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(-) Description

Title :  CRYSTAL STRUCTURE OF MNMC2 FROM AQUIFEX AEOLICUS
 
Authors :  R. Shibata, Y. Bessho, S. Yokoyama, Riken Structural Genomics/Prot Initiative (Rsgi)
Date :  03 Oct 12  (Deposition) - 17 Oct 12  (Release) - 07 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.49
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Trna Wobble Uridine, Modification Enzyme, Genetic Code, 5- Methylaminomethyl-2-Thiouridine, Methyltransferase, 2-Codon Sets, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Kitamura, M. Nishimoto, T. Sengoku, R. Shibata, G. Jager, G. R. Bjork, H. Grosjean, S. Yokoyama, Y. Bessho
Characterization And Structure Of The Aquifex Aeolicus Protein Duf752: A Bacterial Trna-Methyltransferase (Mnmc2) Functioning Without The Usually Fused Oxidase Domain (Mnmc1
J. Biol. Chem. 2012
PubMed-ID: 23091054  |  Reference-DOI: 10.1074/JBC.M112.409300

(-) Compounds

Molecule 1 - MNMC2
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-11B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AQ_1980
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 224324
    Strain: VF5

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric Unit (3, 14)
No.NameCountTypeFull Name
1BEN2Ligand/IonBENZAMIDINE
2MSE8Mod. Amino AcidSELENOMETHIONINE
3SAM4Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1BEN-1Ligand/IonBENZAMIDINE
2MSE2Mod. Amino AcidSELENOMETHIONINE
3SAM1Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
1BEN1Ligand/IonBENZAMIDINE
2MSE2Mod. Amino AcidSELENOMETHIONINE
3SAM1Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 3 (3, 4)
No.NameCountTypeFull Name
1BEN1Ligand/IonBENZAMIDINE
2MSE2Mod. Amino AcidSELENOMETHIONINE
3SAM1Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 4 (2, 3)
No.NameCountTypeFull Name
1BEN-1Ligand/IonBENZAMIDINE
2MSE2Mod. Amino AcidSELENOMETHIONINE
3SAM1Ligand/IonS-ADENOSYLMETHIONINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:67 , HIS A:68 , GLY A:104 , PHE A:105 , GLY A:106 , LEU A:107 , GLY A:108 , TYR A:109 , ASN A:110 , GLU A:133 , LYS A:134 , GLY A:173 , ASP A:174 , ALA A:175 , ASP A:193 , PHE A:195 , ASN A:200 , GLU A:202 , LEU A:203BINDING SITE FOR RESIDUE SAM A 501
2AC2SOFTWARETYR B:67 , HIS B:68 , GLY B:104 , PHE B:105 , GLY B:106 , LEU B:107 , GLY B:108 , TYR B:109 , ASN B:110 , GLU B:133 , LYS B:134 , GLY B:173 , ASP B:174 , ALA B:175 , ASP B:193 , PHE B:195 , ASN B:200 , GLU B:202 , LEU B:203 , HOH B:518BINDING SITE FOR RESIDUE SAM B 401
3AC3SOFTWAREGLU B:12 , LEU B:22 , GLU B:24BINDING SITE FOR RESIDUE BEN B 402
4AC4SOFTWARETYR C:67 , HIS C:68 , GLY C:104 , PHE C:105 , GLY C:106 , LEU C:107 , GLY C:108 , TYR C:109 , ASN C:110 , GLU C:133 , LYS C:134 , GLY C:173 , ASP C:174 , ALA C:175 , ASP C:193 , PHE C:195 , ASN C:200 , GLU C:202 , LEU C:203 , HOH C:514 , HOH C:524BINDING SITE FOR RESIDUE SAM C 401
5AC5SOFTWAREGLU C:12 , GLU C:24 , PHE C:27BINDING SITE FOR RESIDUE BEN C 402
6AC6SOFTWARETYR D:67 , HIS D:68 , GLY D:104 , PHE D:105 , GLY D:106 , LEU D:107 , GLY D:108 , TYR D:109 , ASN D:110 , GLU D:133 , LYS D:134 , GLY D:173 , ASP D:174 , ALA D:175 , ASP D:193 , PHE D:195 , ASN D:200 , GLU D:202 , LEU D:203 , HOH D:504 , HOH D:505BINDING SITE FOR RESIDUE SAM D 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (7, 7)

Asymmetric Unit
No.Residues
1Glu A:145 -Pro A:146
2Val A:158 -Pro A:159
3Glu B:145 -Pro B:146
4Val B:158 -Pro B:159
5Glu C:145 -Pro C:146
6Val C:158 -Pro C:159
7Val D:158 -Pro D:159

