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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ANAPLASTIC LYMPHOMA KINASE CATALYTIC DOMAIN
 
Authors :  C. Lee
Date :  05 Jan 10  (Deposition) - 28 Jul 10  (Release) - 08 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Kinase Domain, Atp-Binding, Glycoprotein, Kinase, Membrane, Nucleotide-Binding, Phosphoprotein, Proto-Oncogene, Receptor, Transferase, Transmembrane, Tyrosine-Protein Kinase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. C. Lee, Y. Jia, N. Li, X. Sun, K. Ng, E. Ambing, M. Y. Gao, S. Hua, C. Chen S. Kim, P. Y. Michellys, S. A. Lesley, J. L. Harris, G. Spraggon
Crystal Structure Of The Alk (Anaplastic Lymphoma Kinase) Catalytic Domain.
Biochem. J. V. 430 425 2010
PubMed-ID: 20632993  |  Reference-DOI: 10.1042/BJ20100609

(-) Compounds

Molecule 1 - ANAPLASTIC LYMPHOMA KINASE
    ChainsA
    EC Number2.7.10.1
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System CommonFALL ARMYWORM
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS
    FragmentCATALYTIC DOMAIN RESIDUES 1072-1410
    GeneALK
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymALK TYROSINE KINASE RECEPTOR

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:28 , HOH A:130 , LEU A:1122 , ALA A:1148 , MET A:1199 , GLY A:1202BINDING SITE FOR RESIDUE GOL A 1
2AC2SOFTWAREPHE A:1245 , ILE A:1246 , ARG A:1248 , ALA A:1274 , TYR A:1278BINDING SITE FOR RESIDUE GOL A 1411
3AC3SOFTWAREHOH A:30 , HOH A:132 , HOH A:181 , SER A:1172 , PHE A:1174 , ASN A:1175 , ARG A:1181 , CYS A:1182 , GOL A:1413BINDING SITE FOR RESIDUE GOL A 1412
4AC4SOFTWAREHOH A:132 , HOH A:165 , SER A:1172 , LYS A:1173 , ASN A:1175 , GOL A:1412BINDING SITE FOR RESIDUE GOL A 1413

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3L9P)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:1190 -Pro A:1191

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (20, 20)

Asymmetric/Biological Unit (20, 20)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_041486G1121DALK_HUMANPolymorphism55760835AG1121D
02UniProtVAR_063851G1128AALK_HUMANDisease (NBLST3)113994088AG1128A
03UniProtVAR_063852T1151MALK_HUMANDisease (NBLST3)113994091AT1151M
04UniProtVAR_063853M1166RALK_HUMANDisease (NBLST3)  ---AM1166R
05UniProtVAR_063854I1171NALK_HUMANDisease (NBLST3)  ---AI1171N
06UniProtVAR_063855F1174CALK_HUMANDisease (NBLST3)  ---AF1174C
07UniProtVAR_063856F1174IALK_HUMANDisease (NBLST3)  ---AF1174I
08UniProtVAR_063857F1174LALK_HUMANDisease (NBLST3)863225281AF1174L
09UniProtVAR_063858F1174VALK_HUMANDisease (NBLST3)281864719AF1174V
10UniProtVAR_063859R1192PALK_HUMANDisease (NBLST3)113994089AR1192P
11UniProtVAR_063860A1234TALK_HUMANDisease (NBLST3)  ---AA1234T
12UniProtVAR_063861F1245CALK_HUMANDisease (NBLST3)863225283AF1245C
13UniProtVAR_063862F1245VALK_HUMANDisease (NBLST3)281864720AF1245V
14UniProtVAR_063863I1250TALK_HUMANDisease (NBLST3)113994092AI1250T
15UniProtVAR_041487A1274TALK_HUMANPolymorphism45502292AA1274T
16UniProtVAR_063864R1275LALK_HUMANUnclassified  ---AR1275L
17UniProtVAR_063865R1275QALK_HUMANDisease (NBLST3)113994087AR1275Q
18UniProtVAR_063866Y1278SALK_HUMANDisease (NBLST3)863225285AY1278S
19UniProtVAR_041488M1328LALK_HUMANPolymorphism56160491AM1328L
20UniProtVAR_055987F1376SALK_HUMANPolymorphism17694720AF1376S

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.ALK_HUMAN1122-1150  1A:1122-1150
2PROTEIN_KINASE_TYRPS00109 Tyrosine protein kinases specific active-site signature.ALK_HUMAN1245-1257  1A:1245-1257
3RECEPTOR_TYR_KIN_IIPS00239 Receptor tyrosine kinase class II signature.ALK_HUMAN1276-1284  1A:1276-1284

(-) Exons   (0, 0)

(no "Exon" information available for 3L9P)

(-) 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:303
 aligned with ALK_HUMAN | Q9UM73 from UniProtKB/Swiss-Prot  Length:1620

