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(-) Description

Title :  STRUCTURE OF HUMAN ADENOSINE KINASE AT 1.50 ANGSTROMS
 
Authors :  I. I. Mathews, M. D. Erion, S. E. Ealick
Date :  13 Oct 98  (Deposition) - 13 Oct 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Human Adenosine Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  I. I. Mathews, M. D. Erion, S. E. Ealick
Structure Of Human Adenosine Kinase At 1. 5 A Resolution.
Biochemistry V. 37 15607 1998
PubMed-ID: 9843365  |  Reference-DOI: 10.1021/BI9815445
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (ADENOSINE KINASE)
    ChainsA
    EC Number2.7.1.20
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21[DE3], B834[DE3]
    Expression System Taxid562
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsNATIVE PROTEIN WAS EXPRESSED IN BL21[DE3] CELLS SELENO METHIONINE PROTEIN IN B834[DE3] CELLS

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1ADN2Ligand/IonADENOSINE
2CL2Ligand/IonCHLORIDE ION
3MG3Ligand/IonMAGNESIUM ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:14 , THR A:66 , ADN A:350BINDING SITE FOR RESIDUE CL A 380
2AC2SOFTWARETHR A:265 , HOH A:556 , HOH A:746BINDING SITE FOR RESIDUE CL A 385
3AC3SOFTWAREHOH A:746 , HOH A:747 , HOH A:748 , HOH A:749 , HOH A:750 , HOH A:751BINDING SITE FOR RESIDUE MG A 360
4AC4SOFTWAREASP A:130 , ASN A:131 , HOH A:752 , HOH A:753 , HOH A:754 , HOH A:755BINDING SITE FOR RESIDUE MG A 365
5AC5SOFTWARESER A:32 , HOH A:402 , HOH A:756 , HOH A:757 , HOH A:758 , HOH A:759BINDING SITE FOR RESIDUE MG A 375
6AC6SOFTWAREASN A:14 , ASP A:18 , LEU A:40 , GLY A:64 , SER A:65 , ASN A:68 , PHE A:170 , ASN A:296 , GLY A:297 , ASP A:300 , CL A:380 , HOH A:415 , HOH A:416 , HOH A:430BINDING SITE FOR RESIDUE ADN A 350
7AC7SOFTWARETHR A:265 , GLY A:267 , ARG A:268 , THR A:271 , ASP A:286 , GLN A:289 , ILE A:292 , ALA A:298 , GLY A:299 , HIS A:324 , ALA A:327 , ILE A:331 , HOH A:408 , HOH A:410 , HOH A:420 , HOH A:425 , HOH A:577 , HOH A:597 , HOH A:637BINDING SITE FOR RESIDUE ADN A 355
8ADAAUTHORADN A:350ADN 350 BINDS IN THE SUBSTRATE BINDING SITE.
9ADBAUTHORADN A:355ADN 355 BINDS IN THE ATP BINDING SITE.

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1BX4)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gln A:79 -Pro A:80

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

Asymmetric/Biological Unit (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_066640G30EADK_HUMANDisease (HMAKD)397514454AG13E
2UniProtVAR_066641D235AADK_HUMANDisease (HMAKD)397514453AD218A
3UniProtVAR_066642A318EADK_HUMANDisease (HMAKD)397514452AA301E

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PFKB_KINASES_2PS00584 pfkB family of carbohydrate kinases signature 2.ADK_HUMAN311-324  1A:294-307

(-) Exons   (11, 11)

Asymmetric/Biological Unit (11, 11)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002866211aENSE00001248887chr10:75910987-75911101115ADK_HUMAN1-22221A:4-52
1.4ENST000002866214ENSE00001248864chr10:75960522-7596059675ADK_HUMAN22-47261A:5-3026
1.5ENST000002866215ENSE00001248860chr10:75984296-7598434954ADK_HUMAN47-65191A:30-4819
1.6ENST000002866216ENSE00001178540chr10:76074425-7607450379ADK_HUMAN65-91271A:48-7427
1.7ENST000002866217ENSE00001024568chr10:76153899-76154071173ADK_HUMAN92-149581A:75-13258
1.8ENST000002866218ENSE00001024570chr10:76158229-76158337109ADK_HUMAN149-185371A:132-16837
1.9aENST000002866219aENSE00001310865chr10:76285014-76285184171ADK_HUMAN186-242571A:169-22557
1.11ENST0000028662111ENSE00001248835chr10:76349040-7634907536ADK_HUMAN243-254121A:226-23712
1.12ENST0000028662112ENSE00001248829chr10:76360137-76360251115ADK_HUMAN255-293391A:238-27639
1.13ENST0000028662113ENSE00001248825chr10:76429941-7643002787ADK_HUMAN293-322301A:276-30530
1.14aENST0000028662114aENSE00001879300chr10:76468079-76468233155ADK_HUMAN322-362411A:305-34541

(-) 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:342
 aligned with ADK_HUMAN | P55263 from UniProtKB/Swiss-Prot  Length:362

