Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE AND RNA BINDING PROPERTIES OF THE RRM/ALKB DOMAINS IN HUMAN ABH8, AN ENZYME CATALYZING TRNA HYPERMODIFICATION, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET HR5601B
 
Authors :  C. Pastore, I. Topalidou, F. Forouhar, A. C. Yan, M. Levy, J. F. Hunt, Nor Structural Genomics Consortium (Nesg)
Date :  19 Aug 11  (Deposition) - 02 Nov 11  (Release) - 10 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (4x)
Biol. Unit 3:  A  (2x)
Keywords :  Structural Genomics, Psi-Biology, Northeast Structural Genomics Consortium, Nesg, Alpha-Beta Two Domain-Protein Containing A Zinc Structure Motif, Trna Modifying Enzyme, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Pastore, I. Topalidou, F. Forouhar, A. C. Yan, M. Levy, J. F. Hunt
Crystal Structure And Rna Binding Properties Of The Rna Recognition Motif (Rrm) And Alkb Domains In Human Alkb Homolog 8 (Abh8), An Enzyme Catalyzing Trna Hypermodification.
J. Biol. Chem. V. 287 2130 2012
PubMed-ID: 22065580  |  Reference-DOI: 10.1074/JBC.M111.286187

(-) Compounds

Molecule 1 - ALKYLATED DNA REPAIR PROTEIN ALKB HOMOLOG 8
    ChainsA
    EC Number1.14.11.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainB834(LAMBDA)(DE3)
    Expression System Taxid562
    Expression System Vector TypePET26
    FragmentRRM AND ALKB DOMAINS OF ABH8
    GeneABH8, ALKBH8
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPROBABLE ALPHA-KETOGLUTARATE-DEPENDENT DIOXYGENASE ABH8

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (1x)A
Biological Unit 2 (4x)A
Biological Unit 3 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric Unit (4, 10)
No.NameCountTypeFull Name
1AKG1Ligand/Ion2-OXOGLUTARIC ACID
2MN1Ligand/IonMANGANESE (II) ION
3MSE7Mod. Amino AcidSELENOMETHIONINE
4ZN1Ligand/IonZINC ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1AKG1Ligand/Ion2-OXOGLUTARIC ACID
2MN-1Ligand/IonMANGANESE (II) ION
3MSE7Mod. Amino AcidSELENOMETHIONINE
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 32)
No.NameCountTypeFull Name
1AKG4Ligand/Ion2-OXOGLUTARIC ACID
2MN-1Ligand/IonMANGANESE (II) ION
3MSE28Mod. Amino AcidSELENOMETHIONINE
4ZN-1Ligand/IonZINC ION
Biological Unit 3 (2, 16)
No.NameCountTypeFull Name
1AKG2Ligand/Ion2-OXOGLUTARIC ACID
2MN-1Ligand/IonMANGANESE (II) ION
3MSE14Mod. Amino AcidSELENOMETHIONINE
4ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:242 , CYS A:341 , CYS A:343 , CYS A:349BINDING SITE FOR RESIDUE ZN A 401
2AC2SOFTWAREHIS A:238 , ASP A:240 , HIS A:292 , AKG A:403BINDING SITE FOR RESIDUE MN A 402
3AC3SOFTWAREASN A:227 , TYR A:229 , HIS A:238 , SER A:251 , MSE A:260 , HIS A:292 , ARG A:328 , SER A:330 , THR A:332 , ARG A:334 , MN A:402BINDING SITE FOR RESIDUE AKG A 403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FE2OG_OXYPS51471 Fe(2+) 2-oxoglutarate dioxygenase domain profile.ALKB8_HUMAN220-337  1A:220-337
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FE2OG_OXYPS51471 Fe(2+) 2-oxoglutarate dioxygenase domain profile.ALKB8_HUMAN220-337  1A:220-337
Biological Unit 2 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FE2OG_OXYPS51471 Fe(2+) 2-oxoglutarate dioxygenase domain profile.ALKB8_HUMAN220-337  4A:220-337
Biological Unit 3 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FE2OG_OXYPS51471 Fe(2+) 2-oxoglutarate dioxygenase domain profile.ALKB8_HUMAN220-337  2A:220-337

(-) Exons   (9, 9)

Asymmetric Unit (9, 9)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2ENST000003895682ENSE00001724312chr11:107436244-10743617966ALKB8_HUMAN-00--
1.3ENST000003895683ENSE00001620533chr11:107435940-10743588853ALKB8_HUMAN-00--
1.4ENST000003895684ENSE00001769102chr11:107434462-107434273190ALKB8_HUMAN-00--
1.5ENST000003895685ENSE00001727109chr11:107433542-107433425118ALKB8_HUMAN-00--
1.6ENST000003895686ENSE00002152837chr11:107431625-107431491135ALKB8_HUMAN1-43431A:28-4316
1.7ENST000003895687ENSE00000990040chr11:107427729-107427492238ALKB8_HUMAN44-123801A:44-12380
1.8aENST000003895688aENSE00000930433chr11:107424704-107424573132ALKB8_HUMAN123-167451A:123-15634
1.9ENST000003895689ENSE00000930432chr11:107423929-10742383496ALKB8_HUMAN167-199331A:174-199 (gaps)26
1.10bENST0000038956810bENSE00000930431chr11:107422638-107422534105ALKB8_HUMAN199-234361A:199-23436
1.11ENST0000038956811ENSE00001506233chr11:107420549-10742047971ALKB8_HUMAN234-257241A:234-25724
1.12bENST0000038956812bENSE00001687648chr11:107403132-107403026107ALKB8_HUMAN258-293361A:258-29336
1.13ENST0000038956813ENSE00001697189chr11:107396318-107396167152ALKB8_HUMAN293-344521A:293-344 (gaps)52
1.14ENST0000038956814ENSE00001611673chr11:107393281-107393025257ALKB8_HUMAN344-429861A:344-360 (gaps)33
1.15ENST0000038956815ENSE00001634419chr11:107381762-107381613150ALKB8_HUMAN430-479500--
1.16cENST0000038956816cENSE00001763825chr11:107375941-107375321621ALKB8_HUMAN480-6641850--

