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(-) Description

Title :  CRYSTAL STRUCTURE OF ALPHA-TUBULIN ACETYLTRANSFERASE DOMAIN OF HUMAN MEC-17 IN COMPLEX WITH ACETOACETYL-COA (P21212 FORM)
 
Authors :  S. Yuzawa, H. Sumimoto
Date :  22 Aug 12  (Deposition) - 28 Aug 13  (Release) - 28 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.25
Chains :  Asym./Biol. Unit :  A
Keywords :  Gnat Fold, Acetyltransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Yuzawa, H. Sumimoto
Crystal Structure Of Alpha-Tubulin Acetyltransferase Domain Of Human Mec-17
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ALPHA-TUBULIN N-ACETYLTRANSFERASE
    ChainsA
    EC Number2.3.1.108
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPRSFDUET-1
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentALPHA-TUBULIN ACETYLTRANSFERASE DOMAIN, UNP RESIDUES 1-194
    GeneATAT1, C6ORF134, MEC17, NBLA00487
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymALPHA-TAT, TAT, ACETYLTRANSFERASE MEC-17 HOMOLOG

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1ACO1Ligand/IonACETYL COENZYME *A
2CL3Ligand/IonCHLORIDE ION
3EDO1Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:56 , GLN A:58 , ILE A:121 , ASP A:123 , PHE A:124 , TYR A:125 , ILE A:126 , GLN A:131 , ARG A:132 , HIS A:133 , GLY A:134 , GLY A:136 , ARG A:137 , ASP A:157 , ARG A:158 , SER A:160 , LYS A:162 , LYS A:165 , PHE A:166 , LYS A:169 , HIS A:170 , CL A:202 , HOH A:301 , HOH A:307 , HOH A:308 , HOH A:312 , HOH A:338 , HOH A:346 , HOH A:349 , HOH A:355 , HOH A:395 , HOH A:398 , HOH A:449 , HOH A:506BINDING SITE FOR RESIDUE ACO A 201
2AC2SOFTWAREALA A:57 , GLU A:128 , GLN A:131 , LYS A:162 , ACO A:201 , HOH A:303BINDING SITE FOR RESIDUE CL A 202
3AC3SOFTWAREARG A:69 , MET A:70 , HIS A:75 , LYS A:98BINDING SITE FOR RESIDUE CL A 203
4AC4SOFTWAREGLY A:188 , PHE A:189 , PHE A:190BINDING SITE FOR RESIDUE CL A 204
5AC5SOFTWAREARG A:23 , VAL A:116 , PHE A:189 , PHE A:190 , HIS A:192 , GLN A:193 , HOH A:344 , HOH A:386BINDING SITE FOR RESIDUE EDO A 205

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Arg A:86 -Pro A:87

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3VWD)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GNAT_ATATPS51730 Alpha-tubulin Gcn5-related N-acetyltransferase (GNAT) domain profile.ATAT_HUMAN1-190  1A:1-190

(-) Exons   (0, 0)

(no "Exon" information available for 3VWD)

(-) 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:196
 aligned with ATAT_HUMAN | Q5SQI0 from UniProtKB/Swiss-Prot  Length:421

