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(-) Description

Title :  X-RAY STRUCTURE OF NORTHEAST STRUCTURAL GENOMICS TARGET PROTEIN SR145 FROM BACILLUS SUBTILIS
 
Authors :  A. P. Kuzin, W. Edstrom, S. M. Vorobiev, R. Shastry, L. -C. Ma, R. Xiao, T. Acton, G. T. Montelione, L. Tong, J. F. Hunt, Northeast Structural Genomics Consortium (Nesg)
Date :  11 Jun 04  (Deposition) - 20 Jul 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Biol. Unit 4:  G,H  (1x)
Keywords :  Structural Genomics, Unknown Function, Psi, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. P. Kuzin, W. Edstrom, S. M. Vorobiev, R. Shastry, L. -C. Ma, R. Xiao, T. Acton, G. T. Montelione, L. Tong, J. F. Hunt
X-Ray Structure Of Northeast Structural Genomics Target Protein Sr145 From Bacillus Subtilis
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL UPF0247 PROTEIN YYDA
    ChainsA, B, C, D, E, F, G, H
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET21
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneYYDA, BSU40230
    Organism ScientificBACILLUS SUBTILIS
    Organism Taxid1423

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit ABCDEFGH
Biological Unit 1 (1x)AB      
Biological Unit 2 (1x)  CD    
Biological Unit 3 (1x)    EF  
Biological Unit 4 (1x)      GH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 46)

Asymmetric Unit (1, 46)
No.NameCountTypeFull Name
1MSE46Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 12)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 12)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (1, 10)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE
Biological Unit 4 (1, 12)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1TO0)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1TO0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1TO0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1TO0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1TO0)

(-) Exons   (0, 0)

(no "Exon" information available for 1TO0)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  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:148
 aligned with RLMH_BACSU | Q45601 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       
           RLMH_BACSU     1 MNINIVTIGKLKEKYLKQGIEEYTKRLSAYAKIDIIELPDEKAPENLSDQDMKIIKDKEGDRILSKISPDAHVIALAIEGKMKTSEELADTIDKLATYGKSKVTFVIGGSLGLSDTVMKRADEKLSFSKMTFPHQLMRLILVEQIYRAFRINRGEPY 157
               SCOP domains d1to0a_ A: Hypothetical protein YydA                                                                                                                          SCOP domains
               CATH domains -1to0A00 A:2-157  [code=3.40.1280.10, no n         ame defined]                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee....hhhhhhhhhhhhhhhh...eeeeeee....---------.hhhhhhhhhhhhh......eeeee....ee.hhhhhhhhhhhhhh....eeeeee......hhhhhhhh.eeee......hhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1to0 A   1 mNINIVTIGKLKEKYLKQGIEEYTKRLSAYAKIDIIELPDEK---------mKIIKDKEGDRILSKISPDAHVIALAIEGKmKTSEELADTIDKLATYGKSKVTFVIGGSLGLSDTVmKRADEKLSFSKmTFPHQLmRLILVEQIYRAFRINRGEPY 157
                            |       10        20        30        40 |       - |      60        70        80 |      90       100       110       120       130      |140       150       
                            |                                       42        52-MSE                        82-MSE                             118-MSE     130-MSE  |                    
                            1-MSE                                                                                                                                 137-MSE                

