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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE METHYLTRANSFERASE (TFU_2867) FROM THERMOBIFIDA FUSCA YX AT 1.95 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  22 Jun 07  (Deposition) - 03 Jul 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  B  (2x)
Biol. Unit 4:  A  (2x)
Keywords :  Putative Methyltransferase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Uncharacterized Protein Tfu_2867 (Yp_290923. 1) From Thermobifida Fusca Yx At 1. 95 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN TFU_2867
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YP_290923.1, TFU_2867
    Mutation: YES
    Organism Scientific: THERMOBIFIDA FUSCA
    Organism Taxid: 269800
    Strain: YX

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (2x):  B
Biological Unit 4 (2x): A 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 30)

Asymmetric Unit (5, 30)
No.NameCountTypeFull Name
1MPD6Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2MSE12Mod. Amino AcidSELENOMETHIONINE
3NEP2Mod. Amino AcidN1-PHOSPHONOHISTIDINE
4SAM2Ligand/IonS-ADENOSYLMETHIONINE
5SO48Ligand/IonSULFATE ION
Biological Unit 1 (5, 14)
No.NameCountTypeFull Name
1MPD3Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2MSE6Mod. Amino AcidSELENOMETHIONINE
3NEP1Mod. Amino AcidN1-PHOSPHONOHISTIDINE
4SAM1Ligand/IonS-ADENOSYLMETHIONINE
5SO43Ligand/IonSULFATE ION
Biological Unit 2 (5, 16)
No.NameCountTypeFull Name
1MPD3Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2MSE6Mod. Amino AcidSELENOMETHIONINE
3NEP1Mod. Amino AcidN1-PHOSPHONOHISTIDINE
4SAM1Ligand/IonS-ADENOSYLMETHIONINE
5SO45Ligand/IonSULFATE ION
Biological Unit 3 (5, 32)
No.NameCountTypeFull Name
1MPD6Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2MSE12Mod. Amino AcidSELENOMETHIONINE
3NEP2Mod. Amino AcidN1-PHOSPHONOHISTIDINE
4SAM2Ligand/IonS-ADENOSYLMETHIONINE
5SO410Ligand/IonSULFATE ION
Biological Unit 4 (5, 28)
No.NameCountTypeFull Name
1MPD6Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2MSE12Mod. Amino AcidSELENOMETHIONINE
3NEP2Mod. Amino AcidN1-PHOSPHONOHISTIDINE
4SAM2Ligand/IonS-ADENOSYLMETHIONINE
5SO46Ligand/IonSULFATE ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:205 , ALA A:220 , HOH A:404BINDING SITE FOR RESIDUE SO4 A 274
02AC2SOFTWAREGLN B:205 , ALA B:220 , HOH B:406BINDING SITE FOR RESIDUE SO4 B 274
03AC3SOFTWARETYR B:242 , MSE B:265BINDING SITE FOR RESIDUE SO4 B 275
04AC4SOFTWARETHR B:89BINDING SITE FOR RESIDUE SO4 B 276
05AC5SOFTWARELEU A:42 , TYR A:45BINDING SITE FOR RESIDUE SO4 A 275
06AC6SOFTWARETHR B:21 , ILE B:111BINDING SITE FOR RESIDUE SO4 B 277
07AC7SOFTWARETYR A:242 , MSE A:265 , HOH A:489 , HOH A:517BINDING SITE FOR RESIDUE SO4 A 276
08AC8SOFTWARETYR B:45BINDING SITE FOR RESIDUE SO4 B 278
09AC9SOFTWAREILE A:22 , ALA A:23 , TYR A:26 , ASN A:60 , ARG A:61 , GLY A:84 , SER A:85 , GLY A:86 , ASP A:110 , ILE A:111 , ALA A:134 , ASP A:135 , VAL A:136 , ARG A:137 , VAL A:163 , GLY A:164 , MSE A:165 , TYR A:168 , HOH A:412 , HOH A:437 , HOH A:451BINDING SITE FOR RESIDUE SAM A 400
10BC1SOFTWAREILE B:22 , ALA B:23 , TYR B:26 , ASN B:60 , ARG B:61 , GLY B:84 , SER B:85 , GLY B:86 , ASP B:110 , ILE B:111 , ALA B:134 , ASP B:135 , VAL B:136 , VAL B:163 , GLY B:164 , MSE B:165 , HOH B:408 , HOH B:418 , HOH B:461BINDING SITE FOR RESIDUE SAM B 400
11BC2SOFTWARESER A:56 , ALA A:57 , ASN A:60 , THR A:194 , SER A:195 , GLY A:264 , MPD A:402 , HOH A:415BINDING SITE FOR RESIDUE MPD A 401
12BC3SOFTWARESER B:56 , ALA B:57 , ASN B:60 , THR B:194 , GLY B:264 , MPD B:402 , HOH B:525BINDING SITE FOR RESIDUE MPD B 401
13BC4SOFTWAREILE B:22 , VAL B:25 , TYR B:26 , ALA B:46 , TYR B:168 , THR B:211 , LEU B:215 , MPD B:401BINDING SITE FOR RESIDUE MPD B 402
14BC5SOFTWARESER B:85 , GLY B:86 , LEU B:87 , PRO B:88 , TYR B:108 , GLY B:119BINDING SITE FOR RESIDUE MPD B 403
15BC6SOFTWAREILE A:22 , TYR A:26 , ALA A:46 , TYR A:168 , THR A:211 , MPD A:401BINDING SITE FOR RESIDUE MPD A 402
16BC7SOFTWAREGLY A:86 , LEU A:87 , PRO A:88 , TYR A:108 , GLY A:119 , LEU A:122 , LEU A:123BINDING SITE FOR RESIDUE MPD A 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2QE6)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Trp A:10 -Pro A:11
2Glu A:237 -Pro A:238
3Trp B:10 -Pro B:11
4Glu B:237 -Pro B:238

