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(-) Description

Title :  THREE DIMENSIONAL STRUCTURE ANALYSIS OF THE R337Q VARIANT OF HUMAN PANCREATIC ALPHA-MYLASE
 
Authors :  S. Numao, R. Maurus, G. Sidhu, Y. Wang, C. M. Overall, G. D. Brayer, S. G. W
Date :  28 Nov 01  (Deposition) - 16 Jan 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha-Amylase, Chloride Binding, Pichia Pastoris, Mutagenesis, Catalysis, Pancreatic, Enzyme, Human, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Numao, R. Maurus, G. Sidhu, Y. Wang, C. M. Overall, G. D. Brayer, S. G. Withers
Probing The Role Of The Chloride Ion In The Mechanism Of Human Pancreatic Alpha-Amylase.
Biochemistry V. 41 215 2002
PubMed-ID: 11772019  |  Reference-DOI: 10.1021/BI0115636

(-) Compounds

Molecule 1 - ALPHA-AMYLASE, PANCREATIC
    ChainsA
    EC Number3.2.1.1
    EngineeredYES
    Expression SystemPICHIA PASTORIS
    Expression System Taxid4922
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Synonym1,4-ALPHA-D-GLUCAN GLUCANOHYDROLASE, PANCREATIC ALPHA- AMYLASE, PA

 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
1CA1Ligand/IonCALCIUM ION
2NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
3PCA1Mod. Amino AcidPYROGLUTAMIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:343 , TRP A:344 , PRO A:345 , ASP A:381 , ASN A:459 , GLY A:460 , ASN A:461BINDING SITE FOR RESIDUE NAG A 497
2AC2SOFTWAREASN A:100 , ARG A:158 , ASP A:167 , HIS A:201 , HOH A:531 , HOH A:532 , HOH A:541BINDING SITE FOR RESIDUE CA A 498

(-) 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 1KGW)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1KGW)

(-) 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_HUMAN | P04746 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_HUMAN    16 QYSPNTQQGRTSIVHLFEWRWVDIALECERYLAPKGFGGVQVSPPNENVAIYNPFRPWWERYQPVSYKLCTRSGNEDEFRNMVTRCNNVGVRIYVDAVINHMCGNAVSAGTSSTCGSYFNPGSRDFPAVPYSGWDFNDGKCKTGSGDIENYNDATQVRDCRLTGLLDLALEKDYVRSKIAEYMNHLIDIGVAGFRLDASKHMWPGDIKAILDKLHNLNSNWFPAGSKPFIYQEVIDLGGEPIKSSDYFGNGRVTEFKYGAKLGTVIRKWNGEKMSYLKNWGEGWGFVPSDRALVFVDNHDNQRGHGAGGASILTFWDARLYKMAVGFMLAHPYGFTRVMSSYRWPRQFQNGNDVNDWVGPPNNNGVIKEVTINPDTTCGNDWVCEHRWRQIRNMVIFRNVVDGQPFTNWYDNGSNQVAFGRGNRGFIVFNNDDWSFSLTLQTGLPAGTYCDVISGDKINGNCTGIKIYVSDDGKAHFSISNSAEDPFIAIHAESKL 511
               SCOP domains d1kgwa2 A:1-403 Animal alpha-amylase                                                                                                                                                                                                                                                                                                                                                                               d1kgwa1 A:404-496 Animal alpha-amylase                                                        SCOP domains
               CATH domains -1kgwA01 A:2-403 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                      1kgwA02 A:404-496 Golgi alpha-mannosidase II                                                  CATH domains
               Pfam domains --------------------Alpha-amylase-1kgwA02 A:21-336                                                                                                                                                                                                                                                                                              ---------------------------------------------------------------------Alpha-amylase_C-1kgwA01 A:406-495                                                         - Pfam domains
         Sec.struct. author ...........eeeee...hhhhhhhhhhhh.......eeee..............hhhhhhh...........hhhhhhhhhhhhhh...eeeeee...eeee...............hhhhh.......hhhhh................hhhhhhhh....eee....hhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhh................eeee..........hhhhhh...eee.hhhhhhhhhhhh.....hhhhhhhhhhhhh..hhh.eee.....hhhhh...hhhhh.hhhhhhhhhhhhhhhhhh...eeeeee.....................ee..ee................hhhhhhhhhhhhhhhhhh....eeeeee....eeeeee...eeeeee.....eeeeee................................eeeeee.......eeeee.hhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kgw A   1 xYSPNTQQGRTSIVHLFEWRWVDIALECERYLAPKGFGGVQVSPPNENVAIYNPFRPWWERYQPVSYKLCTRSGNEDEFRNMVTRCNNVGVRIYVDAVINHMCGNAVSAGTSSTCGSYFNPGSRDFPAVPYSGWDFNDGKCKTGSGDIENYNDATQVRDCRLTGLLDLALEKDYVRSKIAEYMNHLIDIGVAGFRLDASKHMWPGDIKAILDKLHNLNSNWFPAGSKPFIYQEVIDLGGEPIKSSDYFGNGRVTEFKYGAKLGTVIRKWNGEKMSYLKNWGEGWGFVPSDRALVFVDNHDNQRGHGAGGASILTFWDARLYKMAVGFMLAHPYGFTQVMSSYRWPRQFQNGNDVNDWVGPPNNNGVIKEVTINPDTTCGNDWVCEHRWRQIRNMVIFRNVVDGQPFTNWYDNGSNQVAFGRGNRGFIVFNNDDWSFSLTLQTGLPAGTYCDVISGDKINGNCTGIKIYVSDDGKAHFSISNSAEDPFIAIHAESKL 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                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           

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  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

(-) 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)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (AMYP_HUMAN | P04746)
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.
    GO:0044245    polysaccharide digestion    The whole of the physical, chemical, and biochemical processes carried out by living organisms to break down ingested polysaccharides into components that may be easily absorbed and directed into metabolism.
cellular component
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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_HUMAN | P047461b2y 1bsi 1cpu 1hny 1kb3 1kbb 1kbk 1kgu 1kgx 1u2y 1u30 1u33 1xcw 1xcx 1xd0 1xd1 1xgz 1xh0 1xh1 1xh2 2cpu 2qmk 2qv4 3bai 3baj 3bak 3baw 3bax 3bay 3cpu 3ij7 3ij8 3ij9 3old 3ole 3olg 3oli 4gqq 4gqr 4w93 4x9y 5e0f 5emy 5kez 5td4

(-) Related Entries Specified in the PDB File

1bs1 HUMAN PANCREATIC ALPHA-AMYLASE FROM PICHIA PASTORIS, GLYCOSYLATED PROTEIN
1kb3 THREE DIMENSIONAL STRUCTURE ANALYSIS OF THE R195A VARIANT OF HUMAN PANCREATIC ALPHA AMYLASE
1kgu THREE DIMENSIONAL STRUCTURE ANALYSIS OF THE R337A VARIANT OF HUMAN PANCREATIC ALPHA-AMYLASE
1kgx THREE DIMENSIONAL STRUCTURE ANALYSIS OF THE R195Q VARIANT OF HUMAN PANCREATIC ALPHA AMYLASE