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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN BETA SECRETASE COMPLEXED WITH IXS
 
Authors :  S. Munshi
Date :  16 Aug 07  (Deposition) - 22 Apr 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Aspartyl Protease, Bace, Alternative Splicing, Glycoprotein, Hydrolase, Membrane, Transmembrane, Zymogen (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. A. Coburn, S. J. Stachel, K. G. Jones, T. G. Steele, D. M. Rush, J. Dimuzio, B. L. Pietrak, M. T. Lai, Q. Huang, J. Lineberger, L. Jin, S. Munshi, K. M. Holloway, A. Espeseth, A. Simon, D. Hazuda, S. L. Graham, J. P. Vacca
Bace-1 Inhibition By A Series Of Psi[Ch2Nh] Reduced Amide Isosteres
Bioorg. Med. Chem. Lett. V. 16 3635 2006
PubMed-ID: 16690314  |  Reference-DOI: 10.1016/J.BMCL.2006.04.076
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BETA-SECRETASE 1
    ChainsA
    EC Number3.4.23.46
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET11A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 43-446
    GeneBACE1, BACE
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymBETA-SITE APP CLEAVING ENZYME 1, BETA-SITE AMYLOID PROTEIN CLEAVING ENZYME 1, MEMBRANE-ASSOCIATED ASPARTIC PROTEASE 2, MEMAPSIN-2, ASPARTYL PROTEASE 2, ASP 2, ASP2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1IXS1Ligand/IonN-[(1S)-1-BENZYL-2-{[(1S)-2-(ISOBUTYLAMINO)-1-METHYL-2-OXOETHYL]AMINO}ETHYL]-N'-[(1R)-1-(4-FLUOROPHENYL)ETHYL]-5-[METHYL(METHYLSULFONYL)AMINO]ISOPHTHALAMIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:11 , GLN A:12 , GLY A:13 , TYR A:14 , LEU A:30 , ASP A:32 , GLY A:34 , PRO A:70 , TYR A:71 , THR A:72 , GLN A:73 , PHE A:108 , TRP A:115 , TYR A:198 , ASP A:228 , SER A:229 , GLY A:230 , THR A:231 , THR A:232 , ASN A:233 , ARG A:235 , SER A:325 , ALA A:335 , HOH A:604BINDING SITE FOR RESIDUE IXS A 449

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:155 -A:359
2A:217 -A:382
3A:269 -A:319

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ser A:22 -Pro A:23
2Arg A:128 -Pro A:129
3Tyr A:222 -Asp A:223
4Gly A:372 -Pro A:373

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_060692V265ABACE1_HUMANPolymorphism28989503AV204A

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEPTIDASE_A1PS51767 Peptidase family A1 domain profile.BACE1_HUMAN75-416  1A:14-355
2ASP_PROTEASEPS00141 Eukaryotic and viral aspartyl proteases active site.BACE1_HUMAN90-101  1A:29-40

(-) Exons   (9, 9)

Asymmetric/Biological Unit (9, 9)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003130051bENSE00002169377chr11:117186972-117186251722BACE1_HUMAN1-87871A:444-26 (gaps)32
1.2dENST000003130052dENSE00001779698chr11:117167677-11716758989BACE1_HUMAN88-117301A:27-5630
1.4cENST000003130054cENSE00001602221chr11:117166063-117165847217BACE1_HUMAN117-189731A:56-12873
1.5bENST000003130055bENSE00001732292chr11:117164724-117164587138BACE1_HUMAN190-235461A:129-174 (gaps)46
1.6bENST000003130056bENSE00001231658chr11:117163904-117163770135BACE1_HUMAN236-280451A:175-21945
1.7cENST000003130057cENSE00001053358chr11:117162529-117162428102BACE1_HUMAN281-314341A:220-25334
1.8bENST000003130058bENSE00001053366chr11:117161765-117161616150BACE1_HUMAN315-364501A:254-30350
1.9dENST000003130059dENSE00001385289chr11:117161375-117161204172BACE1_HUMAN365-422581A:304-361 (gaps)58
1.10fENST0000031300510fENSE00002041784chr11:117160523-1171564024122BACE1_HUMAN422-501801A:361-38525

(-) 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:375
 aligned with BACE1_HUMAN | P56817 from UniProtKB/Swiss-Prot  Length:501

