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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   N298S VARIANT OF HUMAN PANCREATIC ALPHA-AMYLASE IN COMPLEX WITH AZIDE

Authors :   R. Maurus, G. D. Brayer

Date :   08 Nov 07 (Deposition) - 25 Mar 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym./Biol. Unit : A

Keywords :   Amylase, Diabetes, Human, Pancreatic, Enzyme, Hydrolase, Catalysis, Anion Activation, Chloride, Azide, Carbohydrate Metabolism, Glycoprotein, Glycosidase, Metal-Binding, Pyrrolidone Carboxylic Acid, Secreted (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Maurus, A. Begum, L. K. Williams, J. R. Fredriksen, R. Zhang, S. G. Withers, G. D. Brayer
Alternative Catalytic Anions Differentially Modulate Human Alpha-Amylase Activity And Specificity
Biochemistry V. 47 3332 2008
PubMed-ID: 18284212 | Reference-DOI: 10.1021/BI701652T

Molecule 1 - PANCREATIC ALPHA-AMYLASE
	Chains	:	A
	EC Number	:	3.2.1.1
	Engineered	:	YES
	Expression System	:	PICHIA PASTORIS
	Expression System Taxid	:	4922
	Gene	:	AMY2A
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PA, 1,4-ALPHA-D- GLUCAN GLUCANOHYDROLASE

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (6, 9)

No.	Name	Count	Type	Full Name
1	AZI	2	Ligand/Ion	AZIDE ION
2	CA	1	Ligand/Ion	CALCIUM ION
3	CL	1	Ligand/Ion	CHLORIDE ION
4	NA	3	Ligand/Ion	SODIUM ION
5	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
6	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:176 , TRP A:203 , ASP A:206 , ASN A:459 , ASN A:461 , HOH A:522 , HOH A:756 , HOH A:898 , HOH A:922 , HOH A:965 , HOH A:1083	BINDING SITE FOR RESIDUE NAG A 497
2	AC2	SOFTWARE	ASN A:100 , ARG A:158 , ASP A:167 , HIS A:201 , HOH A:562 , HOH A:891 , HOH A:892	BINDING SITE FOR RESIDUE CA A 498
3	AC3	SOFTWARE	ARG A:195 , ARG A:337	BINDING SITE FOR RESIDUE CL A 499
4	AC4	SOFTWARE	ALA A:198 , LYS A:200 , HIS A:201 , GLU A:233 , ILE A:235 , HOH A:602 , HOH A:724	BINDING SITE FOR RESIDUE AZI A 500
5	AC5	SOFTWARE	PHE A:136 , ASN A:137 , ASP A:138 , GLY A:139 , LYS A:140 , HOH A:508 , HOH A:989	BINDING SITE FOR RESIDUE AZI A 501
6	AC6	SOFTWARE	ASP A:197 , GLU A:233 , HOH A:608 , HOH A:620 , HOH A:724 , HOH A:1054 , HOH A:1106	BINDING SITE FOR RESIDUE NA A 502
7	AC7	SOFTWARE	GLU A:76 , LYS A:227	BINDING SITE FOR RESIDUE NA A 504

Asymmetric/Biological Unit

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

Asymmetric/Biological Unit

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

(no "SAP(SNP)/Variant" information available for 3BAX)

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

(no "Exon" information available for 3BAX)

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 d3baxa2 A:1-408 Animal alpha-amylase                                                                                                                                                                                                                                                                                                                                                                                    d3baxa1 A:409-496 Animal alpha-amylase                                                   SCOP domains
               CATH domains -3baxA01 A:2-403 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                      3baxA02 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....hhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhh................eeee..........hhhhhh...eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhh.eee.....hhhhh...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 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bax A   1 xYSPNTQQGRTSIVHLFEWRWVDIALECERYLAPKGFGGVQVSPPNENVAIYNPFRPWWERYQPVSYKLCTRSGNEDEFRNMVTRCNNVGVRIYVDAVINHMCGNAVSAGTSSTCGSYFNPGSRDFPAVPYSGWDFNDGKCKTGSGDIENYNDATQVRDCRLTGLLDLALEKDYVRSKIAEYMNHLIDIGVAGFRLDASKHMWPGDIKAILDKLHNLNSNWFPAGSKPFIYQEVIDLGGEPIKSSDYFGNGRVTEFKYGAKLGTVIRKWNGEKMSYLKNWGEGWGFVPSDRALVFVDSHDNQRGHGAGGASILTFWDARLYKMAVGFMLAHPYGFTRVMSSYRWPRQFQNGNDVNDWVGPPNNNGVIKEVTINPDTTCGNDWVCEHRWRQIRNMVIFRNVVDGQPFTNWYDNGSNQVAFGRGNRGFIVFNNDDWSFSLTLQTGLPAGTYCDVISGDKINGNCTGIKIYVSDDGKAHFSISNSAEDPFIAIHAESKL 496
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                            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 '\|'

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Glycosidases (843)

Human (Homo sapiens) (94)

3baxA01

A:2-403

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Golgi alpha-mannosidase II (346)

Human (Homo sapiens) (76)

3baxA02

A:404-496

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

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.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
		AZI	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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	Cis Peptide Bonds
		Asn A:53 - Pro A:54	[ RasMol ]
		Val A:129 - Pro A:130	[ RasMol ]

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	3bax
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	AMYP_HUMAN \| P04746
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	3.2.1.1
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1bsi	WILD-TYPE HPA EXPRESSED IN PICHIA PASTORIS.
1cpu	WILD-TYPE HPA IN COMPLEX WITH ACARBOSE.
1hny	WILD-TYPE HPA ISOLATED FROM PANCREATIC TISSUE.
2qmk	WILD-TYPE HPA IN COMPLEX WITH NITRITE.
2qv4	WILD-TYPE HPA IN COMPLEX WITH NITRITE AND ACARBOSE.
3bai	WILD-TYPE HPA IN COMPLEX WITH NITRATE
3baj	WILD-TYPE HPA IN COMPLEX WITH NITRATE AND ACARBOSE
3bak	N298S VARIANT HPA IN COMPLEX WITH NITRATE
3baw	WILD-TYPE HPA IN COMPLEX WITH AZIDE
3bay

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 9)

Sites (7, 7)

SS Bonds (5, 5)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 2)

CATH Domains (2, 2)

Pfam Domains (0, 0)

Gene Ontology (15, 15)

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Related Entries Specified in the PDB File