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(-) Description

Title :  X-RAY CRYSTALLOGRAPHIC ANALYSIS OF PIG PANCREATIC ALPHA-AMYLASE WITH LIMIT DEXTRIN AND OLIGOSACCHARIDE
 
Authors :  S. B. Larson, J. S. Day, A. Mcpherson
Date :  15 Dec 09  (Deposition) - 14 Apr 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.11
Chains :  Asym./Biol. Unit :  A
Keywords :  Catalytic Domain, Carbohydrate Binding Module, Oligosaccharide, Limit Dextrin, Glucose, Carbohydrate Metabolism, Glycoprotein, Glycosidase, Metal-Binding, Pyrrolidone Carboxylic Acid, Secreted, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. B. Larson, J. S. Day, A. Mcpherson
X-Ray Crystallographic Analyses Of Pig Pancreatic Alpha-Amylase With Limit Dextrin, Oligosaccharide, And Alpha-Cyclodextrin.
Biochemistry V. 49 3101 2010
PubMed-ID: 20222716  |  Reference-DOI: 10.1021/BI902183W
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PANCREATIC ALPHA-AMYLASE
    Chains: A
    EC Number: 3.2.1.1
    Fragment: RESIDUES 16-511
    Organism Common: PIG
    Organism Scientific: SUS SCROFA
    Organism Taxid: 9823
    Other Details: PANCREAS
    Synonym: PA, 1,4-ALPHA-D-GLUCAN GLUCANOHYDROLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 14)

Asymmetric/Biological Unit (4, 14)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2CL1Ligand/IonCHLORIDE ION
3GLC11Ligand/IonALPHA-D-GLUCOSE
4PCA1Mod. Amino AcidPYROGLUTAMIC ACID

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:108 , HOH A:569 , HOH A:570 , GLC A:603 , HOH A:606BINDING SITE FOR RESIDUE GLC A 604
02AC2SOFTWARETHR A:52 , ASN A:53 , GLU A:272 , ASN A:279 , GLC A:602 , GLC A:604 , HOH A:696BINDING SITE FOR RESIDUE GLC A 603
03AC3SOFTWARETHR A:52 , ASN A:53 , LYS A:261 , TRP A:284 , GLY A:285 , HOH A:573 , HOH A:574 , GLC A:601 , GLC A:603 , HOH A:979 , HOH A:998BINDING SITE FOR RESIDUE GLC A 602
04AC4SOFTWAREASN A:53 , PRO A:54 , HOH A:530 , HOH A:571 , HOH A:572 , GLC A:602 , HOH A:979 , HOH A:1034 , HOH A:1035BINDING SITE FOR RESIDUE GLC A 601
05AC5SOFTWARETYR A:62 , HIS A:101 , ASP A:197 , ALA A:198 , GLU A:233 , ILE A:235 , ASP A:300 , HOH A:552 , HOH A:582 , HOH A:583 , HOH A:584 , GLC A:704BINDING SITE FOR RESIDUE GLC A 705
06AC6SOFTWARETRP A:58 , TRP A:59 , TYR A:62 , GLN A:63 , ASP A:300 , HOH A:582 , HOH A:584 , GLC A:703 , GLC A:705 , HOH A:1023BINDING SITE FOR RESIDUE GLC A 704
07AC7SOFTWAREGLN A:63 , VAL A:163 , GLC A:702 , GLC A:704 , GLC A:706BINDING SITE FOR RESIDUE GLC A 703
08AC8SOFTWAREHOH A:578 , GLC A:701 , GLC A:703BINDING SITE FOR RESIDUE GLC A 702
09AC9SOFTWAREGLY A:147 , HOH A:550 , HOH A:551 , HOH A:575 , HOH A:576 , HOH A:577 , HOH A:622 , GLC A:702BINDING SITE FOR RESIDUE GLC A 701
10BC1SOFTWARETRP A:59 , GLN A:63 , GLY A:104 , SER A:105 , GLY A:106 , ALA A:107 , HOH A:579 , HOH A:580 , HOH A:581 , HOH A:679 , GLC A:703BINDING SITE FOR RESIDUE GLC A 706
11BC2SOFTWARELYS A:140 , GLU A:171 , TRP A:203 , ASP A:206 , HOH A:778 , HOH A:805 , HOH A:949 , HOH A:1093BINDING SITE FOR RESIDUE GLC A 801
12BC3SOFTWAREASN A:100 , ARG A:158 , ASP A:167 , HIS A:201 , HOH A:760 , HOH A:767 , HOH A:852BINDING SITE FOR RESIDUE CA A 501
13BC4SOFTWAREARG A:195 , ASN A:298 , ARG A:337BINDING SITE FOR RESIDUE CL A 502

