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(-) Description

Title :  CRYSTAL STRUCTURE OF N5-GLUTAMINE METHYLTRANSFERASE, HEMK(EC 2.1.1.-) (TM0488) FROM THERMOTOGA MARITIMA AT 2.80 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  02 Dec 04  (Deposition) - 01 Feb 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Tm0488, N5-Glutamine Methyltransferase, Hemk(Ec 2. 1. 1. -), Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of N5-Glutamine Methyltransferase, Hemk(E 2. 1. 1. -) (Tm0488) From Thermotoga Maritima At 2. 80 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - N5-GLUTAMINE METHYLTRANSFERASE, HEMK
    Chains: A, B
    EC Number: 2.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TM0488
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 243274
    Strain: MSB8

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2SAM2Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
2SAM1Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
2SAM1Ligand/IonS-ADENOSYLMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:100 , THR A:106 , GLY A:129 , THR A:130 , GLY A:131 , ASP A:151 , VAL A:152 , GLY A:178 , GLU A:179 , PHE A:180 , ASN A:197 , PRO A:198 , PRO A:199 , ALA A:218 , PHE A:228 , HOH A:303BINDING SITE FOR RESIDUE SAM A 301
2AC2SOFTWAREPHE B:100 , GLY B:129 , THR B:130 , GLY B:131 , ILE B:135 , ASP B:151 , VAL B:152 , GLU B:179 , PHE B:180 , ASN B:197 , PRO B:198 , PRO B:199 , GLU B:217 , ALA B:218 , PHE B:228BINDING SITE FOR RESIDUE SAM B 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VQ1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1VQ1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VQ1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VQ1)

(-) Exons   (0, 0)

(no "Exon" information available for 1VQ1)

(-) 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 PRMC_THEMA | Q9WYV8 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:271
                                    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 
           PRMC_THEMA    12 RKIWSLIRDCSGKLEGVTETSVLEVLLIVSRVLGIRKEDLFLKDLGVSPTEEKRILELVEKRASGYPLHYILGEKEFMGLSFLVEEGVFVPRPETEELVELALELIRKYGIKTVADIGTGSGAIGVSVAKFSDAIVFATDVSSKAVEIARKNAERHGVSDRFFVRKGEFLEPFKEKFASIEMILSNPPYVKSSAHLPKDVLFEPPEALFGGEDGLDFYREFFGRYDTSGKIVLMEIGEDQVEELKKIVSDTVFLKDSAGKYRFLLLNRRSS 282
               SCOP domains d1vq1a_ A: automated matches                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1vq1A01 A:12-85 DNA helicase RuvA subunit, C-terminal domain              1vq1A02 A:86-282 Vaccinia Virus protein VP39                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhh.......hhhhhhhhhhhhhhhhhh.hhhhhhh.eee..eee..........hhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhh...eeeeee.hhhhhhhhhhhhhh......eeeee...hhhhhhhh....eeee..........-----...hhhhhh.....hhhhhhhhhhh.....eeeee.hhhhhhhhhhhh...eeee.....eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vq1 A  12 RKIWSLIRDCSGKLEGVTETSVLEVLLIVSRVLGIRKEDLFLKDLGVSPTEEKRILELVEKRASGYPLHYILGEKEFmGLSFLVEEGVFVPRPETEELVELALELIRKYGIKTVADIGTGSGAIGVSVAKFSDAIVFATDVSSKAVEIARKNAERHGVSDRFFVRKGEFLEPFKEKFASIEmILSNPPYVKSSAH-----LFEPPEALFGGEDGLDFYREFFGRYDTSGKIVLmEIGEDQVEELKKIVSDTVFLKDSAGKYRFLLLNRRSS 282
                                    21        31        41        51        61        71        81       |91       101       111       121       131       141       151       161       171       181       191 |     201    |    -|      221       231       241   |   251       261       271       281 
                                                                                                        89-MSE                                                                                                 193-MSE      206   212                              245-MSE                                 


Chain B from PDB  Type:PROTEIN  Length:264
 aligned with PRMC_THEMA | Q9WYV8 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:271
                                    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 
           PRMC_THEMA    12 RKIWSLIRDCSGKLEGVTETSVLEVLLIVSRVLGIRKEDLFLKDLGVSPTEEKRILELVEKRASGYPLHYILGEKEFMGLSFLVEEGVFVPRPETEELVELALELIRKYGIKTVADIGTGSGAIGVSVAKFSDAIVFATDVSSKAVEIARKNAERHGVSDRFFVRKGEFLEPFKEKFASIEMILSNPPYVKSSAHLPKDVLFEPPEALFGGEDGLDFYREFFGRYDTSGKIVLMEIGEDQVEELKKIVSDTVFLKDSAGKYRFLLLNRRSS 282
               SCOP domains d1vq1b_ B: automated matches                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1vq1B01 B:12-85 DNA helicase RuvA subunit, C-terminal domain              1vq1B02 B:86-282 Vaccinia Virus protein VP39                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhh.......hhhhhhhhhhhhhhhhhh.hhhhhhh.eee..eee..........hhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhh...eeeeee.hhhhhhhhhhhhhh......eeeee...hhhhhhhh....eeee........-------...hhhhhh.....hhhhhhhhhhh.....eeeee.hhhhhhhhhhhh...eeee.....eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vq1 B  12 RKIWSLIRDCSGKLEGVTETSVLEVLLIVSRVLGIRKEDLFLKDLGVSPTEEKRILELVEKRASGYPLHYILGEKEFmGLSFLVEEGVFVPRPETEELVELALELIRKYGIKTVADIGTGSGAIGVSVAKFSDAIVFATDVSSKAVEIARKNAERHGVSDRFFVRKGEFLEPFKEKFASIEmILSNPPYVKSS-------LFEPPEALFGGEDGLDFYREFFGRYDTSGKIVLmEIGEDQVEELKKIVSDTVFLKDSAGKYRFLLLNRRSS 282
                                    21        31        41        51        61        71        81       |91       101       111       121       131       141       151       161       171       181       191 |     201  |      -|      221       231       241   |   251       261       271       281 
                                                                                                        89-MSE                                                                                                 193-MSE    204     212                              245-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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1VQ1)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PRMC_THEMA | Q9WYV8)
molecular function
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0008276    protein methyltransferase activity    Catalysis of the transfer of a methyl group (CH3-) to a protein.
    GO:0036009    protein-glutamine N-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + protein L-glutamine = S-adenosyl-L-homocysteine + protein N-methyl-L-glutamine.
    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:0018364    peptidyl-glutamine methylation    The addition of a methyl group to a glutamine residue in a protein.
    GO:0006479    protein methylation    The addition of a methyl group to a protein amino acid. A methyl group is derived from methane by the removal of a hydrogen atom.

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