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(-) Description

Title :  PROBING THE ROLE OF AROMATIC RESIDUES AT THE SECONDARY SACCHARIDE BINDING SITES OF HUMAN SALIVARY ALPHA-AMYLASE IN SUBSTRATE HYDROLYSIS AND BACTERIAL BINDING
 
Authors :  C. Ragunath, S. G. A Manuel, H. M. Sait, C. Kasinathan
Date :  18 Jun 08  (Deposition) - 01 Jul 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Amylase Acarbose Aromatic Residues Mutagenesis, Calcium, Carbohydrate Metabolism, Chloride, Glycoprotein, Glycosidase, Hydrolase, Metal-Binding, Pyrrolidone Carboxylic Acid, Secreted (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Ragunath, S. G. A Manuel, H. M. Sait, C. Kasinathan, N. Ramasubbu
Probing The Role Of Aromatic Residues
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALPHA-AMYLASE 1
    Chains: A
    EC Number: 3.2.1.1
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Plasmid: PVL1392
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: 1,4-ALPHA-D-GLUCAN GLUCANOHYDROLASE 1, SALIVARY ALPHA-AMYLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 7)

Asymmetric/Biological Unit (6, 7)
No.NameCountTypeFull Name
1AGL1Ligand/Ion4,6-DIDEOXY-4-AMINO-ALPHA-D-GLUCOSE
2CA1Ligand/IonCALCIUM ION
3CL1Ligand/IonCHLORIDE ION
4GLC2Ligand/IonALPHA-D-GLUCOSE
5HMC1Ligand/Ion5-HYDROXYMETHYL-CHONDURITOL
6PCA1Mod. Amino AcidPYROGLUTAMIC ACID

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:58 , TRP A:59 , TYR A:62 , GLN A:63 , HIS A:305BINDING SITE FOR RESIDUE GLC A 503
2AC2SOFTWARETYR A:151 , LYS A:200 , ILE A:235 , GLU A:240 , GLY A:306 , ALA A:307 , HOH A:659 , HOH A:717 , HOH A:887BINDING SITE FOR RESIDUE GLC A 506
3AC3SOFTWAREALA A:198 , HIS A:201 , GLU A:233 , ASP A:300 , GLY A:306 , HOH A:554 , HOH A:576BINDING SITE FOR RESIDUE AGL A 505
4AC4SOFTWAREASN A:100 , ARG A:158 , ASP A:167 , HIS A:201 , HOH A:529 , HOH A:536 , HOH A:562BINDING SITE FOR RESIDUE CA A 497
5AC5SOFTWAREARG A:195 , ASN A:298 , ARG A:337BINDING SITE FOR RESIDUE CL A 498
6AC6SOFTWARETRP A:58 , TYR A:62 , HIS A:101 , ARG A:195 , ASP A:197 , GLU A:233 , HIS A:299 , ASP A:300BINDING SITE FOR RESIDUE HMC A 504

(-) 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 3DHP)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (10, 10)

Asymmetric/Biological Unit (10, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1cENST000003700831cENSE00001800716chr1:104198377-104198550174AMY1_HUMAN-00--
1.3ENST000003700833ENSE00001618329chr1:104198907-104199120214AMY1_HUMAN1-56561A:1-4141
1.4bENST000003700834bENSE00002198690chr1:104199466-104199612147AMY1_HUMAN57-105491A:42-9049
1.5ENST000003700835ENSE00001722064chr1:104200416-104200613198AMY1_HUMAN106-171661A:91-15666
1.6bENST000003700836bENSE00002145789chr1:104201062-104201292231AMY1_HUMAN172-248771A:157-23377
1.7ENST000003700837ENSE00001650327chr1:104202032-104202165134AMY1_HUMAN249-293451A:234-27845
1.8ENST000003700838ENSE00001669527chr1:104202982-104203104123AMY1_HUMAN293-334421A:278-31942
1.9ENST000003700839ENSE00001786647chr1:104203199-104203298100AMY1_HUMAN334-367341A:319-35234
1.10aENST0000037008310aENSE00001615366chr1:104205279-104205397119AMY1_HUMAN368-407401A:353-39240
1.11ENST0000037008311ENSE00001680728chr1:104205508-104205633126AMY1_HUMAN407-449431A:392-43443
1.13aENST0000037008313aENSE00001671242chr1:104206953-104207173221AMY1_HUMAN449-511631A:434-49663