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3VYW)

(-) 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:303
 aligned with O67789_AQUAE | O67789 from UniProtKB/TrEMBL  Length:308

    Alignment length:306
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301      
         O67789_AQUAE     2 KREEYLKNYLESYLRKKEVSLTEEEFNVILREFLRFAYNPEESGQEIADTADGSKTLIHKTYGEPYHSQTAGAIRESLYKFVRPSRILEKAKERKVIRILDVGFGLGYNLAVALKHLWEVNPKLRVEIISFEKELLKEFPILPEPYREIHEFLLERVPEYEGERLSLKVLLGDARKRIKEVENFKADAVFHDAFSPYKNPELWTLDFLSLIKERIDEKGYWVSYSSSLSVRKSLLTLGFKVGSSREIGRKRKGTVASLKAPVPPMEENEVRKLVLSPFAVPMRDEKLDKEPLEILIDYLLKVYKIS 307
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.......eeeee.....eeeee....ee......hhhhhhhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhhhhhhhhhhh...eeeeeeee.............hhhhhhhhhhhh.eee...eeeeeee.hhhhhhhhh....eeeeee.......hhhhhhhhhhhhhhh.eeeeeeeee...hhhhhhhhhhh..eeeeee..---.eeeeee........hhhhhhhhhhh.............hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3vyw A   2 KREEYLKNYLESYLRKKEVSLTEEEFNVILREFLRFAYNPEESGQEIADTADGSKTLIHKTYGEPYHSQTAGAIRESLYKFVRPSRILEKAKERKVIRILDVGFGLGYNLAVALKHLWEVNPKLRVEIISFEKELLKEFPILPEPYREIHEFLLERVPEYEGERLSLKVLLGDARKRIKEVENFKADAVFHDAFSPYKNPELWTLDFLSLIKERIDEKGYWVSYSSSLSVRKSLLTLGFKVGSSREI---RKGTVASLKAPVPPmEENEVRKLVLSPFAVPmRDEKLDKEPLEILIDYLLKVYKIS 307
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241      |  -|      261    |  271       281 |     291       301      
                                                                                                                                                                                                                                                                                248 252           266-MSE          283-MSE                    


Chain B from PDB  Type:PROTEIN  Length:305
 aligned with O67789_AQUAE | O67789 from UniProtKB/TrEMBL  Length:308

    Alignment length:305
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301     
         O67789_AQUAE     2 KREEYLKNYLESYLRKKEVSLTEEEFNVILREFLRFAYNPEESGQEIADTADGSKTLIHKTYGEPYHSQTAGAIRESLYKFVRPSRILEKAKERKVIRILDVGFGLGYNLAVALKHLWEVNPKLRVEIISFEKELLKEFPILPEPYREIHEFLLERVPEYEGERLSLKVLLGDARKRIKEVENFKADAVFHDAFSPYKNPELWTLDFLSLIKERIDEKGYWVSYSSSLSVRKSLLTLGFKVGSSREIGRKRKGTVASLKAPVPPMEENEVRKLVLSPFAVPMRDEKLDKEPLEILIDYLLKVYKI 306
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.......eeeee.....eeeee....ee......hhhhhhhhhhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhhhh...eeeeeeee.............hhhhhhhhhhhh.eee...eeeeeee.hhhhhhhhh....eeeeee.......hhhhhhhhhhhhhhhheeeeeeeee...hhhhhhhhhhh..eeeeee......eeeeee........hhhhhhhhhhh.............hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vyw B   2 KREEYLKNYLESYLRKKEVSLTEEEFNVILREFLRFAYNPEESGQEIADTADGSKTLIHKTYGEPYHSQTAGAIRESLYKFVRPSRILEKAKERKVIRILDVGFGLGYNLAVALKHLWEVNPKLRVEIISFEKELLKEFPILPEPYREIHEFLLERVPEYEGERLSLKVLLGDARKRIKEVENFKADAVFHDAFSPYKNPELWTLDFLSLIKERIDEKGYWVSYSSSLSVRKSLLTLGFKVGSSREIGRKRKGTVASLKAPVPPmEENEVRKLVLSPFAVPmRDEKLDKEPLEILIDYLLKVYKI 306
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261    |  271       281 |     291       301     
                                                                                                                                                                                                                                                                                                  266-MSE          283-MSE                   