Chain B from PDB  Type:PROTEIN  Length:148
 aligned with RLMH_BACSU | Q45601 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       
           RLMH_BACSU     1 MNINIVTIGKLKEKYLKQGIEEYTKRLSAYAKIDIIELPDEKAPENLSDQDMKIIKDKEGDRILSKISPDAHVIALAIEGKMKTSEELADTIDKLATYGKSKVTFVIGGSLGLSDTVMKRADEKLSFSKMTFPHQLMRLILVEQIYRAFRINRGEPY 157
               SCOP domains d1to0b_ B: Hypothetical protein YydA                                                                                                                          SCOP domains
               CATH domains -1to0B00 B:2-157  [code=3.40.1280.10, no          name defined]                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee....hhhhhhhhhhhhhhhh...eeeeeee...---------..hhhhhhhhhhhhh......eeeee.......hhhhhhhhhhhhhhh...eeeeee......hhhhhhhh.eee.......hhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1to0 B   1 mNINIVTIGKLKEKYLKQGIEEYTKRLSAYAKIDIIELPDE---------DmKIIKDKEGDRILSKISPDAHVIALAIEGKmKTSEELADTIDKLATYGKSKVTFVIGGSLGLSDTVmKRADEKLSFSKmTFPHQLmRLILVEQIYRAFRINRGEPY 157
                            |       10        20        30        40|        -||      60        70        80 |      90       100       110       120       130      |140       150       
                            1-MSE                                  41        51|                            82-MSE                             118-MSE     130-MSE  |                    
                                                                              52-MSE                                                                              137-MSE                

Chain C from PDB  Type:PROTEIN  Length:148
 aligned with RLMH_BACSU | Q45601 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:155
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150     
           RLMH_BACSU     1 MNINIVTIGKLKEKYLKQGIEEYTKRLSAYAKIDIIELPDEKAPENLSDQDMKIIKDKEGDRILSKISPDAHVIALAIEGKMKTSEELADTIDKLATYGKSKVTFVIGGSLGLSDTVMKRADEKLSFSKMTFPHQLMRLILVEQIYRAFRINRGE 155
               SCOP domains d1to0c_ C: Hypothetical protein YydA                                                                                                                        SCOP domains
               CATH domains -1to0C00 C:2-155  [code=3.40.1280.10, no n       ame defined]                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....hhhhhhhhhhhhhhhhh...eeeeee....-------...hhhhhhhhhhhhhh....eeeeee....ee.hhhhhhhhhhhh......eeeeee......hhhhhhhh.eeee......hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1to0 C   1 mNINIVTIGKLKEKYLKQGIEEYTKRLSAYAKIDIIELPDEK-------QDmKIIKDKEGDRILSKISPDAHVIALAIEGKmKTSEELADTIDKLATYGKSKVTFVIGGSLGLSDTVmKRADEKLSFSKmTFPHQLmRLILVEQIYRAFRINRGE 155
                            |       10        20        30        40 |      50 |      60        70        80 |      90       100       110       120       130      |140       150     
                            1-MSE                                   42      50 |                            82-MSE                             118-MSE     130-MSE  |                  
                                                                              52-MSE                                                                              137-MSE              

Chain D from PDB  Type:PROTEIN  Length:151
 aligned with RLMH_BACSU | Q45601 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       
           RLMH_BACSU     1 MNINIVTIGKLKEKYLKQGIEEYTKRLSAYAKIDIIELPDEKAPENLSDQDMKIIKDKEGDRILSKISPDAHVIALAIEGKMKTSEELADTIDKLATYGKSKVTFVIGGSLGLSDTVMKRADEKLSFSKMTFPHQLMRLILVEQIYRAFRINRGEPY 157
               SCOP domains d1to0d_ D: Hypothetical protein YydA                                                                                                                          SCOP domains
               CATH domains -1to0D00 D:2-157  [code=3.40.1280.10, no       name defined]                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee....hhhhhhhhhhhhhhhhh..eeeeeee..------..hhhhhhhhhhhhhhhhh......eeeee.......hhhhhhhhhhhhhhh...eeeeee......hhhhhhhh.eee.......hhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1to0 D   1 mNINIVTIGKLKEKYLKQGIEEYTKRLSAYAKIDIIELPD------LSDQDmKIIKDKEGDRILSKISPDAHVIALAIEGKmKTSEELADTIDKLATYGKSKVTFVIGGSLGLSDTVmKRADEKLSFSKmTFPHQLmRLILVEQIYRAFRINRGEPY 157
                            |       10        20        30        40      | 50 |      60        70        80 |      90       100       110       120       130      |140       150       
                            1-MSE                                 40     47    |                            82-MSE                             118-MSE     130-MSE  |                    
                                                                              52-MSE                                                                              137-MSE                

