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(-) Description

Title :  THE STRUCTURE OF A PROBABLE METHYLASE FAMILY PROTEIN FROM HAEMOPHILUS INFLUENZAE RD KW20
 
Authors :  K. Tan, H. Li, K. Buck, A. Joachimiak, Midwest Center For Structural (Mcsg)
Date :  07 Aug 09  (Deposition) - 01 Sep 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.01
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Apc63004, Methylase Family Protein, Haemophilus Influenzae Rd Kw20, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Methyltransferase, Transferase, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Tan, H. Li, K. Buck, A. Joachimiak
The Structure Of A Probable Methylase Family Protein From Haemophilus Influenzae Rd Kw20
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UNCHARACTERIZED TRNA/RRNA METHYLTRANSFERASE HI0380
    Chains: A, B
    EC Number: 2.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG19
    Expression System Strain: PPK1037
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: HAEMOPHILUS INFLUENZAE, HI0380
    Organism Scientific: HAEMOPHILUS INFLUENZAE
    Organism Taxid: 727
    Strain: RD KW20

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 22)

Asymmetric/Biological Unit (4, 22)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2EDO5Ligand/Ion1,2-ETHANEDIOL
3MSE14Mod. Amino AcidSELENOMETHIONINE
4SO42Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:78 , GLY A:111 , LEU A:140 , EDO A:243BINDING SITE FOR RESIDUE EDO A 242
2AC2SOFTWARESER A:79 , LEU A:129 , ASN A:130 , ILE A:131 , EDO A:242BINDING SITE FOR RESIDUE EDO A 243
3AC3SOFTWARESER B:79 , ASN B:130 , ILE B:131 , LEU B:140 , SO4 B:247BINDING SITE FOR RESIDUE EDO B 242
4AC4SOFTWARESER B:73 , ARG B:83 , HIS B:84 , HIS B:126BINDING SITE FOR RESIDUE EDO B 243
5AC5SOFTWAREASN B:141BINDING SITE FOR RESIDUE EDO B 244
6AC6SOFTWAREASN B:130 , ILE B:131 , PRO B:132 , ALA B:133 , PRO B:135BINDING SITE FOR RESIDUE ACT B 245
7AC7SOFTWAREARG A:23 , HIS B:14 , ASN B:17 , GLU B:113 , ARG B:114 , ASN B:141BINDING SITE FOR RESIDUE SO4 B 246
8AC8SOFTWAREARG B:112 , LEU B:140 , LEU B:142 , EDO B:242BINDING SITE FOR RESIDUE SO4 B 247

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3ILK)

(-) 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:239
 aligned with Y380_HAEIN | P44676 from UniProtKB/Swiss-Prot  Length:241

    Alignment length:240
                              1                                                                                                                                                                                                                                             
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238
           Y380_HAEIN     - --MLENIRIVLIETSHSGNIGSAARAMKTMGLTQLCLVSPKSVDEQSYALSAGAENIVKNARVVDSFDEAVDDCSLVIGTSARLRHLQNTLIEPRECAEKVVAYKGKIAIVFGRERIGLTNEELLKCHYHLNIPANPDYSSLNLAMAVQLVSYELRMAFLVQNNKKNSLSLIEKNYPTTDQLAYFFDYTERIYQSLGFIQNQGVMRKLKRLYYRAKLEKNELNILNGMLSAVEKRIDLTK 238
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeee...hhhhhhhhhhhhhhh...eeeee.....hhhhhhh...hhhhhhhheee.hhhhhh....eeeee...hhhhh..eehhhhhhhhhhhh...eeeee.......hhhhhhh..eee...........hhhhhhhhhhhhhhhhhhhhhhhhhhh..-.....hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ilk A  -1 NAmLENIRIVLIETSHSGNIGSAARAmKTmGLTQLCLVSPKSVDEQSYALSAGAENIVKNARVVDSFDEAVDDCSLVIGTSARLRHLQNTLIEPRECAEKVVAYKGKIAIVFGRERIGLTNEELLKCHYHLNIPANPDYSSLNLAmAVQLVSYELRmAFLVQNNKKNSLSL-EKNYPTTDQLAYFFDYTERIYQSLGFIQNQGVmRKLKRLYYRAKLEKNELNILNGmLSAVEKRIDLTK 238
                              |      8        18      | 28        38        48        58        68        78        88        98       108       118       128       138     | 148      |158       168| |    178       188       198    |  208       218       228       238
                              |                      25-MSE                                                                                                                144-MSE    155-MSE       169 |                             203-MSE                226-MSE        
                              1-MSE                     28-MSE                                                                                                                                        171                                                                   


Chain B from PDB  Type:PROTEIN  Length:233
 aligned with Y380_HAEIN | P44676 from UniProtKB/Swiss-Prot  Length:241

    Alignment length:238
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230        
           Y380_HAEIN     1 MLENIRIVLIETSHSGNIGSAARAMKTMGLTQLCLVSPKSVDEQSYALSAGAENIVKNARVVDSFDEAVDDCSLVIGTSARLRHLQNTLIEPRECAEKVVAYKGKIAIVFGRERIGLTNEELLKCHYHLNIPANPDYSSLNLAMAVQLVSYELRMAFLVQNNKKNSLSLIEKNYPTTDQLAYFFDYTERIYQSLGFIQNQGVMRKLKRLYYRAKLEKNELNILNGMLSAVEKRIDLTK 238
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhh.eeeeee...hhhhhhhhhhhhhhh...eeeee.....hhhhhhhhh.hhhhhhh.eee.hhhhhh....eeeee...hhhhh..eehhhhhhhhhhhh...eeeee.......hhhhhh...eee...........hhhhhhhhhhhhhhhhhhhhhh..-----......hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ilk B   1 mLENIRIVLIETSHSGNIGSAARAmKTmGLTQLCLVSPKSVDEQSYALSAGAENIVKNARVVDSFDEAVDDCSLVIGTSARLRHLQNTLIEPRECAEKVVAYKGKIAIVFGRERIGLTNEELLKCHYHLNIPANPDYSSLNLAmAVQLVSYELRmAFLVQNNKK-----IEKNYPTTDQLAYFFDYTERIYQSLGFIQNQGVmRKLKRLYYRAKLEKNELNILNGmLSAVEKRIDLTK 238
                            |       10        20    |  |30        40        50        60        70        80        90       100       110       120       130       140   |   150    |  160   |   170       180       190       200  |    210       220     | 230        
                            1-MSE                  25-MSE                                                                                                                144-MSE    155-MSE  164   170                              203-MSE                226-MSE        
                                                      28-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 3ILK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Y380_HAEIN | P44676)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0008173    RNA methyltransferase activity    Catalysis of the transfer of a methyl group from a donor to a nucleoside residue in an RNA molecule.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0052666    tRNA (cytosine-2'-O-)-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing 2'-O-methylcytosine.
    GO:0052665    tRNA (uracil-2'-O-)-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing 2'-O-methyluracil.
    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:0006396    RNA processing    Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0002128    tRNA nucleoside ribose methylation    The process that results in the modification of the sugar of a nucleoside in tRNA at the 2'O position.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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