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1Q4N|pdb_00001q4n
Structural studies of Phe256Trp of human salivary alpha-amylase: implications for the role of a conserved water molecule and its associated chain in enzyme activity
- PDB DOI: https://doi.org/10.2210/pdb1Q4N/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Spodoptera frugiperda
- Mutation(s): Yes
- Deposited: 2003-08-04 Released: 2004-03-16
- Deposition Author(s): Ramasubbu, N.
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.07 Å
- R-Value Free: 0.206 (Depositor), 0.220 (DCC)
- R-Value Work: 0.156 (Depositor), 0.170 (DCC)
- R-Value Observed: 0.159 (Depositor)
Starting Model:experimental
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Download MendeleyStructural studies of a Phe256Trp mutant of human salivary alpha-amylase: implications for the role of a conserved water molecule in enzyme activity
Ramasubbu, N., Sundar, K., Ragunath, C., Rafi, M.M.(2004) Arch Biochem Biophys 421: 115-124
- PubMed: 14678792 Search on PubMed
- DOI: https://doi.org/10.1016/j.abb.2003.10.007
- Primary Citation of Related Structures:
1Q4N - PubMed Abstract:
In the mechanism of hydrolysis of starch by alpha-amylases, a conserved water molecule bridging two catalytic residues has been implicated. In human salivary alpha-amylase (HSAmy), this water (W641), observed in many alpha-amylase structures, is part of a chain of water molecules. To test the hypothesis that W641 may be involved in the mechanism, Phe256 in the close vicinity was mutated to a Trp residue. X-ray structure of F256W complexed to 2-amino-2-(hydroxyethyl)-1,3-propanediol at 2.1A revealed that the water chain is disrupted. In the F256W structure exhibits a positional shift in His305, characteristic of alpha-amylase complex structures. Kinetic analysis, in comparison with HSAmy, revealed that the mutant exhibited a 70-fold decrease in the specific activity for starch and significantly reduced k(cat) (20-fold) and K(m) (4-fold) for maltoheptaoside. Collectively, these results suggest that W641 and the chain of water molecules may be critical for the alpha-amylase activity.
- Department of Oral Biology, New Jersey Dental School, University of Medicine and Dentistry, Newark, NJ 07103, USA. n.ramasubbu@umdnj.edu
Organizational Affiliation:
Explore in 3D: Structure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (TAM)
Global Symmetry: Asymmetric - C1
Global Stoichiometry: Monomer - A1
Find Similar Assemblies
Biological assembly 1 assigned by authors.
Macromolecule Content
- Total Structure Weight: 56.23 kDa
- Atom Count: 4,286
- Modeled Residue Count: 496
- Deposited Residue Count: 496
- Unique protein chains: 1
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Alpha-amylase, salivary | A [auth X] | 496 | Homo sapiens | Mutation(s): 1 Gene Names: AMY1A OR AMY1 EC: 3.2.1.1 |  |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P0DUB6 (Homo sapiens) Explore P0DUB6 Go to UniProtKB: P0DUB6 | |||||
GTEx: ENSG00000237763 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P0DUB6 | ||||
Sequence AnnotationsExpand | |||||
| |||||
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| TAM Query on TAM Download Ideal Coordinates CCD File | D [auth X] | TRIS(HYDROXYETHYL)AMINOMETHANE C7 H17 N O3 GKODZWOPPOTFGA-UHFFFAOYSA-N |  | ||
| CA Query on CA Download Ideal Coordinates CCD File | B [auth X] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
| CL Query on CL Download Ideal Coordinates CCD File | C [auth X] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| PCA Query on PCA | A [auth X] | L-PEPTIDE LINKING | C5 H7 N O3 |  | GLN |
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.07 Å
- R-Value Free: 0.206 (Depositor), 0.220 (DCC)
- R-Value Work: 0.156 (Depositor), 0.170 (DCC)
- R-Value Observed: 0.159 (Depositor)
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 51.9 | α = 90 |
| b = 74.2 | β = 90 |
| c = 134.82 | γ = 90 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| REFMAC | refinement |
| AMoRE | phasing |
Deposition Data
- Released Date: 2004-03-16 Deposition Author(s): Ramasubbu, N.
Revision History (Full details and data files)
- Version 1.0: 2004-03-16
Type: Initial release - Version 1.1: 2008-04-29
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Version format compliance - Version 1.3: 2018-01-31
Changes: Experimental preparation - Version 2.0: 2019-12-25
Changes: Database references, Derived calculations, Polymer sequence - Version 2.1: 2021-10-27
Changes: Database references, Derived calculations - Version 2.2: 2023-08-16
Changes: Data collection, Refinement description - Version 2.3: 2024-11-06
Changes: Structure summary
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RCSB PDB Core Operations are funded by theU.S. National Science Foundation (DBI-2321666), theUS Department of Energy (DE-SC0019749), and theNational Cancer Institute,National Institute of Allergy and Infectious Diseases, andNational Institute of General Medical Sciences of theNational Institutes of Health under grant R01GM157729.