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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   MYRISTOYL-COA:PROTEIN N-MYRISTOYLTRANSFERASE BOUND TO MYRISTOYL-COA AND PEPTIDE ANALOGS

Authors :   K. Fuetterer, R. S. Bhatnagar, G. Waksman

Date :   14 Jul 98 (Deposition) - 06 Jan 99 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

Chains :   Asym./Biol. Unit : A

Keywords :   Transferase Acyltransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. S. Bhatnagar, K. Futterer, T. A. Farazi, S. Korolev, C. L. Murray, E. Jackson-Machelski, G. W. Gokel, J. I. Gordon, G. Waksman
Structure Of N-Myristoyltransferase With Bound Myristoylcoa And Peptide Substrate Analogs.
Nat. Struct. Biol. V. 5 1091 1998
PubMed-ID: 9846880 | Reference-DOI: 10.1038/4202

Molecule 1 - MYRISTOYL-COA:PROTEIN N-MYRISTOYLTRANSFERASE
	Chains	:	A
	EC Number	:	2.3.1.97
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PBB131
	Expression System Strain	:	JM101
	Expression System Taxid	:	562
	Gene	:	NMT1
	Mutation	:	YES
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE, PEPTIDE N- MYRISTOYLTRANSFERASE, NMT

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 14)

No.	Name	Count	Type	Full Name
1	GOL	12	Ligand/Ion	GLYCEROL
2	MIM	1	Ligand/Ion	[CYCLOHEXYLETHYL]-[[[[4-[2-METHYL-1-IMIDAZOLYL-BUTYL]PHENYL]ACETYL]-SERYL]-LYSINYL]-AMINE
3	NHM	1	Ligand/Ion	S-(2-OXO)PENTADECYLCOA

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:38 , LYS A:39 , PHE A:40 , TRP A:41 , ASN A:102 , TYR A:103 , VAL A:104 , ILE A:168 , ASN A:169 , PHE A:170 , LEU A:171 , CYS A:172 , VAL A:173 , ARG A:178 , SER A:179 , ARG A:181 , LEU A:182 , THR A:183 , PRO A:184 , ILE A:187 , THR A:191 , TRP A:200 , HIS A:201 , ALA A:202 , TYR A:204 , THR A:205 , PHE A:425 , MIM A:700 , HOH A:1003	BINDING SITE FOR RESIDUE NHM A 500
02	AC2	SOFTWARE	VAL A:104 , ASP A:106 , ASP A:108 , PHE A:113 , TYR A:115 , ASN A:169 , THR A:205 , GLY A:207 , TYR A:219 , HIS A:221 , PRO A:223 , PHE A:234 , THR A:235 , PHE A:334 , GLY A:416 , ASP A:417 , GLY A:418 , LEU A:455 , NHM A:500 , HOH A:1016	BINDING SITE FOR RESIDUE MIM A 700
03	AC3	SOFTWARE	MET A:246 , GLU A:249 , GOL A:812 , HOH A:1034	BINDING SITE FOR RESIDUE GOL A 801
04	AC4	SOFTWARE	ASP A:132 , ASP A:245 , GOL A:809	BINDING SITE FOR RESIDUE GOL A 802
05	AC5	SOFTWARE	CYS A:197 , GOL A:809	BINDING SITE FOR RESIDUE GOL A 803
06	AC6	SOFTWARE	HIS A:296 , HOH A:1043 , HOH A:1055	BINDING SITE FOR RESIDUE GOL A 804
07	AC7	SOFTWARE	LYS A:263 , PHE A:298 , GLY A:300 , ILE A:311 , SER A:313	BINDING SITE FOR RESIDUE GOL A 805
08	AC8	SOFTWARE	ASP A:270 , LYS A:291 , ASP A:307	BINDING SITE FOR RESIDUE GOL A 806
09	AC9	SOFTWARE	PRO A:58 , HIS A:201	BINDING SITE FOR RESIDUE GOL A 807
10	BC1	SOFTWARE	GLU A:80 , TRP A:81 , CYS A:82 , SER A:83 , GLN A:91 , ARG A:138	BINDING SITE FOR RESIDUE GOL A 808
11	BC2	SOFTWARE	ASP A:132 , THR A:242 , GLU A:244 , ASP A:245 , GOL A:802 , GOL A:803	BINDING SITE FOR RESIDUE GOL A 809
12	BC3	SOFTWARE	GLU A:317 , PRO A:319 , ASP A:320 , GLY A:321	BINDING SITE FOR RESIDUE GOL A 810
13	BC4	SOFTWARE	ASP A:70 , LYS A:196 , GLU A:244	BINDING SITE FOR RESIDUE GOL A 811
14	BC5	SOFTWARE	ASP A:85 , HIS A:241 , GLU A:249 , GOL A:801 , HOH A:1034	BINDING SITE FOR RESIDUE GOL A 812