    Alignment length:390
                                    66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446
          BACE1_HUMAN    57 RGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYN 446
               SCOP domains d2qzla_ A: beta-secretase (memapsin)                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------2qzlA01 A:14-146 Acid Proteases                                                                                                      2qzlA02 A:1           47-385 Acid Proteases                                                                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhh..eee......eeeeee....eeeeeeee.....eeee...........hhhhh...eeeeeeeeee....eeeeeeeeeeee........eeeeeeeeeeee..........eeee..hhhhh.......hhhhhhhhhh.....eeeeee..-----------.eeeeeee...hhh.eeeeeeeee.......ee.eeeeee..ee...hhhhhh...eee......eeeehhhhhhhhhhhhhhh.....hhhhhh....eeee....hhhhh..eeeeee.....eeeeeeehhhhheeee.----..eeeeee.eeee...eeehhhhhh.eeeeeehhh.eeeeeee...........eeeeeee..hhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------PEPTIDASE_A1  PDB: A:14-355 UniProt: 75-416                                                                                                                                                                                                                                                                                                           ------------------------------ PROSITE (1)
                PROSITE (2) ---------------------------------ASP_PROTEASE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1b  PDB: A:444-26 (gaps)Exon 1.2d  PDB: A:27-56       ------------------------------------------------------------------------Exon 1.5b  PDB: A:129-174 (gaps)              Exon 1.6b  PDB: A:175-219 UniProt: 236-280   Exon 1.7c  PDB: A:220-253         Exon 1.8b  PDB: A:254-303 UniProt: 315-364        ---------------------------------------------------------Exon 1.10f  PDB: A:361-38 Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------Exon 1.4c  PDB: A:56-128 UniProt: 117-189                                -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9d  PDB: A:304-361 (gaps) UniProt: 365-422         ------------------------ Transcript 1 (2)
                 2qzl A 444 RGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGAWAGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGA-----------SVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVE----SQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYN 385
                                ||   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155 |       -   |   175       185       195       205       215       225       235       245       255       265       275       285       295       305    |  315       325       335       345       355       365       375       385
                              448|                                                                                                                                                         157         169                                                                                                                                          310  315                                                                      
                                 1                                                                                                                                                                                                                                                                                                                                                                                                

   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  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2QZL)

(-) Gene Ontology  (30, 30)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (BACE1_HUMAN | P56817)
molecular function
    GO:0001540    amyloid-beta binding    Interacting selectively and non-covalently with amyloid-beta peptide/protein and/or its precursor.
    GO:0004190    aspartic-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
    GO:0008798    beta-aspartyl-peptidase activity    Catalysis of the cleavage of a beta-linked aspartic residue from the N-terminus of a polypeptide.
    GO:0004175    endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    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:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    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:0050435    amyloid-beta metabolic process    The chemical reactions and pathways involving amyloid-beta, a glycoprotein associated with Alzheimer's disease, and its precursor, amyloid precursor protein (APP).
    GO:0044267    cellular protein metabolic process    The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
    GO:0006509    membrane protein ectodomain proteolysis    The proteolytic cleavage of transmembrane proteins and release of their ectodomain (extracellular domain).
    GO:0030163    protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0070931    Golgi-associated vesicle lumen    The volume enclosed by the membrane of a Golgi-associated vesicle.
    GO:0030424    axon    The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0030659    cytoplasmic vesicle membrane    The lipid bilayer surrounding a cytoplasmic vesicle.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005788    endoplasmic reticulum lumen    The volume enclosed by the membranes of the endoplasmic reticulum.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0010008    endosome membrane    The lipid bilayer surrounding an endosome.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005770    late endosome    A prelysosomal endocytic organelle differentiated from early endosomes by lower lumenal pH and different protein composition. Late endosomes are more spherical than early endosomes and are mostly juxtanuclear, being concentrated near the microtubule organizing center.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005771    multivesicular body    A type of endosome in which regions of the limiting endosomal membrane invaginate to form internal vesicles; membrane proteins that enter the internal vesicles are sequestered from the cytoplasm.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0005802    trans-Golgi network    The network of interconnected tubular and cisternal structures located within the Golgi apparatus on the side distal to the endoplasmic reticulum, from which secretory vesicles emerge. The trans-Golgi network is important in the later stages of protein secretion where it is thought to play a key role in the sorting and targeting of secreted proteins to the correct destination.

