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(-) Description

Title :  STRUCTURE OF ADENYLATE KINASE 1 IN COMPLEX WITH P1,P4-DI (ADENOSINE)TETRAPHOSPHATE
 
Authors :  G. Bunkoczi, P. Filippakopoulos, A. Jansson, E. Longman, F. Von Delft A. Edwards, C. Arrowsmith, M. Sundstrom, S. Knapp
Date :  09 Dec 05  (Deposition) - 20 Feb 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.71
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Transferase, Ap4A, Nucleotide Kinase, Transferase Atp-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. Bunkoczi, P. Filippakopoulos, A. Jansson, E. Longman, F. Von Delft, A. Edwards, C. Arrowsmith, M. Sundstrom, J. Weigelt, S. Knapp
Structure Of Adenylate Kinase 1 In Complex With P1, P4-Di(Adenosine)Tetraphosphate
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ADENYLATE KINASE 1
    ChainsA, B
    EC Number2.7.4.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPLIC-SGC
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymATP-AMP TRANSPHOSPHORYLASE, AK1, MYOKINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1B4P2Ligand/IonBIS(ADENOSINE)-5'-TETRAPHOSPHATE
2MLI2Ligand/IonMALONATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1B4P1Ligand/IonBIS(ADENOSINE)-5'-TETRAPHOSPHATE
2MLI1Ligand/IonMALONATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1B4P1Ligand/IonBIS(ADENOSINE)-5'-TETRAPHOSPHATE
2MLI1Ligand/IonMALONATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:17 , GLY A:18 , SER A:19 , GLY A:20 , LYS A:21 , GLY A:22 , THR A:23 , THR A:39 , GLY A:40 , LEU A:43 , ARG A:44 , MET A:61 , GLN A:65 , VAL A:67 , GLY A:94 , TYR A:95 , ARG A:97 , GLN A:101 , ARG A:128 , ARG A:132 , ARG A:138 , ARG A:149 , ARG A:167 , GLY A:177 , SER A:178 , VAL A:179 , HOH A:2040 , HOH A:2065 , HOH A:2159 , HOH A:2179 , HOH A:2180 , HOH A:2181 , HOH A:2182 , HOH A:2183 , HOH A:2184 , HOH A:2185 , HOH A:2186 , HOH A:2187 , HOH A:2189 , HOH A:2190BINDING SITE FOR RESIDUE B4P A1195
2AC2SOFTWAREGLU A:62 , GLY A:137 , ARG A:138 , VAL A:139 , ASP A:140 , HOH A:2191 , HOH B:2120BINDING SITE FOR RESIDUE MLI A1196
3AC3SOFTWAREPRO B:17 , GLY B:18 , SER B:19 , GLY B:20 , LYS B:21 , GLY B:22 , THR B:23 , THR B:39 , GLY B:40 , LEU B:43 , ARG B:44 , MET B:61 , GLN B:65 , VAL B:67 , GLY B:94 , TYR B:95 , ARG B:97 , GLN B:101 , ARG B:128 , ARG B:132 , ARG B:138 , ARG B:149 , ARG B:167 , GLY B:177 , SER B:178 , VAL B:179 , HOH B:2067 , HOH B:2070 , HOH B:2095 , HOH B:2175 , HOH B:2176 , HOH B:2177 , HOH B:2178 , HOH B:2179 , HOH B:2180 , HOH B:2181 , HOH B:2182 , HOH B:2183 , HOH B:2184 , HOH B:2185 , HOH B:2186 , HOH B:2187BINDING SITE FOR RESIDUE B4P B1196
4AC4SOFTWARESER B:58 , MET B:61 , ASP B:140 , HOH B:2189BINDING SITE FOR RESIDUE MLI B1197

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2C95)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Tyr A:95 -Pro A:96
2Tyr B:95 -Pro B:96

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (5, 10)

Asymmetric Unit (5, 10)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_055337G40RKAD1_HUMANDisease (HAAKD)137853204A/BG40R
2UniProtVAR_055338G64RKAD1_HUMANDisease (HAAKD)137853205A/BG64R
3UniProtVAR_034046E123QKAD1_HUMANPolymorphism8192462A/BE123Q
4UniProtVAR_004021R128WKAD1_HUMANDisease (HAAKD)28930974A/BR128W
5UniProtVAR_055340Y164CKAD1_HUMANDisease (HAAKD)137853203A/BY164C