(-) SS Bonds  (5, 5)

Asymmetric/Biological 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/Biological 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 3L2L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3L2L)

(-) Exons   (0, 0)

(no "Exon" information available for 3L2L)

(-) 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: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 d3l2la1 A:1-403 automated matches                                                                                                                                                                                                                                                                                                                                                                                  d3l2la2 A:404-496 automated matches                                                           SCOP domains
               CATH domains -3l2lA01 A:2-403 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                      3l2lA02 A:404-496 Golgi alpha-mannosidase II                                                  CATH domains
               Pfam domains ---------------------Alpha-amylase-3l2lA02 A:22-336                                                                                                                                                                                                                                                                                             ------------------------------------------------------------------------Alpha-amylase_C-3l2lA01 A:409-495                                                      - Pfam domains
         Sec.struct. author ...........eeeee...hhhhhhhhhhhh.......eeee..............hhhhhhh...........hhhhhhhhhhhhhhh..eeeeee...eeee...............hhhhh.......hhhhh................hhhhhhhhhhh.eee....hhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhh................eeee..........hhhhhh...eee.hhhhhhhhhhhh.....hhhhhhhhhhhhh..hhh.eee.....hhhhh...hhhhh.hhhhhhhhhhhhhhhhhh...eeeeee.....................ee..ee................hhhhhhhhhhhhhhhhhhh...eeeeee....eeeeee...eeeeee.....eeeeee.....eeee......ee..ee...eeee....eeeeee.......eeeee.hhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l2l A   1 xYAPQTQSGRTSIVHLFEWRWVDIALECERYLGPKGFGGVQVSPPNENIVVTNPSRPWWERYQPVSYKLCTRSGNENEFRDMVTRCNNVGVRIYVDAVINHMCGSGAAAGTGTTCGSYCNPGNREFPAVPYSAWDFNDGKCKTASGGIESYNDPYQVRDCQLVGLLDLALEKDYVRSMIADYLNKLIDIGVAGFRIDASKHMWPGDIKAVLDKLHNLNTNWFPAGSRPFIFQEVIDLGGEAIQSSEYFGNGRVTEFKYGAKLGTVVRKWSGEKMSYLKNWGEGWGFMPSDRALVFVDNHDNQRGHGAGGASILTFWDARLYKVAVGFMLAHPYGFTRVMSSYRWARNFVNGQDVNDWIGPPNNNGVIKEVTINADTTCGNDWVCEHRWRQIRNMVWFRNVVDGQPFANWWDNGSNQVAFGRGNRGFIVFNNDDWQLSSTLQTGLPGGTYCDVISGDKVGNSCTGIKVYVSSDGTAQFSISNSAEDPFIAIHAESKL 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
   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  (2, 2)

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

(-) Pfam Domains  (2, 2)

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

(-) Gene Ontology  (13, 13)

Asymmetric/Biological 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.

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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

3l2m X-RAY CRYSTALLOGRAPHIC ANALYSIS OF PIG PANCREATIC ALPHA- AMYLASE WITH ALPHA-CYCLODEXTRIN