    Alignment length:244
                             1                                                                                                                                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239    
           ATAT_HUMAN     - -MEFPFDVDALFPERITVLDQHLRPPARRPGTTTPARVDLQQQIMTIIDELGKASAKAQNLSAPITSASRMQSNRHVVYILKDSSARPAGKGAIIGFIKVGYKKLFVLDDREAHNEVEPLCILDFYIHESVQRHGHGRELFQYMLQKERVEPHQLAIDRPSQKLLKFLNKHYNLETTVPQVNNFVIFEGFFAHQHRPPAPSLRATRHSRAAAVDPTPAAPARKLPPKRAEGDIKPYSSSDREFL 243
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhh...eeee...................hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhh..eeeeee........--.eeeeeeeee..eeee.....eeee..eeeeeeee.hhhh..hhhhhhhhhhhhhhh.hhhhheee..hhhhhhhhhhhhh..........ee.....hhhhh----------------------------------------------hhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -GNAT_ATAT  PDB: A:1-190 UniProt: 1-190                                                                                                                                                        ----------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vwd A   0 SMEFPFDVDALFPERITVLDQHLRPPARRPGTTTPARVDLQQQIMTIIDELGKASAKAQNLSAPITSASRMQSNRHVVYILKDSSARPAG--AIIGFIKVGYKKLFVLDDREAHNEVEPLCILDFYIHESVQRHGHGRELFQYMLQKERVEPHQLAIDRPSQKLLKFLNKHYNLETTVPQVNNFVIFEGFFAHQH----------------------------------------------EFG 197
                                     9        19        29        39        49        59        69        79        89  |     99       109       119       129       139       149       159       169       179       189    |    -         -         -         -         - |  
                                                                                                                    89 92                                                                                                   194                                            195  

   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  (0, 0)

(no "SCOP Domain" information available for 3VWD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VWD)

(-) Gene Ontology  (27, 27)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ATAT_HUMAN | Q5SQI0)
molecular function
    GO:0050662    coenzyme binding    Interacting selectively and non-covalently with a coenzyme, any of various nonprotein organic cofactors that are required, in addition to an enzyme and a substrate, for an enzymatic reaction to proceed.
    GO:0004468    lysine N-acetyltransferase activity, acting on acetyl phosphate as donor    Catalysis of the reaction: acetyl phosphate + L-lysine = phosphate + N6-acetyl-L-lysine.
    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:0016746    transferase activity, transferring acyl groups    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
    GO:0019799    tubulin N-acetyltransferase activity    Catalysis of the reaction: acetyl-CoA + (alpha-tubulin) L-lysine = CoA + (alpha-tubulin) N6-acetyl-L-lysine.
biological process
    GO:0071929    alpha-tubulin acetylation    The addition of an acetyl group to the lysine 40 residue of alpha-tubulin.
    GO:0021542    dentate gyrus development    The process whose specific outcome is the progression of the dentate gyrus over time, from its formation to the mature structure. The dentate gyrus is one of two interlocking gyri of the hippocampus. It contains granule cells, which project to the pyramidal cells and interneurons of the CA3 region of the ammon gyrus.
    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:0006996    organelle organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.
    GO:1900227    positive regulation of NLRP3 inflammasome complex assembly    Any process that activates or increases the frequency, rate or extent of NLRP3 inflammasome complex assembly.
    GO:0045598    regulation of fat cell differentiation    Any process that modulates the frequency, rate or extent of adipocyte differentiation.
    GO:0070507    regulation of microtubule cytoskeleton organization    Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins.
    GO:0007283    spermatogenesis    The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
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: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:0030054    cell junction    A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005905    clathrin-coated pit    A part of the endomembrane system in the form of an invagination of a membrane upon which a clathrin coat forms, and that can be converted by vesicle budding into a clathrin-coated vesicle. Coated pits form on the plasma membrane, where they are involved in receptor-mediated selective transport of many proteins and other macromolecules across the cell membrane, in the trans-Golgi network, and on some endosomes.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    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:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005874    microtubule    Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.
    GO:0097427    microtubule bundle    An arrangement of closely apposed microtubules running parallel to each other.
    GO:0072686    mitotic spindle    A spindle that forms as part of mitosis. Mitotic and meiotic spindles contain distinctive complements of proteins associated with microtubules.
    GO:0005819    spindle    The array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during mitosis or meiosis and serves to move the duplicated chromosomes apart.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ATAT_HUMAN | Q5SQI03vwe 4b5o 4b5p 4gs4 4if5 4pk2 4pk3 4u9y 4u9z

(-) Related Entries Specified in the PDB File

3vwe