(-) 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:304
 aligned with ALKB8_HUMAN | Q96BT7 from UniProtKB/Swiss-Prot  Length:664

    Alignment length:349
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367         
          ALKB8_HUMAN    28 TLLRHEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVEKVQWKELRPQALPPGLMVVEEIISSEEEKMLLESVDWTEDTDNQNSQKSLKHRRVKHFGYEFHYENNNVDKDKPLSGGLPDICESFLEKWLRKGYIKHKPDQMTINQYEPGQGIPAHIDTHSAFEDEIVSLSLGSEIVMDFKHPDGIAVPVMLPRRSLLVMTGESRYLWTHGITCRKFDTVQASESLKSGIITSDVGDLTLSKRGLRTSFTFRKVRQTPCNCSYPLVCDSQRKETPPSFPESDKEASRLEQEYVH 376
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................ee..hhhhh.hhhhhhhhhh....eeeee......eeeeee.hhhhhhhhhhhh...eee.....eee......................eeee....hhhhhhhhhh..-----------------.eeeee..----------.........hhhhhhhhhhhhhhh.......eeeeeee...................eeeeee...eeeeee.....eeeeee...eeeee.hhhhhh.........eeeee...--...........eeeee...eeeeeee..........hhhhh.....----------------...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FE2OG_OXY  PDB: A:220-337 UniProt: 220-337                                                                            --------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.6        Exon 1.7  PDB: A:44-123 UniProt: 44-123                                         ---------------------------------------------------------------------------Exon 1.10b  PDB: A:199-234          -----------------------Exon 1.12b  PDB: A:258-293          --------------------------------------------------Exon 1.14  PDB: A:344-360 (gaps)  Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------Exon 1.8a  PDB: A:123-156 UniProt: 123-167   ------------------------------------------------------------------Exon 1.11  PDB: A:234-25-----------------------------------Exon 1.13  PDB: A:293-344 (gaps) UniProt: 293-344   -------------------------------- Transcript 1 (2)
           Transcript 1 (3) -------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9  PDB: A:174-199 (gaps)  --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (3)
                 3thp A  28 TLLRHEGIETVSYATQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLmPPNKPYSFARYRTTEESKRAYVTLNGKEVVDDLGQKITLYLNFVEKVQWKELRPQALPPGLmVVEEIISSEEEKmLLESV-----------------RRVKHFGY----------KDKPLSGGLPDICESFLEKWLRKGYIKHKPDQmTINQYEPGQGIPAHIDTHSAFEDEIVSLSLGSEIVmDFKHPDGIAVPVmLPRRSLLVmTGESRYLWTHGITCRKFDTVQASE--KSGIITSDVGDLTLSKRGLRTSFTFRKVRQTPCNCSYPLVCDSQRK----------------ENLYFQ 360
                                    37        47        57        67        77        87        97       107       117       127       137|      147   |    |-         -      |177   |     -    |  197       207       217      |227       237       247       257  |    267     | 277    |  287       297        |- |     317       327       337       347      |  -         -   |     
                                                                           76-MSE                                                       138-MSE      151-MSE6               174    181        192                             224-MSE                             260-MSE      273-MSE  282-MSE                 306  |                                          354              355     
                                                                                                                                                                                                                                                                                                                   309                                                                   

   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 3THP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (24, 24)

Asymmetric Unit(hide GO term definitions)
Chain A   (ALKB8_HUMAN | Q96BT7)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    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:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016706    oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors    Catalysis of the reaction: A + 2-oxoglutarate + O2 = B + succinate + CO2. This is an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from 2-oxoglutarate and one other donor, and one atom of oxygen is incorporated into each donor.
    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:0016300    tRNA (uracil) methyltransferase activity    Catalysis of the transfer of a methyl group from a donor to a uracil residue in a tRNA molecule.
    GO:0000049    tRNA binding    Interacting selectively and non-covalently with transfer RNA.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0030488    tRNA methylation    The posttranscriptional addition of methyl groups to specific residues in a tRNA molecule.
    GO:0002098    tRNA wobble uridine modification    The process in which a uridine in position 34 of a tRNA is post-transcriptionally modified.
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:0015630    microtubule cytoskeleton    The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins.
    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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    AKG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3thp)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3thp
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  ALKB8_HUMAN | Q96BT7
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.14.11.-
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  ALKB8_HUMAN | Q96BT7
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        ALKB8_HUMAN | Q96BT72cq2 3tht

(-) Related Entries Specified in the PDB File

3tht