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 Related Entries

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

UniProtKB/Swiss-Prot
        BACE1_HUMAN | P568171fkn 1m4h 1py1 1sgz 1tqf 1ujj 1ujk 1w50 1w51 1xn2 1xn3 1xs7 1ym2 1ym4 2b8l 2b8v 2f3e 2f3f 2fdp 2g94 2hiz 2hm1 2iqg 2irz 2is0 2ntr 2oah 2of0 2ohk 2ohl 2ohm 2ohn 2ohp 2ohq 2ohr 2ohs 2oht 2ohu 2p4j 2p83 2p8h 2ph6 2ph8 2q11 2q15 2qk5 2qmd 2qmf 2qmg 2qp8 2qu2 2qu3 2qzk 2va5 2va6 2va7 2vie 2vij 2viy 2viz 2vj6 2vj7 2vj9 2vkm 2vnm 2vnn 2wez 2wf0 2wf1 2wf2 2wf3 2wf4 2wjo 2xfi 2xfj 2xfk 2zdz 2ze1 2zhr 2zhs 2zht 2zhu 2zhv 2zjh 2zji 2zjj 2zjk 2zjl 2zjm 2zjn 3bra 3buf 3bug 3buh 3cib 3cic 3cid 3ckp 3ckr 3dm6 3duy 3dv1 3dv5 3exo 3fkt 3h0b 3hvg 3hw1 3i25 3igb 3in3 3in4 3ind 3ine 3inf 3inh 3ivh 3ivi 3ixj 3ixk 3k5c 3k5d 3k5f 3k5g 3kmx 3kmy 3kn0 3kyr 3l38 3l3a 3l58 3l59 3l5b 3l5c 3l5d 3l5e 3l5f 3lhg 3lnk 3lpi 3lpj 3lpk 3msj 3msk 3msl 3n4l 3nsh 3ohf 3ohh 3ooz 3pi5 3qbh 3qi1 3r1g 3r2f 3rsv 3rsx 3rth 3rtm 3rtn 3ru1 3rvi 3s2o 3s7l 3s7m 3skf 3skg 3tpj 3tpl 3tpp 3tpr 3u6a 3udh 3udj 3udk 3udm 3udn 3udp 3udq 3udr 3udy 3ufl 3uqp 3uqr 3uqu 3uqw 3uqx 3veu 3vf3 3vg1 3vv6 3vv7 3vv8 3wb4 3wb5 3zmg 3zov 4acu 4acx 4azy 4b00 4b05 4b0q 4b1c 4b1d 4b1e 4b70 4b72 4b77 4b78 4bek 4bfd 4d83 4d85 4d88 4d89 4d8c 4dh6 4di2 4dju 4djv 4djw 4djx 4djy 4dpf 4dpi 4dus 4dv9 4dvf 4ewo 4exg 4fco 4fgx 4fm7 4fm8 4fri 4frj 4frk 4frs 4fs4 4fse 4fsl 4gid 4gmi 4h1e 4h3f 4h3g 4h3i 4h3j 4ha5 4hzt 4i0d 4i0e 4i0f 4i0g 4i0h 4i0i 4i0j 4i0z 4i10 4i11 4i12 4i1c 4ivs 4ivt 4j0p 4j0t 4j0v 4j0y 4j0z 4j17 4j1c 4j1e 4j1f 4j1h 4j1i 4j1k 4joo 4jp9 4jpc 4jpe 4k8s 4k9h 4ke0 4ke1 4l7g 4l7h 4l7j 4lc7 4lxa 4lxk 4lxm 4n00 4pzw 4pzx 4r5n 4r8y 4r91 4r92 4r93 4r95 4rcd 4rce 4rcf 4rrn 4rro 4rrs 4trw 4try 4trz 4wtu 4wy1 4wy6 4x2l 4x7i 4xkx 4xxs 4ybi 4zpe 4zpf 4zpg 4zsm 4zsp 4zsq 4zsr 5clm 5dqc 5enk 5enm 5ezx 5ezz 5f00 5f01 5hd0 5hdu 5hdv 5hdx 5hdz 5he4 5he5 5he7 5htz 5hu0 5hu1 5i3v 5i3w 5i3x 5i3y 5ie1 5kqf 5kr8 5t1u 5t1w 5tol 5uyu 5v0n

(-) Related Entries Specified in the PDB File

2qzk SAME PROTEIN COMPLEXED WITH I21