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QE6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2QE6)

(-) Exons   (0, 0)

(no "Exon" information available for 2QE6)

(-) 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:266
 aligned with Q47KX2_THEFY | Q47KX2 from UniProtKB/TrEMBL  Length:273

    Alignment length:266
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267      
         Q47KX2_THEFY     8 SVWPPPGLDFSKPTIARAYDALLGGKDNFEADRALADYACKHIPGLKESAIENRKVLVRGVRFLAGEAGISQFLDLGSGLPTVQNTHEVAQSVNPDARVVYVDIDPMVLTHGRALLAKDPNTAVFTADVRDPEYILNHPDVRRMIDFSRPAAIMLVGMLHYLSPDVVDRVVGAYRDALAPGSYLFMTSLVDTGLPAQQKLARITRENLGEGWARTPEEIERQFGDFELVEPGVVYTALWRPDEPVDPDNLSPGEQLGMAGIGRKKA 273
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2qe6A00 A:8-273 Vaccinia Virus protein VP39                                                                                                                                                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh....hhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.....eeeee........hhhhhhhhhh...eeeeee.hhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhh......eeee..hhhhh...hhhhhhhhhhhhh....eeeeeee....hhhhhhhhhhhhhhhh.....hhhhhhhh....ee.....ee.hhh...........hhhhh.eeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qe6 A   8 SVWPPPGLDFSKPTIARVYDALLGGKDNFEADRALADYACKhIPGLKESAIENRKVLVRGVRFLAGEAGISQFLDLGSGLPTVQNTHEVAQSVNPDARVVYVDIDPmVLTHGRALLAKDPNTAVFTADVRDPEYILNHPDVRRmIDFSRPAAImLVGmLHYLSPDVVDRVVGAYRDALAPGSYLFmTSLVDTGLPAQQKLARITRENLGEGWARTPEEIERQFGDFELVEPGVVYTALWRPDEPVDPDNLSPGEQLGmAGIGRKKA 273
                                    17        27        37        47 |      57        67        77        87        97       107      |117       127       137       147   |   157   |   167       177       187     | 197       207       217       227       237       247       257       267      
                                                                    49-NEP                                                          114-MSE                              151-MSE   161-MSE                         193-MSE                                                                 265-MSE    
                                                                                                                                                                                       165-MSE                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:266
 aligned with Q47KX2_THEFY | Q47KX2 from UniProtKB/TrEMBL  Length:273

    Alignment length:266
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267      
         Q47KX2_THEFY     8 SVWPPPGLDFSKPTIARAYDALLGGKDNFEADRALADYACKHIPGLKESAIENRKVLVRGVRFLAGEAGISQFLDLGSGLPTVQNTHEVAQSVNPDARVVYVDIDPMVLTHGRALLAKDPNTAVFTADVRDPEYILNHPDVRRMIDFSRPAAIMLVGMLHYLSPDVVDRVVGAYRDALAPGSYLFMTSLVDTGLPAQQKLARITRENLGEGWARTPEEIERQFGDFELVEPGVVYTALWRPDEPVDPDNLSPGEQLGMAGIGRKKA 273
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2qe6B00 B:8-273 Vaccinia Virus protein VP39                                                                                                                                                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh....hhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.....eeeee........hhhhhhhhhh...eeeeee.hhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhh......eeee..hhhhh...hhhhhhhhhhhhh....eeeeeee....hhhhhhhhhhhhhhhh.....hhhhhhhh....ee.....ee.hhh...........hhhhh.eeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qe6 B   8 SVWPPPGLDFSKPTIARVYDALLGGKDNFEADRALADYACKhIPGLKESAIENRKVLVRGVRFLAGEAGISQFLDLGSGLPTVQNTHEVAQSVNPDARVVYVDIDPmVLTHGRALLAKDPNTAVFTADVRDPEYILNHPDVRRmIDFSRPAAImLVGmLHYLSPDVVDRVVGAYRDALAPGSYLFmTSLVDTGLPAQQKLARITRENLGEGWARTPEEIERQFGDFELVEPGVVYTALWRPDEPVDPDNLSPGEQLGmAGIGRKKA 273
                                    17        27        37        47 |      57        67        77        87        97       107      |117       127       137       147   |   157   |   167       177       187     | 197       207       217       227       237       247       257       267      
                                                                    49-NEP                                                          114-MSE                              151-MSE   161-MSE                         193-MSE                                                                 265-MSE    
                                                                                                                                                                                       165-MSE
   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 2QE6)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2QE6)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q47KX2_THEFY | Q47KX2)
molecular function
    GO:0051539    4 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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