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(-) Description

Title :  STRUCTURE OF HUMAN ADENYLATE KINASE 3 LIKE 1
 
Authors :  J. Choe, A. Atanassova, C. Arrowsmith, A. Edwards, M. Sundstrom, A. Bochkarev, H. Park, Structural Genomics Consortium (Sgc)
Date :  14 Apr 05  (Deposition) - 17 May 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.48
Chains :  Asym./Biol. Unit :  A
Keywords :  Atp:Amp Phosphotransferase, Myokinase, Structural Genomics, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Atanassova, J. Choe, C. Arrowsmith, A. Edwards, M. Sundstrom, A. Bochkarev, H. Park
Structure Of Human Adenylate Kinase 3 Like 1
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1
    ChainsA
    EC Number2.7.4.10
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET28
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneAK3L1, AKL3L
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymAK3, ADENYLATE KINASE 3 ALPHA LIKE 1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1ZD8)

(-) Sites  (0, 0)

(no "Site" information available for 1ZD8)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1ZD8)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Phe A:91 -Pro A:92

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ZD8)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADENYLATE_KINASEPS00113 Adenylate kinase signature.KAD3_HUMAN87-98  1A:86-97

(-) Exons   (5, 5)

Asymmetric/Biological Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000003818092aENSE00001914265chr9:4741318-4740937382KAD3_HUMAN1-51511A:6-5045
1.3ENST000003818093ENSE00001668355chr9:4722625-4722506120KAD3_HUMAN51-91411A:50-9041
1.4ENST000003818094ENSE00000982089chr9:4719307-4719135173KAD3_HUMAN91-148581A:90-14758
1.5ENST000003818095ENSE00000982090chr9:4718537-4718419119KAD3_HUMAN149-188401A:148-18740
1.6cENST000003818096cENSE00001929396chr9:4713096-47111551942KAD3_HUMAN188-227401A:187-21731

(-) 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
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Chain A from PDB  Type:PROTEIN  Length:212
 aligned with KAD3_HUMAN | Q9UIJ7 from UniProtKB/Swiss-Prot  Length:227

    Alignment length:212
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216  
           KAD3_HUMAN     7 LLRAVIMGAPGSGKGTVSSRITTHFELKHLSSGDLLRDNMLRGTEIGVLAKAFIDQGKLIPDDVMTRLALHELKNLTQYSWLLDGFPRTLPQAEALDRAYQIDTVINLNVPFEVIKQRLTARWIHPASGRVYNIEFNPPKTVGIDDLTGEPLIQREDDKPETVIKRLKAYEDQTKPVLEYYQKKGVLETFSGTETNKIWPYVYAFLQTKVPQ 218
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1zd8A00 A:6-217 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                 CATH domains
           Pfam domains (1) -----ADK-1zd8A01 A:11-191                                                                                                                                                                 -------------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------ADK_lid-1zd8A02 A:127-162           ------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ..eeeeee....hhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.....eeee....hhhhhhhhhh.....eeeeee.hhhhhhhhhh.eeee....eeee.....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------ADENYLATE_KI------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: A:6-50 UniProt: 1-51         ---------------------------------------Exon 1.4  PDB: A:90-147 UniProt: 91-148                   Exon 1.5  PDB: A:148-187                ------------------------------ Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------Exon 1.3  PDB: A:50-90 UniProt: 51-91    ------------------------------------------------------------------------------------------------Exon 1.6c  PDB: A:187-217       Transcript 1 (2)
                 1zd8 A   6 LLRAVIMGAPGSGKGTVSSRITTHFELKHLSSGDLLRDNMLRGTEIGVLAKAFIDQGKLIPDDVMTRLALHELKNLTQYSWLLDGFPRTLPQAEALDRAYQIDTVINLNVPFEVIKQRLTARWIHPASGRVYNIEFNPPKTVGIDDLTGEPLIQREDDKPETVIKRLKAYEDQTKPVLEYYQKKGVLETFSGTETNKIWPYVYAFLQTKVPQ 217
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215  

   Legend:   → Mismatch (orange background)
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  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  (0, 0)

(no "SCOP Domain" information available for 1ZD8)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (KAD3_HUMAN | Q9UIJ7)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0004017    adenylate kinase activity    Catalysis of the reaction: ATP + AMP = 2 ADP.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0019205    nucleobase-containing compound kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP or GTP, to a nucleobase, nucleoside, nucleotide or polynucleotide substrate.
    GO:0046899    nucleoside triphosphate adenylate kinase activity    Catalysis of the reaction: nucleoside triphosphate + AMP = nucleoside diphosphate + ADP.
    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:0016776    phosphotransferase activity, phosphate group as acceptor    Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to a phosphate group (acceptor).
    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: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:0006172    ADP biosynthetic process    The chemical reactions and pathways resulting in the formation of ADP, adenosine 5'-diphosphate.
    GO:0046033    AMP metabolic process    The chemical reactions and pathways involving AMP, adenosine monophosphate.
    GO:0046039    GTP metabolic process    The chemical reactions and pathways involving GTP, guanosine triphosphate.
    GO:0046041    ITP metabolic process    The chemical reactions and pathways involving ITP, inosine triphosphate.
    GO:0046051    UTP metabolic process    The chemical reactions and pathways involving UTP, uridine (5'-)triphosphate.
    GO:0007596    blood coagulation    The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
    GO:0006139    nucleobase-containing compound metabolic process    Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
    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.
cellular component
    GO:0005759    mitochondrial matrix    The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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    Phe A:91 - Pro A:92   [ RasMol ]  
 

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