Chain C from PDB  Type:PROTEIN  Length:305
 aligned with O67789_AQUAE | O67789 from UniProtKB/TrEMBL  Length:308

    Alignment length:305
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301     
         O67789_AQUAE     2 KREEYLKNYLESYLRKKEVSLTEEEFNVILREFLRFAYNPEESGQEIADTADGSKTLIHKTYGEPYHSQTAGAIRESLYKFVRPSRILEKAKERKVIRILDVGFGLGYNLAVALKHLWEVNPKLRVEIISFEKELLKEFPILPEPYREIHEFLLERVPEYEGERLSLKVLLGDARKRIKEVENFKADAVFHDAFSPYKNPELWTLDFLSLIKERIDEKGYWVSYSSSLSVRKSLLTLGFKVGSSREIGRKRKGTVASLKAPVPPMEENEVRKLVLSPFAVPMRDEKLDKEPLEILIDYLLKVYKI 306
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.......eeeee.....eeeee....ee......hhhhhhhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhhhhhhhhhhh...eeeeeeee.............hhhhhhhhhhhh.eee...eeeeeee.hhhhhhhhh....eeeeee.......hhhhhhhhhhhhhhhheeeeeeeee...hhhhhhhhhhh..eeeeee......eeeeee........hhhhhhhhhhh.............hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vyw C   2 KREEYLKNYLESYLRKKEVSLTEEEFNVILREFLRFAYNPEESGQEIADTADGSKTLIHKTYGEPYHSQTAGAIRESLYKFVRPSRILEKAKERKVIRILDVGFGLGYNLAVALKHLWEVNPKLRVEIISFEKELLKEFPILPEPYREIHEFLLERVPEYEGERLSLKVLLGDARKRIKEVENFKADAVFHDAFSPYKNPELWTLDFLSLIKERIDEKGYWVSYSSSLSVRKSLLTLGFKVGSSREIGRKRKGTVASLKAPVPPmEENEVRKLVLSPFAVPmRDEKLDKEPLEILIDYLLKVYKI 306
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261    |  271       281 |     291       301     
                                                                                                                                                                                                                                                                                                  266-MSE          283-MSE                   


Chain D from PDB  Type:PROTEIN  Length:306
 aligned with O67789_AQUAE | O67789 from UniProtKB/TrEMBL  Length:308

    Alignment length:306
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301      
         O67789_AQUAE     2 KREEYLKNYLESYLRKKEVSLTEEEFNVILREFLRFAYNPEESGQEIADTADGSKTLIHKTYGEPYHSQTAGAIRESLYKFVRPSRILEKAKERKVIRILDVGFGLGYNLAVALKHLWEVNPKLRVEIISFEKELLKEFPILPEPYREIHEFLLERVPEYEGERLSLKVLLGDARKRIKEVENFKADAVFHDAFSPYKNPELWTLDFLSLIKERIDEKGYWVSYSSSLSVRKSLLTLGFKVGSSREIGRKRKGTVASLKAPVPPMEENEVRKLVLSPFAVPMRDEKLDKEPLEILIDYLLKVYKIS 307
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.......eeee.......eeee....ee......hhhhhhhhhhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhhhh...eeeeeeee.............hhhhhhhhhhh..eee...eeeeeee.hhhhhhhhh....eeeeee.......hhhhhhhhhhhhhhhheeeeeeeee...hhhhhhhhhhh..eeeee........eeeee........hhhhhhhhhhh.............hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3vyw D   2 KREEYLKNYLESYLRKKEVSLTEEEFNVILREFLRFAYNPEESGQEIADTADGSKTLIHKTYGEPYHSQTAGAIRESLYKFVRPSRILEKAKERKVIRILDVGFGLGYNLAVALKHLWEVNPKLRVEIISFEKELLKEFPILPEPYREIHEFLLERVPEYEGERLSLKVLLGDARKRIKEVENFKADAVFHDAFSPYKNPELWTLDFLSLIKERIDEKGYWVSYSSSLSVRKSLLTLGFKVGSSREIGRKRKGTVASLKAPVPPmEENEVRKLVLSPFAVPmRDEKLDKEPLEILIDYLLKVYKIS 307
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261    |  271       281 |     291       301      
                                                                                                                                                                                                                                                                                                  266-MSE          283-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 3VYW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (O67789_AQUAE | O67789)
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.
    GO:0016645    oxidoreductase activity, acting on the CH-NH group of donors    Catalysis of an oxidation-reduction (redox) reaction in which a CH-NH group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
biological process
    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.

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  3vyw
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 Related Entries

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