    Alignment length:342
                                    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  
            ADK_HUMAN    21 LRENILFGMGNPLLDISAVVDKDFLDKYSLKPNDQILAEDKHKELFDELVKKFKVEYHAGGSTQNSIKVAQWMIQQPHKAATFFGCIGIDKFGEILKRKAAEAHVDAHYYEQNEQPTGTCAACITGDNRSLIANLAAANCYKKEKHLDLEKNWMLVEKARVCYIAGFFLTVSPESVLKVAHHASENNRIFTLNLSAPFISQFYKESLMKVMPYVDILFGNETEAATFAREQGFETKDIKEIAKKTQALPKMNSKRQRIVIFTQGRDDTIMATESEVTAFAVLDQDQKEIIDTNGAGDAFVGGFLSQLVSDKPLTECIRAGHYAASIIIRRTGCTFPEKPDFH 362
               SCOP domains d1bx4a_ A: Adenosine kinase                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1bx4A01      1bx4A02 A:17-62,A:121-137                     1bx4A01 A:4-16,A:63-120,A:138-345                         1bx4A02          1bx4A01 A:4-16,A:63-120,A:138-345  [code=3.40.1190.20, no name defined]                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeee...eeeeeee..hhhhhh......eeee..hhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhh......eeeeeeee..hhhhhhhhhhhh...eeeeeee......eeeeeee..eeeeeee.hhhhh..hhh....hhhhhhhhh..eeeeehhhhh..hhhhhhhhhhhhh...eeeee...hhhhhh.hhhhhhhhhh..eeeeehhhhhhhhhh.......hhhhhhhhh...........eeeee.....eeee....eeee............hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ---------E------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A----------------------------------------------------------------------------------E-------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PFKB_KINASES_2-------------------------------------- PROSITE
           Transcript 1 (1) 1.------------------------Exon 1.5           --------------------------Exon 1.7  PDB: A:75-132 UniProt: 92-149                   ------------------------------------Exon 1.9a  PDB: A:169-225 UniProt: 186-242               Exon 1.11   Exon 1.12  PDB: A:238-276              ----------------------------Exon 1.14a  PDB: A:305-345                Transcript 1 (1)
           Transcript 1 (2) -Exon 1.4  PDB: A:5-30     -----------------Exon 1.6  PDB: A:48-74     ---------------------------------------------------------Exon 1.8  PDB: A:132-168             -----------------------------------------------------------------------------------------------------------Exon 1.13  PDB: A:276-305     ---------------------------------------- Transcript 1 (2)
                 1bx4 A   4 VRENILFGMGNPLLDISAVVDKDFLDKYSLKPNDQILAEDKHKELFDELVKKFKVEYHAGGSTQNSIKVAQWMIQQPHKAATFFGCIGIDKFGEILKRKAAEAHVDAHYYEQNEQPTGTCAACITGDNRSLIANLAAANCYKKEKHLDLEKNWMLVEKARVCYIAGFFLTVSPESVLKVAHHASENNRIFTLNLSAPFISQFYKESLMKVMPYVDILFGNETEAATFAREQGFETKDIKEIAKKTQALPKMNSKRQRIVIFTQGRDDTIMATESEVTAFAVLDQDQKEIIDTNGAGDAFVGGFLSQLVSDKPLTECIRAGHYAASIIIRRTGCTFPEKPDFH 345
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343  

   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1BX4)

(-) Gene Ontology  (23, 23)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ADK_HUMAN | P55263)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004001    adenosine kinase activity    Catalysis of the reaction: ATP + adenosine = ADP + AMP.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0016773    phosphotransferase activity, alcohol group as acceptor    Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor).
    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.
biological process
    GO:0006167    AMP biosynthetic process    The chemical reactions and pathways resulting in the formation of AMP, adenosine monophosphate.
    GO:0044209    AMP salvage    The chemical reactions and pathways resulting in the formation of adenosine monophosphate (AMP) from derivatives of it (either adenine, ADP or adenosine 3',5'-bisphosphate) without de novo synthesis.
    GO:0046085    adenosine metabolic process    The chemical reactions and pathways involving adenosine, adenine riboside, a ribonucleoside found widely distributed in cells of every type as the free nucleoside and in combination in nucleic acids and various nucleoside coenzymes.
    GO:0032922    circadian regulation of gene expression    Any process that modulates the frequency, rate or extent of gene expression such that an expression pattern recurs with a regularity of approximately 24 hours.
    GO:0006175    dATP biosynthetic process    The chemical reactions and pathways resulting in the formation of dATP, deoxyadenosine triphosphate (2'-deoxyadenosine 5'-triphosphate).
    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:0042102    positive regulation of T cell proliferation    Any process that activates or increases the rate or extent of T cell proliferation.
    GO:0010613    positive regulation of cardiac muscle hypertrophy    Any process that increases the rate, frequency or extent of the enlargement or overgrowth of all or part of the heart due to an increase in size (not length) of individual cardiac muscle fibers, without cell division.
    GO:0006166    purine ribonucleoside salvage    Any process which produces a purine nucleoside from derivatives of it, without de novo synthesis.
    GO:0043101    purine-containing compound salvage    Any process that generates a purine-containing compound, any nucleobase, nucleoside, nucleotide or nucleic acid that contains a purine base, from derivatives of them without de novo synthesis.
    GO:0009156    ribonucleoside monophosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of a ribonucleoside monophosphate, a compound consisting of a nucleobase linked to a ribose sugar esterified with phosphate on the sugar.
    GO:0044342    type B pancreatic cell proliferation    The multiplication or reproduction of pancreatic B cells, resulting in the expansion of an pancreatic B cell population. Pancreatic B cell are cells of the pancreas that secrete insulin.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ADK_HUMAN | P552632i6a 2i6b 4o1l

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1BX4)