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (5, 5)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_055337G40RKAD1_HUMANDisease (HAAKD)137853204AG40R
2UniProtVAR_055338G64RKAD1_HUMANDisease (HAAKD)137853205AG64R
3UniProtVAR_034046E123QKAD1_HUMANPolymorphism8192462AE123Q
4UniProtVAR_004021R128WKAD1_HUMANDisease (HAAKD)28930974AR128W
5UniProtVAR_055340Y164CKAD1_HUMANDisease (HAAKD)137853203AY164C

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (5, 5)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_055337G40RKAD1_HUMANDisease (HAAKD)137853204BG40R
2UniProtVAR_055338G64RKAD1_HUMANDisease (HAAKD)137853205BG64R
3UniProtVAR_034046E123QKAD1_HUMANPolymorphism8192462BE123Q
4UniProtVAR_004021R128WKAD1_HUMANDisease (HAAKD)28930974BR128W
5UniProtVAR_055340Y164CKAD1_HUMANDisease (HAAKD)137853203BY164C

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADENYLATE_KINASEPS00113 Adenylate kinase signature.KAD1_HUMAN90-101
 
  2A:90-101
B:90-101
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADENYLATE_KINASEPS00113 Adenylate kinase signature.KAD1_HUMAN90-101
 
  1A:90-101
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADENYLATE_KINASEPS00113 Adenylate kinase signature.KAD1_HUMAN90-101
 
  1-
B:90-101

(-) Exons   (6, 12)

Asymmetric Unit (6, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003731761aENSE00001459734chr9:130640022-130639902121KAD1_HUMAN-00--
1.3aENST000003731763aENSE00002044723chr9:130636928-13063689039KAD1_HUMAN1-332A:1-3
B:2-3
3
2
1.4cENST000003731764cENSE00001604283chr9:130635340-13063530536KAD1_HUMAN3-15132A:3-15
B:3-15
13
13
1.4eENST000003731764eENSE00000729990chr9:130635132-130634969164KAD1_HUMAN15-69552A:15-69
B:15-69
55
55
1.5ENST000003731765ENSE00000729987chr9:130634218-130634102117KAD1_HUMAN70-108392A:70-108
B:70-108
39
39
1.6ENST000003731766ENSE00000729985chr9:130630791-130630600192KAD1_HUMAN109-172642A:109-172
B:109-172
64
64
1.7eENST000003731767eENSE00001459722chr9:130630355-1306287591597KAD1_HUMAN173-194222A:173-194
B:173-194
22
22

(-) Sequences/Alignments

Asymmetric 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:195
 aligned with KAD1_HUMAN | P00568 from UniProtKB/Swiss-Prot  Length:194

    Alignment length:195
                             1                                                                                                                                                                                                 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189     
           KAD1_HUMAN     - -MEEKLKKTKIIFVVGGPGSGKGTQCEKIVQKYGYTHLSTGDLLRSEVSSGSARGKKLSEIMEKGQLVPLETVLDMLRDAMVAKVNTSKGFLIDGYPREVQQGEEFERRIGQPTLLLYVDAGPETMTQRLLKRGETSGRVDDNEETIKKRLETYYKATEPVIAFYEKRGIVRKVNAEGSVDSVFSQVCTHLDALK 194
               SCOP domains d2c95a_ A: automated matches                                                                                                                                                                        SCOP domains
               CATH domains 2c95A00 A:0-194 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh...eeeeee....hhhhhhhhhhhhhh.eeeehhhhhhhhhhh.hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------R-----------------------R----------------------------------------------------------Q----W-----------------------------------C------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ADENYLATE_KI--------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) -1.3-----------Exon 1.4e  PDB: A:15-69 UniProt: 15-69                 Exon 1.5  PDB: A:70-108 UniProt: 70-108Exon 1.6  PDB: A:109-172 UniProt: 109-172                       Exon 1.7e              Transcript 1 (1)
           Transcript 1 (2) ---Exon 1.4c    ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2c95 A   0 SMEEKLKKTNIIFVVGGPGSGKGTQCEKIVQKYGYTHLSTGDLLRSEVSSGSARGKKLSEIMEKGQLVPLETVLDMLRDAMVAKVNTSKGFLIDGYPREVQQGEEFERRIGQPTLLLYVDAGPETMTQRLLKRGETSGRVDDNEETIKKRLETYYKATEPVIAFYEKRGIVRKVNAEGSVDSVFSQVCTHLDALL 194
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189     