Chain E from PDB  Type:PROTEIN  Length:139
 aligned with RLMH_BACSU | Q45601 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:153
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150   
           RLMH_BACSU     1 MNINIVTIGKLKEKYLKQGIEEYTKRLSAYAKIDIIELPDEKAPENLSDQDMKIIKDKEGDRILSKISPDAHVIALAIEGKMKTSEELADTIDKLATYGKSKVTFVIGGSLGLSDTVMKRADEKLSFSKMTFPHQLMRLILVEQIYRAFRINR 153
               SCOP domains d1to0e_ E: Hypothetical protein YydA                                                                                                                      SCOP domains
               CATH domains -1to0E00 E:2-153  [code=3.40.1280.10, no               name defined]                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....hhhhhhhhhhhhhhhhh...eeeeee..--------------.hhhhhhhhhh......eeeee....ee.hhhhhhhhhhhhhhh....eeee.......hhhhhhhh.eeee......hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1to0 E   1 mNINIVTIGKLKEKYLKQGIEEYTKRLSAYAKIDIIELPD--------------IKDKEGDRILSKISPDAHVIALAIEGKmKTSEELADTIDKLATYGKSKVTFVIGGSLGLSDTVmKRADEKLSFSKmTFPHQLmRLILVEQIYRAFRINR 153
                            |       10        20        30        40         -    |   60        70        80 |      90       100       110       120       130      |140       150   
                            1-MSE                                 40             55                         82-MSE                             118-MSE     130-MSE  |                
                                                                                                                                                                  137-MSE            

Chain F from PDB  Type:PROTEIN  Length:142
 aligned with RLMH_BACSU | Q45601 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:154
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150    
           RLMH_BACSU     1 MNINIVTIGKLKEKYLKQGIEEYTKRLSAYAKIDIIELPDEKAPENLSDQDMKIIKDKEGDRILSKISPDAHVIALAIEGKMKTSEELADTIDKLATYGKSKVTFVIGGSLGLSDTVMKRADEKLSFSKMTFPHQLMRLILVEQIYRAFRINRG 154
               SCOP domains d1to0f_ F: Hypothetical protein YydA                                                                                                                       SCOP domains
               CATH domains -1to0F00 F:2-154  [code=3.40.1280.10, no             name defined]                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee....hhhhhhhhhhhhhhhhh..eeeeeee..------------..hhhhhhhhhhh......eeeee....ee.hhhhhhhhhhhh......eeeeee......hhhhhhhh.eeee......hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1to0 F   1 mNINIVTIGKLKEKYLKQGIEEYTKRLSAYAKIDIIELPD------------KIIKDKEGDRILSKISPDAHVIALAIEGKmKTSEELADTIDKLATYGKSKVTFVIGGSLGLSDTVmKRADEKLSFSKmTFPHQLmRLILVEQIYRAFRINRG 154
                            |       10        20        30        40         -  |     60        70        80 |      90       100       110       120       130      |140       150    
                            1-MSE                                 40           53                           82-MSE                             118-MSE     130-MSE  |                 
                                                                                                                                                                  137-MSE             