    Alignment length:308
                                  1102      1112      1122      1132      1142      1152      1162      1172      1182      1192      1202      1212      1222      1232      1242      1252      1262      1272      1282      1292      1302      1312      1322      1332      1342      1352      1362      1372      1382      1392        
           ALK_HUMAN   1093 NPNYCFAGKTSSISDLKEVPRKNITLIRGLGHGAFGEVYEGQVSGMPNDPSPLQVAVKTLPEVCSEQDELDFLMEALIISKFNHQNIVRCIGVSLQSLPRFILLELMAGGDLKSFLRETRPRPSQPSSLAMLDLLHVARDIACGCQYLEENHFIHRDIAARNCLLTCPGPGRVAKIGDFGMARDIYRASYYRKGGCAMLPVKWMPPEAFMEGIFTSKTDTWSFGVLLWEIFSLGYMPYPSKSNQEVLEFVTSGGRMDPPKNCPGPVYRIMTQCWQHQPEDRPNFAIILERIEYCTQDPDVINTALPIE 1400
               SCOP domains d3l9pa_ A: automated matches                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------Pkinase_Tyr-3l9pA01 A:     1116-1383                                                                                                                                                                                                                                        ----------------- Pfam domains
         Sec.struct. author ...eee..eeehhhhh...hhh.eeeeee........eeeeee..-----..eeeeeee.....hhhhhhhhhhhhhhhhhh.......eeeee......eeeee....eehhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee........eee..hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
             SAPs(SNPs) (1) ----------------------------D------A----------------------M--------------R----N--C-----------------P-----------------------------------------T----------C----T-----------------------TL--S-------------------------------------------------L-----------------------------------------------S------------------------ SAPs(SNPs) (1)
             SAPs(SNPs) (2) ---------------------------------------------------------------------------------I----------------------------------------------------------------------V-----------------------------Q----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) ---------------------------------------------------------------------------------L---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (3)
             SAPs(SNPs) (4) ---------------------------------------------------------------------------------V---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (4)
                    PROSITE -----------------------------PROTEIN_KINASE_ATP           ----------------------------------------------------------------------------------------------PROTEIN_KINAS------------------RECEPTOR_-------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3l9p A 1093 NPNYCFAGKTSSISDLKEVPRKNITLIRGLGHGAFGEVYEGQVSG-----SPLQVAVKTLPEVCSEQDELDFLMEALIISKFNHQNIVRCIGVSLQSLPRFILLELMAGGDLKSFLRETRPRPSQPSSLAMLDLLHVARDIACGCQYLEENHFIHRDIAARNCLLTCPGPGRVAKIGDFGMARDIYRAGYYRKGGCAMLPVKWMPPEAFMEGIFTSKTDTWSFGVLLWEIFSLGYMPYPSKSNQEVLEFVTSGGRMDPPKNCPGPVYRIMTQCWQHQPEDRPNFAIILERIEYCTQDPDVINTALPIE 1400
                                  1102      1112      1122      1132    |    -|     1152      1162      1172      1182      1192      1202      1212      1222      1232      1242      1252      1262      1272      1282      1292      1302      1312      1322      1332      1342      1352      1362      1372      1382      1392        
                                                                     1137  1143                                                                                                                                                                                                                                                                 

   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  (0, 0)

(no "CATH Domain" information available for 3L9P)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: PKinase (934)

(-) Gene Ontology  (30, 30)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ALK_HUMAN | Q9UM73)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004704    NF-kappaB-inducing kinase activity    Catalysis of the phosphorylation of the alpha or beta subunit of the inhibitor of kappaB kinase complex (IKK).
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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).
    GO:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0004713    protein tyrosine kinase activity    Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0004714    transmembrane receptor protein tyrosine kinase activity    Combining with a signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity by catalysis of the reaction: ATP + a protein-L-tyrosine = ADP + a protein-L-tyrosine phosphate.
biological process
    GO:0038061    NIK/NF-kappaB signaling    The process in which a signal is passed on to downstream components within the cell through the NIK-dependent processing and activation of NF-KappaB. Begins with activation of the NF-KappaB-inducing kinase (NIK), which in turn phosphorylates and activates IkappaB kinase alpha (IKKalpha). IKKalpha phosphorylates the NF-Kappa B2 protein (p100) leading to p100 processing and release of an active NF-KappaB (p52).
    GO:0000187    activation of MAPK activity    The initiation of the activity of the inactive enzyme MAP kinase (MAPK).
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0048666    neuron development    The process whose specific outcome is the progression of a neuron over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell.
    GO:0018108    peptidyl-tyrosine phosphorylation    The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0051092    positive regulation of NF-kappaB transcription factor activity    Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB.
    GO:0046777    protein autophosphorylation    The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0042981    regulation of apoptotic process    Any process that modulates the occurrence or rate of cell death by apoptotic process.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0007169    transmembrane receptor protein tyrosine kinase signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription.
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: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:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ALK_HUMAN | Q9UM732kup 2kuq 2xb7 2xba 2xp2 2yfx 2yhv 2yjr 2yjs 2ys5 2yt2 3aox 3lcs 3lct 4anl 4anq 4ans 4ccb 4ccu 4cd0 4cli 4clj 4cmo 4cmt 4cmu 4cnh 4ctb 4ctc 4dce 4fnw 4fnx 4fny 4fnz 4fob 4foc 4fod 4joa 4mkc 4tt7 4z55 5a9u 5aa8 5aa9 5aaa 5aab 5aac 5fto 5ftq 5imx 5iug 5iuh 5iui 5j7h 5kz0

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3L9P)