1NV8 - JenaLib

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Title :   N5-GLUTAMINE METHYLTRANSFERASE, HEMK

Authors :   H. L. Schubert, J. D. Phillips, C. P. Hill

Date :   02 Feb 03 (Deposition) - 27 May 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Class I Adomet-Dependent Methyltransferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. L. Schubert, J. D. Phillips, C. P. Hill
Structures Along The Catalytic Pathway Of Prmc/Hemk, An N(5)-Glutamine Adomet-Dependent Methyltransferase
Biochemistry V. 42 5592 2003
PubMed-ID: 12741815 | Reference-DOI: 10.1021/BI034026P
(for further references see the PDB file header)

Molecule 1 - HEMK PROTEIN
	Chains	:	A, B
	EC Number	:	2.1.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PHIS.PARELLEL3
	Expression System Strain	:	BL21(DE3)CODON+
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	HEMK
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	2336

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	MEQ	2	Ligand/Ion	N5-METHYLGLUTAMINE
2	SAM	2	Ligand/Ion	S-ADENOSYLMETHIONINE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	MEQ	1	Ligand/Ion	N5-METHYLGLUTAMINE
2	SAM	1	Ligand/Ion	S-ADENOSYLMETHIONINE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	MEQ	1	Ligand/Ion	N5-METHYLGLUTAMINE
2	SAM	1	Ligand/Ion	S-ADENOSYLMETHIONINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:100 , PRO A:102 , GLY A:129 , THR A:130 , GLY A:131 , ASP A:151 , VAL A:152 , GLU A:179 , PHE A:180 , ASN A:197 , PRO A:199 , GLU A:217 , ALA A:218 , MEQ A:400 , HOH A:401 , HOH A:402 , HOH A:404 , HOH A:408 , HOH A:464 , HOH A:467	BINDING SITE FOR RESIDUE SAM A 300
2	AC2	SOFTWARE	PHE B:100 , PRO B:102 , GLY B:129 , THR B:130 , GLY B:131 , ASP B:151 , VAL B:152 , GLY B:178 , GLU B:179 , PHE B:180 , ASN B:197 , PRO B:199 , GLU B:217 , ALA B:218 , MEQ B:401 , HOH B:406 , HOH B:407 , HOH B:409 , HOH B:410 , HOH B:436 , HOH B:488	BINDING SITE FOR RESIDUE SAM B 301
3	AC3	SOFTWARE	ARG A:103 , ASN A:197 , PRO A:198 , PRO A:199 , TYR A:200 , VAL A:201 , ALA A:218 , LEU A:219 , SAM A:300	BINDING SITE FOR RESIDUE MEQ A 400
4	AC4	SOFTWARE	ASN B:197 , PRO B:198 , PRO B:199 , TYR B:200 , LEU B:219 , SAM B:301	BINDING SITE FOR RESIDUE MEQ B 401

(no "SS Bond" information available for 1NV8)

(no "Cis Peptide Bond" information available for 1NV8)

(no "SAP(SNP)/Variant" information available for 1NV8)

(no "PROSITE Motif" information available for 1NV8)

(no "Exon" information available for 1NV8)

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
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Chain A from PDB  Type:PROTEIN  Length:271
 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 d1nv8a_ A: N5-glutamine methyltransferase, HemK                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1nv8A01 A:12-85 DNA helicase RuvA subunit, C-terminal domain              1nv8A02 A:86-282 Vaccinia Virus protein VP39                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhh......hhhhhhhhhhhhhhhhh..hhhhhhheeee..eeee..........hhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh.....eeeee...hhhhhhhh....eeee.....hhhhh........hhhhhh.....hhhhhhhhhhh.....eeeee....hhhhhh......eeee.....eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nv8 A  12 RKIWSLIRDCSGKLEGVTETSVLEVLLIVSRVLGIRKEDLFLKDLGVSPTEEKRILELVEKRASGYPLHYILGEKEFMGLSFLVEEGVFVPRPETEELVELALELIRKYGIKTVADIGTGSGAIGVSVAKFSDAIVFATDVSSKAVEIARKNAERHGVSDRFFVRKGEFLEPFKEKFASIEMILSNPPYVKSSAHLPKDVLFEPPEALFGGEDGLDFYREFFGRYDTSGKIVLMEIGEDQVEELKKIVSDTVFLKDSAGKYRFLLLNRRSS 282
                                    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

Chain B from PDB  Type:PROTEIN  Length:267
 aligned with PRMC_THEMA | Q9WYV8 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:269
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272         
           PRMC_THEMA    13 KIWSLIRDCSGKLEGVTETSVLEVLLIVSRVLGIRKEDLFLKDLGVSPTEEKRILELVEKRASGYPLHYILGEKEFMGLSFLVEEGVFVPRPETEELVELALELIRKYGIKTVADIGTGSGAIGVSVAKFSDAIVFATDVSSKAVEIARKNAERHGVSDRFFVRKGEFLEPFKEKFASIEMILSNPPYVKSSAHLPKDVLFEPPEALFGGEDGLDFYREFFGRYDTSGKIVLMEIGEDQVEELKKIVSDTVFLKDSAGKYRFLLLNRRS 281
               SCOP domains d1nv8b_ B: N5-glutamine methyltransferase  , HemK                                                                                                                                                                                                                             SCOP domains
               CATH domains 1nv8B01 B:13-85 DNA helicase RuvA subunit  , C-terminal domain           1nv8B02 B:86-281 Vaccinia Virus protein VP39                                                                                                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh......hhhhhhhhhhhhhhh.hhhhhh.--...hhhhhhhhhhhhhhhhh..hhhhhhheeee..eeee.........hhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhh.eeee............hhhhhhhhhhh......hhhhhhhhhhh.....eeeee....hhhhhhhhh...eeee.....eeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nv8 B  13 KIWSLIRDCSGKLEGVTETSVLEVLLIVSRVLGIRKEDLFL--LGVSPTEEKRILELVEKRASGYPLHYILGEKEFMGLSFLVEEGVFVPRPETEELVELALELIRKYGIKTVADIGTGSGAIGVSVAKFSDAIVFATDVSSKAVEIARKNAERHGVSDRFFVRKGEFLEPFKEKFASIEMILSNPPYVKSSAHLPKDVLFEPPEALFGGEDGLDFYREFFGRYDTSGKIVLMEIGEDQVEELKKIVSDTVFLKDSAGKYRFLLLNRRS 281
                                    22        32        42        52|  |    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272         
                                                                   53 56

Legend:		→ Mismatch	(orange background)
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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 '\|'

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: Vaccinia Virus protein VP39 (378)

Thermotoga maritima. Organism_taxid: 2336. (5)

1a	1nv8A02	A:86-282
1b	1nv8B02	B:86-281

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Helicase, Ruva Protein; domain 3 (218)

Homologous Superfamily: DNA helicase RuvA subunit, C-terminal domain (65)

Thermotoga maritima. Organism_taxid: 2336. (2)

2a	1nv8B01	B:13-85
2b	1nv8A01	A:12-85

(no "Pfam Domain" information available for 1NV8)

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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1nv9	HEMK, APO STRUCTURE

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