Chain G from PDB  Type:PROTEIN  Length:148
 aligned with RLMH_BACSU | Q45601 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       
           RLMH_BACSU     1 MNINIVTIGKLKEKYLKQGIEEYTKRLSAYAKIDIIELPDEKAPENLSDQDMKIIKDKEGDRILSKISPDAHVIALAIEGKMKTSEELADTIDKLATYGKSKVTFVIGGSLGLSDTVMKRADEKLSFSKMTFPHQLMRLILVEQIYRAFRINRGEPY 157
               SCOP domains d1to0g_ G: Hypothetical protein YydA                                                                                                                          SCOP domains
               CATH domains -1to0G00 G:2-157  [code=3.40.1280.10, no          name defined]                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee....hhhhhhhhhhhhhhhh...eeeeeee...---------hhhhhhhhhhhhhhh......eeeee.......hhhhhhhhhhhhhhh...eeeeee......hhhhhhhh.eee.......hhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1to0 G   1 mNINIVTIGKLKEKYLKQGIEEYTKRLSAYAKIDIIELPDE---------DmKIIKDKEGDRILSKISPDAHVIALAIEGKmKTSEELADTIDKLATYGKSKVTFVIGGSLGLSDTVmKRADEKLSFSKmTFPHQLmRLILVEQIYRAFRINRGEPY 157
                            |       10        20        30        40|        -||      60        70        80 |      90       100       110       120       130      |140       150       
                            1-MSE                                  41        51|                            82-MSE                             118-MSE     130-MSE  |                    
                                                                              52-MSE                                                                              137-MSE                

Chain H from PDB  Type:PROTEIN  Length:150
 aligned with RLMH_BACSU | Q45601 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:157
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       
           RLMH_BACSU     1 MNINIVTIGKLKEKYLKQGIEEYTKRLSAYAKIDIIELPDEKAPENLSDQDMKIIKDKEGDRILSKISPDAHVIALAIEGKMKTSEELADTIDKLATYGKSKVTFVIGGSLGLSDTVMKRADEKLSFSKMTFPHQLMRLILVEQIYRAFRINRGEPY 157
               SCOP domains d1to0h_ H: Hypothetical protein YydA                                                                                                                          SCOP domains
               CATH domains -1to0H00 H:2-157  [code=3.40.1280.10, no n       ame defined]                                                                                                 CATH domains
           Pfam domains (1) SPOUT_MTase-1to0H01 H:1-157                                                                                                                                   Pfam domains (1)
           Pfam domains (2) SPOUT_MTase-1to0H02 H:1-157                                                                                                                                   Pfam domains (2)
           Pfam domains (3) SPOUT_MTase-1to0H03 H:1-157                                                                                                                                   Pfam domains (3)
           Pfam domains (4) SPOUT_MTase-1to0H04 H:1-157                                                                                                                                   Pfam domains (4)
           Pfam domains (5) SPOUT_MTase-1to0H05 H:1-157                                                                                                                                   Pfam domains (5)
           Pfam domains (6) SPOUT_MTase-1to0H06 H:1-157                                                                                                                                   Pfam domains (6)
           Pfam domains (7) SPOUT_MTase-1to0H07 H:1-157                                                                                                                                   Pfam domains (7)
           Pfam domains (8) SPOUT_MTase-1to0H08 H:1-157                                                                                                                                   Pfam domains (8)
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhhhhh...eeeeeee....-------....hhhhhhhhhhhh......eeeee.......hhhhhhhhhhhhhhh...eeeeee......hhhhhhhh.eee.......hhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1to0 H   1 mNINIVTIGKLKEKYLKQGIEEYTKRLSAYAKIDIIELPDEK-------QDmKIIKDKEGDRILSKISPDAHVIALAIEGKmKTSEELADTIDKLATYGKSKVTFVIGGSLGLSDTVmKRADEKLSFSKmTFPHQLmRLILVEQIYRAFRINRGEPY 157
                            |       10        20        30        40 |      50 |      60        70        80 |      90       100       110       120       130      |140       150       
                            1-MSE                                   42      50 |                            82-MSE                             118-MSE     130-MSE  |                    
                                                                              52-MSE                                                                              137-MSE                

   Legend:   → Mismatch (orange background)
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    → 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, 8)

Asymmetric Unit

(-) CATH Domains  (1, 8)

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

(-) Pfam Domains  (1, 8)

Asymmetric Unit
(-)
Clan: SPOUT (28)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F,G,H   (RLMH_BACSU | Q45601)
molecular function
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0070038    rRNA (pseudouridine-N3-)-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing N3-methylpseudouridine.
    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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