Chain B from PDB  Type:PROTEIN  Length:194
 aligned with KAD1_HUMAN | P00568 from UniProtKB/Swiss-Prot  Length:194

    Alignment length:194
                                                                                                                                                                                                                          194 
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191  | 
           KAD1_HUMAN     2 EEKLKKTKIIFVVGGPGSGKGTQCEKIVQKYGYTHLSTGDLLRSEVSSGSARGKKLSEIMEKGQLVPLETVLDMLRDAMVAKVNTSKGFLIDGYPREVQQGEEFERRIGQPTLLLYVDAGPETMTQRLLKRGETSGRVDDNEETIKKRLETYYKATEPVIAFYEKRGIVRKVNAEGSVDSVFSQVCTHLDALK-   -
               SCOP domains d2c95b_ B: automated matches                                                                                                                                                                       SCOP domains
               CATH domains 2c95B00 B:2-195 P-loop containing nucleotide triphosphate hydrolases                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh..eeeeee....hhhhhhhhhhhhhh.eeeehhhhhhhhhhh.hhhhhhhhhhhhh....hhhhhhhhhhhhhhh.......eeee....hhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------R-----------------------R----------------------------------------------------------Q----W-----------------------------------C------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------ADENYLATE_KI---------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.-----------Exon 1.4e  PDB: B:15-69 UniProt: 15-69                 Exon 1.5  PDB: B:70-108 UniProt: 70-108Exon 1.6  PDB: B:109-172 UniProt: 109-172                       Exon 1.7e             - Transcript 1 (1)
           Transcript 1 (2) -Exon 1.4c    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 2c95 B   2 EEKLKKTNIIFVVGGPGSGKGTQCEKIVQKYGYTHLSTGDLLRSEVSSGSARGKKLSEIMEKGQLVPLETVLDMLRDAMVAKVNTSKGFLIDGYPREVQQGEEFERRIGQPTLLLYVDAGPETMTQRLLKRGETSGRVDDNEETIKKRLETYYKATEPVIAFYEKRGIVRKVNAEGSVDSVFSQVCTHLDALLN 195
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191    

   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, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2C95)

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (KAD1_HUMAN | P00568)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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:0004550    nucleoside diphosphate kinase activity    Catalysis of the reaction: ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.
    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: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:0046034    ATP metabolic process    The chemical reactions and pathways involving ATP, adenosine triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0007050    cell cycle arrest    A regulatory process that halts progression through the cell cycle during one of the normal phases (G1, S, G2, M).
    GO:0006139    nucleobase-containing compound metabolic process    Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
    GO:0015949    nucleobase-containing small molecule interconversion    The chemical reactions and pathways by which a nucleobase, nucleoside or nucleotide small molecule is synthesized from another nucleobase, nucleoside or nucleotide small molecule.
    GO:0006165    nucleoside diphosphate phosphorylation    The process of introducing a phosphate group into a nucleoside diphosphate to produce a nucleoside triphosphate.
    GO:0009142    nucleoside triphosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of a nucleoside triphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with triphosphate on the sugar.
    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: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: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:0001520    outer dense fiber    A supramolecular fiber found in the flagella of mammalian sperm that surrounds the nine microtubule doublets. These dense fibers are stiff and noncontractile. In human, they consist of about 10 major and at least 15 minor proteins, where all major proteins are ODF1, ODF2 or ODF2-related proteins.
    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:0036126    sperm flagellum    A microtubule-based flagellum (or cilium) that is part of a sperm, a mature male germ cell that develops from a spermatid.

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 Related Entries

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

UniProtKB/Swiss-Prot
        KAD1_HUMAN | P005681z83

(-) Related Entries Specified in the PDB File

1z83 CRYSTAL STRUCTURE OF HUMAN AK1A IN COMPLEX WITH AP5A