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(-) Description

Title :  THE STRUCTURE OF HCINAP-SO4 COMPLEX AT 1.95 ANGSTROMS RESOLUTION
 
Authors :  S. E. Zographos, C. E. Drakou, D. D. Leonidas
Date :  02 Aug 09  (Deposition) - 06 Oct 10  (Release) - 18 Jan 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha And Beta Proteins (A/B), Protein Binding, Transferase, Phosphotransferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. E. Drakou, A. Malekkou, J. M. Hayes, C. W. Lederer, D. D. Leonidas, N. G. Oikonomakos, A. I. Lamond, N. Santama, S. E. Zographos
Hcinap Is An Atypical Mammalian Nuclear Adenylate Kinase With An Atpase Motif: Structural And Functional Studies.
Proteins V. 80 206 2012
PubMed-ID: 22038794  |  Reference-DOI: 10.1002/PROT.23186

(-) Compounds

Molecule 1 - COILIN-INTERACTING NUCLEAR ATPASE PROTEIN
    ChainsA
    EC Number2.7.4.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-6P-3
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneCINAP, TAF9, HCG_37060
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCOILIN-INTERACTING NUCLEAR ATPASE PROTEIN, TAF9 RNA POLYMERASE II, TATA BOX BINDING PROTEIN (TBP)-ASSOCIATED FACTOR, 32KDA, ISOFORM CRA_B, HUMAN ADENYLATE KINASE 6

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric/Biological Unit (1, 5)
No.NameCountTypeFull Name
1SO45Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:12 , GLY A:13 , VAL A:14 , GLY A:15 , LYS A:16 , THR A:17 , ARG A:109 , HOH A:208 , HOH A:212 , HOH A:218BINDING SITE FOR RESIDUE SO4 A 173
2AC2SOFTWAREGLY A:35 , ARG A:39 , HIS A:79 , HOH A:204 , HOH A:207 , HOH A:231BINDING SITE FOR RESIDUE SO4 A 174
3AC3SOFTWARETYR A:129 , VAL A:141 , HIS A:142 , GLN A:143 , HOH A:340 , HOH A:341BINDING SITE FOR RESIDUE SO4 A 175
4AC4SOFTWARELYS A:137 , GLU A:138 , GLU A:139 , HOH A:249 , HOH A:299 , HOH A:342BINDING SITE FOR RESIDUE SO4 A 176
5AC5SOFTWAREARG A:105 , ASN A:147 , LYS A:148 , PRO A:149 , HOH A:363BINDING SITE FOR RESIDUE SO4 A 177

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3IIK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3IIK)

(-) Exons   (5, 5)

Asymmetric/Biological Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2bENST000003808222bENSE00001867641chr5:68665369-6866529080KAD6_HUMAN1-10101A:1-1010
1.5bENST000003808225bENSE00001756532chr5:68662422-6866233093KAD6_HUMAN10-41321A:10-4132
1.7ENST000003808227ENSE00001486415chr5:68651780-6865172259KAD6_HUMAN41-60201A:41-6020
1.8ENST000003808228ENSE00001486410chr5:68651621-68651476146KAD6_HUMAN61-109491A:61-10949
1.9dENST000003808229dENSE00001549839chr5:68648080-686468111270KAD6_HUMAN109-172641A:109-17264

(-) 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:175
 aligned with KAD6_HUMAN | Q9Y3D8 from UniProtKB/Swiss-Prot  Length:172

    Alignment length:175
                               1                                                                                                                                                                           
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167     
           KAD6_HUMAN     - ---MLLPNILLTGTPGVGKTTLGKELASKSGLKYINVGDLAREEQLYDGYDEEYDCPILDEDRVVDELDNQMREGGVIVDYHGCDFFPERWFHIVFVLRTDTNVLYERLETRGYNEKKLTDNIQCEIFQVLYEEATASYKEEIVHQLPSNKPEELENNVDQILKWIEQWIKDHNS 172
               SCOP domains d3iika_ A: automated matches                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.....hhhhhhhhhhhhhh.eeeehhhhhhhhh.eeeee....eeeehhhhhhhhhhhhhhhh.eeee.......hhhhh.eeeeee.hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) ---Exon 1.2b ------------------------------Exon 1.7            Exon 1.8  PDB: A:61-109 UniProt: 61-109          --------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------Exon 1.5b  PDB: A:10-41         -------------------------------------------------------------------Exon 1.9d  PDB: A:109-172 UniProt: 109-172                       Transcript 1 (2)
                 3iik A  -2 PEFMLLPNILLTGTPGVGKTTLGKELASKSGLKYINVGDLAREEQLYDGYDEEYDCPILDEDRVVDELDNQMREGGVIVDYHGCDFFPERWFHIVFVLRTDTNVLYERLETRGYNEKKLTDNIQCEIFQVLYEEATASYKEEIVHQLPSNKPEELENNVDQILKWIEQWIKDHNS 172
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167     

   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 3IIK)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (KAD6_HUMAN | Q9Y3D8)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    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:0050145    nucleoside phosphate kinase activity    Catalysis of the reaction: ATP + nucleoside phosphate = ADP + nucleoside diphosphate.
    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: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: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:0046940    nucleoside monophosphate phosphorylation    The process of introducing one or more phosphate groups into a nucleoside monophosphate to produce a polyphosphorylated nucleoside.
    GO:0046939    nucleotide phosphorylation    The process of introducing one or more phosphate groups into a nucleotide to produce a phosphorylated nucleoside.
    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:0015030    Cajal body    A class of nuclear body, first seen after silver staining by Ramon y Cajal in 1903, enriched in small nuclear ribonucleoproteins, and certain general RNA polymerase II transcription factors; ultrastructurally, they appear as a tangle of coiled, electron-dense threads roughly 0.5 micrometers in diameter; involved in aspects of snRNP biogenesis; the protein coilin serves as a marker for Cajal bodies. Some argue that Cajal bodies are the sites for preassembly of transcriptosomes, unitary particles involved in transcription and processing of RNA.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    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
        KAD6_HUMAN | Q9Y3D81rkb 3iij 3iil 3iim 5jzv

(-) Related Entries Specified in the PDB File

1rkb THE STRUCTURE OF ADRENAL GLAND PROTEIN AD-004
3iij THE STRUCTURE OF HCINAP-ADP COMPLEX AT 1.76 ANGSTROMS RESOLUTION.
3iil THE STRUCTURE OF HCINAP-MGADP-PI COMPLEX AT 2.0 ANGSTROMS RESOLUTION
3iim THE STRUCTURE OF HCINAP-DADP COMPLEX AT 2.0 ANGSTROMS RESOLUTION