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(-) Description

Title :  CRYSTAL STRUCTURE OF UPF0341 PROTEIN (YHIQ) FROM SHIGELLA FLEXNERI IN COMPLEX WITH S-ADENOSYL HOMOCYSTEINE, NORTHEAST STRUCTURAL GENOMICS TARGET SFR275
 
Authors :  F. Forouhar, M. Su, J. Seetharaman, H. Janjua, Y. Fang, R. Xiao, M. C. Baran, J. Liu, T. B. Acton, G. T. Montelione, L. Tong, J. F. Hunt, Northeast Structural Genomics Consortium (Nesg)
Date :  22 Feb 07  (Deposition) - 06 Mar 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha-Beta Protein, Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Forouhar, M. Su, J. Seetharaman, H. Janjua, Y. Fang, R. Xiao, M. C. Baran, J. Liu, T. B. Acton, G. T. Montelione, L. Tong, J. F. Hunt
Crystal Structure Of Upf0341 Protein (Yhiq) From Shigella Flexneri In Complex With S-Adenosyl Homocysteine, Northeast Structural Genomics Target Sfr275
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UPF0341 PROTEIN YHIQ
    Atcc: 700930
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21
    Expression System Strain: BL21(DE3)+MAGIC
    Expression System Taxid: 562
    Expression System Vector: BL21
    Expression System Vector Type: PLASMID
    Gene: YHIQ, SF3528, S_4240
    Organism Scientific: SHIGELLA FLEXNERI 2A
    Organism Taxid: 42897
    Strain: 2457T, 301

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:95 , THR A:96 , ALA A:97 , GLY A:98 , LEU A:99 , ARG A:101 , ASP A:102 , LEU A:116 , GLU A:117 , ARG A:118 , ALA A:152 , SER A:153 , SER A:154 , LEU A:155 , ASP A:171 , ASP A:197 , HOH A:305 , HOH A:465 , HOH A:476 , HOH A:537BINDING SITE FOR RESIDUE SAH A 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Thr A:162 -Pro A:163

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2OYR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2OYR)

(-) Exons   (0, 0)

(no "Exon" information available for 2OYR)

(-) 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:245
 aligned with RSMJ_SHIFL | Q7UAV7 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:250
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250
           RSMJ_SHIFL     1 MKICLIDETGAGDGALSVLAARWGLEHDEDNLMALVLTPEHLELRKRDEPKLGGIFVDFVGGAMAHRRKFGGGRGEAVAKAVGIKGDYLPDVVDATAGLGRDAFVLASVGCRVRMLERNPVVAALLDDGLARGYADAEIGGWLQERLQLIHASSLTALTDITPRPQVVYLDPMFPHKQKSALVKKEMRVFQSLVGPDLDADGLLEPARLLATKRVVVKRPDYAPPLANVATPNAVVTKGHRFDIYAGTPV 250
               SCOP domains d2oyra1 A:1-250 Hypothetical protein YhiQ                                                                                                                                                                                                                  SCOP domains
               CATH domains -2oyrA01 A:2-56 YhiQ-like domain                        2oyrA02 A:57-250 Vaccinia Virus protein VP39                                                                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......hhhhhhhhhhh.ee.....eeeee....eeeee..hhhh.ee.....hhhhhhhhhhhhhhhhhhhhhh.........eee.....hhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhh..hhhhhhhheeeee.hhhhhh........eeee........-----hhhhhhhhhhh....hhhhhhhhhhhhh..eeeeeee....hhhhh...eeee...eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2oyr A   1 mKICLIDETGAGDGALSVLAARWGLEHDEDNLmALVLTPEHLELRKRDEPKLGGIFVDFVGGAmAHRRKFGGGRGEAVAKAVGIKGDYLPDVVDATAGLGRDAFVLASVGCRVRmLERNPVVAALLDDGLARGYADAEIGGWLQERLQLIHASSLTALTDITPRPQVVYLDPmFPHKQ-----KKEmRVFQSLVGPDLDADGLLEPARLLATKRVVVKRPDYAPPLANVATPNAVVTKGHRFDIYAGTPV 250
                            |       10        20        30  |     40        50        60   |    70        80        90       100       110    |  120       130       140       150       160       170  |    | -   |  |190       200       210       220       230       240       250
                            |                              33-MSE                         64-MSE                                            115-MSE                                                   173-MSE8   184  |                                                               
                            1-MSE                                                                                                                                                                                   187-MSE
   Legend:   → Mismatch (orange background)
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  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
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RSMJ_SHIFL | Q7UAV7)
molecular function
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0008990    rRNA (guanine-N2-)-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing N2-methylguanine.
    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:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0031167    rRNA methylation    The posttranscriptional addition of methyl groups to specific residues in an rRNA molecule.
    GO:0006364    rRNA processing    Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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