(-) 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 AMY1_HUMAN | P04745 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      
           AMY1_HUMAN    16 QYSSNTQQGRTSIVHLFEWRWVDIALECERYLAPKGFGGVQVSPPNENVAIHNPFRPWWERYQPVSYKLCTRSGNEDEFRNMVTRCNNVGVRIYVDAVINHMCGNAVSAGTSSTCGSYFNPGSRDFPAVPYSGWDFNDGKCKTGSGDIENYNDATQVRDCRLSGLLDLALGKDYVRSKIAEYMNHLIDIGVAGFRIDASKHMWPGDIKAILDKLHNLNSNWFPEGSKPFIYQEVIDLGGEPIKSSDYFGNGRVTEFKYGAKLGTVIRKWNGEKMSYLKNWGEGWGFMPSDRALVFVDNHDNQRGHGAGGASILTFWDARLYKMAVGFMLAHPYGFTRVMSSYRWPRYFENGKDVNDWVGPPNDNGVTKEVTINPDTTCGNDWVCEHRWRQIRNMVNFRNVVDGQPFTNWYDNGSNQVAFGRGNRGFIVFNNDDWTFSLTLQTGLPAGTYCDVISGDKINGNCTGIKIYVSDDGKAHFSISNSAEDPFIAIHAESKL 511
               SCOP domains d3dhpa2 A:1-408 automated matches                                                                                                                                                                                                                                                                                                                                                                                       d3dhpa1 A:409-496 automated matches                                                      SCOP domains
               CATH domains -3dhpA01 A:2-403 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                      3dhpA02 A:404-496 Golgi alpha-mannosidase II                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeee...hhhhhhhhhhhh.......eeee..............hhhhhhh...........hhhhhhhhhhhhhhh..eeeeee...eeee...........................hhhhh................hhhhhhhhhhh.eee....hhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhh................eeee..........hhhhhh...eee.hhhhhhhhhhhhh....hhhhhhhhhhhhh......eee.....hhhhh.........hhhhhhhhhhhhhhhhhh...eeeeee.......ee..ee........ee..ee................hhhhhhhhhhhhhhhhhh....eeeeee....eeeeee...eeeeee.....eeeeee.....eeee......ee..ee...eeee....eeeeee.......eeeee.hhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: A:1-41 UniProt: 1-56      Exon 1.4b  PDB: A:42-90 UniProt: 57-105          Exon 1.5  PDB: A:91-156 UniProt: 106-171                          Exon 1.6b  PDB: A:157-233 UniProt: 172-248                                   Exon 1.7  PDB: A:234-278 UniProt: 249-293    ----------------------------------------Exon 1.9  PDB: A:319-352          Exon 1.10a  PDB: A:353-392              -----------------------------------------Exon 1.13a  PDB: A:434-496 UniProt: 449-511                     Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.8  PDB: A:278-319 UniProt: 293-334 ------------------------------------------------------------------------Exon 1.11  PDB: A:392-434 UniProt: 407-449 -------------------------------------------------------------- Transcript 1 (2)
                 3dhp A   1 xYSSNTQQGRTSIVHLFEWRWVDIALECERYLAPKGFGGVQVSPPNENVAIHNPFRPWWERYQPVSYKLCTRSGNEDEFRNMVTRCNNVGVRIYVDAVINHMCGNAVSAGTSSTCGSYFNPGSRDFPAVPYSGADFNDGKCKTGSGDIENYNDATQVRDCRLSGLLDLALGKDYVRSKIAEYMNHLIDIGVAGFRIDASKHMAPGDIKAILDKLHNLNSNWFPEGSKPFIYQEVIDLGGEPIKSSDYFGNGRVTEFKYGAKLGTVIRKWNGEKMSALKNWGEGAGFMPSDRALVFVDNHDNQRGHGAGGASILTFADARLYKMAVGFMLAHPYGFTRVMSSYRWPRYFENGKDVNDWVGPPNDNGVTKEVTINPDTTCGNDWVCEHRARQIRNMVNFRNVVDGQPFTNWYDNGSNQVAFGRGNRGFIVFNNDDWTFSLTLQTGLPAGTYCDVISGDKINGNCTGIKIYVSDDGKAHFSISNSAEDPFIAIHAESKL 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  (0, 0)

(no "Pfam Domain" information available for 3DHP)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (AMY1_HUMAN | P04745)
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.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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:0007586    digestion    The whole of the physical, chemical, and biochemical processes carried out by multicellular organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism.
    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: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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  3dhp
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 Related Entries

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

UniProtKB/Swiss-Prot
        AMY1_HUMAN | P04745: 1c8q 1jxj 1jxk 1mfu 1mfv 1nm9 1q4n 1smd 1xv8 1z32 3blk 3blp

(-) Related Entries Specified in the PDB File

1mfv RECOMBINANT ENZYME ACARBOSE COMPLEX
1smd NATIVE ENZYME