                                                                                                                                                                                                               d1dhka1 A:404-496 Animal alpha-amylase                                                        SCOP domains
               CATH domains -1dhkA01 A:2-403 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                      1dhkA02 A:404-496 Golgi alpha-mannosidase II                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) ...........eeeee....hhhhhhhhhh.......eeeee..eeeeee.......hhhhh......eee.---hhhhhhhhhhhhhh..eeeeee..eeeeee....eeeee....-hhhhh---...eee.eee........eee.....hhhhhh.ee.eeeeee...hhhhhhhhhhhhhhhhh..eeeeee......hhhhhhhhhh...............eeeee..........hhhh....eeeehhhhhhhhhhhh......hhhhhh.hhhhh..hhhhh--....................hhhhhhhhhhhhhhhh....eeeeee......eee..eee................eee..eeee....hhhhhhhhhhhhhhhhh....eeeeeeee..eeeeeeee.eeeeeeee....eeeeeee....eeeee....eee..eee.eeeeee..eeeeeee......eeeeeee.... Sec.struct. author (1)
     Sec.struct. author (2) ------------------------------------------------------------------------eeee------------------------------------------eee--eeee-------------------------------------------------------------------------------------------------------------------------------------------------------------------eeee---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dhk A   1 xYAPQTQSGRTSIVHLFEWRWVDIALECERYLGPKGFGGVQVSPPNENVVVTNPSRPWWERYQPVSYKLCTRSGNENEFRDMVTRCNNVGVRIYVDAVINHMCGSGAAAGTGTTCGSYCNPGSREFPAVPYSAWDFNDGKCKTASGGIESYNDPYQVRDCQLVGLLDLALEKDYVRSMIADYLNKLIDIGVAGFRIDASKHMWPGDIKAVLDKLHNLNTNWFPAGSRPFIFQEVIDLGGEAIQSSEYFGNGRVTEFKYGAKLGTVVRKWSGEKMSYLKNWGEGWGFMPSDRALVFVDNHDNQRGHGAGGASILTFWDARLYKVAVGFMLAHPYGFTRVMSSYRWARNFVNGEDVNDWIGPPNNNGVIKEVTINADTTCGNDWVCEHRWREIRNMVWFRNVVDGQPFANWWDNGSNQVAFGRGNRGFIVFNNDDWQLSSTLQTGLPGGTYCDVISGDKVGNSCTGIKVYVSSDGTAQFSISNSAEDPFIAIHAESKL 496
                            |       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      
                            |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
                            1-PCA                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:195
 aligned with LEA1_PHAVU | P02873 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:204
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223    
           LEA1_PHAVU    24 ATETSFIIDAFNKTNLILQGDATVSSNGNLQLSYNSYDSMSRAFYSAPIQIRDSTTGNVASFDTNFTMNIRTHRQANSAVGLDFVLVPVQPESKGDTVTVEFDTFLSRISIDVNNNDIKSVPWDVHDYDGQNAEVRITYNSSTKVFSVSLSNPSTGKSNNVSTTVELEKEVYDWVSVGFSATSGAYQWSYETHDVLSWSFSSKF 227
               SCOP domains d1dhkb_ B: Phytohemagglutinin-L, PHA-L, also arcelin                                                                                                                                                         SCOP domains
               CATH domains 1dhkB00 B:1-204  [code=2.60.120.200, no name defined]                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee.......eeee..eee.....eee......eeeeeee...............eeeeeeeeeee...---...eeeeeeee.------..eeeeee....eeeeee..eeeeeee..........eeeeeeee....eeeeeeee....eeeeeeee..........eeeeeeeee........eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------LECTIN_------------------------------------------------------------------LECTIN_LEG------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1dhk B   1 ATETSFIIDAFNKTNLILQGDATVSSNGNLQLSYNSYDSMSRAFYSAPIQIRDSTTGNVASFDTNFTMNIRTHR---SAVGLDFVLVPV------DTVTVEFDTFLSRISIDVNNNDIKSVPWDVHDYDGQNAEVRITYNSSTKVFSVSLSNPSTGKSNNVSTTVELEKEVYDWVSVGFSATSGAYQWSYETHDVLSWSFSSKF 204
                                    10        20        30        40        50        60        70   |   |80        |-     | 100       110       120       130       140       150       160       170       180       190       200    
                                                                                                    74  78         89     96
   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 Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 3)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A   (AMYP_PIG | P00690)
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:0043169    cation binding    Interacting selectively and non-covalently with cations, charged atoms or groups of atoms with a net positive charge.
    GO:0031404    chloride ion binding    Interacting selectively and non-covalently with chloride ions (Cl-).
    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:0016052    carbohydrate catabolic process    The chemical reactions and pathways resulting in the breakdown of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
    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.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

Chain B   (LEA1_PHAVU | P02873)
molecular function
    GO:0015066    alpha-amylase inhibitor activity    Stops, prevents or reduces the activity of alpha-amylase.
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
biological process
    GO:0043086    negative regulation of catalytic activity    Any process that stops or reduces the activity of an enzyme.

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  1dhk
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 Related Entries

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

UniProtKB/Swiss-Prot
        AMYP_PIG | P00690: 1bvn 1hx0 1jfh 1kxq 1kxt 1kxv 1ose 1pif 1pig 1ppi 1ua3 1vah 1wo2 3l2l 3l2m 4x0n
        LEA1_PHAVU | P02873: 1viw

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1DHK)