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

(no "Cis Peptide Bond" information available for 2NMT)

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

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NMT_1	PS00975	Myristoyl-CoA:protein N-myristoyltransferase signature 1.	NMT_YEAST	167-175	1	A:167-175
2	NMT_2	PS00976	Myristoyl-CoA:protein N-myristoyltransferase signature 2.	NMT_YEAST	412-418	1	A:412-418

Asymmetric/Biological Unit (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YLR195C	1	YLR195C.1	XII:543306-541939	1368	NMT_YEAST	1-455	455	1	A:34-455	422

Asymmetric/Biological 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
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Chain A from PDB  Type:PROTEIN  Length:422
 aligned with NMT_YEAST | P14743 from UniProtKB/Swiss-Prot  Length:455

    Alignment length:422
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453  
            NMT_YEAST    34 AMKDHKFWRTQPVKDFDEKVVEEGPIDKPKTPEDISDKPLPLLSSFEWCSIDVDNKKQLEDVFVLLNENYVEDRDAGFRFNYTKEFFNWALKSPGWKKDWHIGVRVKETQKLVAFISAIPVTLGVRGKQVPSVEINFLCVHKQLRSKRLTPVLIKEITRRVNKCDIWHALYTAGIVLPAPVSTCRYTHRPLNWKKLYEVDFTGLPDGHTEEDMIAENALPAKTKTAGLRKLKKEDIDQVFELFKRYQSRFELIQIFTKEEFEHNFIGEESLPLDKQVIFSYVVEQPDGKITDFFSFYSLPFTILNNTKYKDLGIGYLYYYATDADFQFKDRFDPKATKALKTRLCELIYDACILAKNANMDVFNALTSQDNTLFLDDLKFGPGDGFLNFYLFNYRAKPITGGLNPDNSNDIKRRSNVGVVML 455
               SCOP domains d2nmta1 A:34-218 N-myristoyl transferase, NMT                                                                                                                                            d2nmta2 A:219-455 N-myristoyl transferase, NMT                                                                                                                                                                                                SCOP domains
               CATH domains 2nmtA01 A:34-206  [code=3.40.630.30, no name defined]                                                                                                                        2nmtA02 A:207-454  [code=3.40.630.30, no name defined]                                                                                                                                                                                                  - CATH domains
               Pfam domains ----------------------NMT-2nmtA01 A:56-217                                                                                                                                              -------------NMT_C-2nmtA02 A:231-454                                                                                                                                                                                                         - Pfam domains
     Sec.struct. author (1) .hhh...hhh.....................hhh...........eeeee.....hhhhhhhhhhhhhh........eee...hhhhhhh.......hhheeeeee........----------hhheeeeeeeee.....hhh.....hhhhhhhhhhhhhhh...eeeeee........eeee.eeee..hhhhhhh..........hhhhhhh................hhhhhhhhhhhhhhhhh..eee....hhhhhhh............eeeeee........eeeeeee..eee..........eeee..eee..hhh......hhhhhhhhhhhhhhhhhhhhhhhh....eeee.....hhhhhhhh.......eeeeeee.............................. Sec.struct. author (1)
     Sec.struct. author (2) ------------------------------------------------------------------------------------------------------------------eeeeeeeeeee--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------NMT_1    --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NMT_2  ------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:34-455 UniProt: 1-455 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                    Transcript 1
                 2nmt A  34 AMKDHKFWRTQPVKDFDEKVVEEGPIDKPKTPEDISDKPLPLLSSFEWCSIDVDNKKQLEDVFVLLNENYVEDRDAGFRFNYTKEFFNWALKSPGWKKDWHIGVRVKETQKLVAFISAIPVTLGVRGKQVPSVEINFLCVHKQLRSKRLTPVLIKEITRRVNKCDIWHALYTAGIVLPAPVSTCRYTHRPLNWKKLYEVDFTGLPDGHTEEDMIAENALPAKTKTAGLRKLKKEDIDQVFELFKRYQSRFELIQIFTKEEFEHNFIGEESLPLDKQVIFSYVVEQPDGKITDFFSFYSLPFTILNNTKYKDLGIGYLYYYATDADFQFKDRFDPKATKALKTRLCELIYDACILAKNANMDVFNALTSQDNTLFLDDLKFGPGDGFLNFYLFNYRAKPITGGLNPDNSNDIKRRSNVGVVML 455
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

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Class: Alpha and beta proteins (a+b) (23004)

Fold: Acyl-CoA N-acyltransferases (Nat) (250)

Superfamily: Acyl-CoA N-acyltransferases (Nat) (250)

Family: N-myristoyl transferase, NMT (7)

Protein domain: N-myristoyl transferase, NMT (7)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (3)

1a	d2nmta1	A:34-218
1b	d2nmta2	A:219-455

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Aminopeptidase (284)

Homologous Superfamily: [code=3.40.630.30, no name defined] (126)

Baker's yeast (Saccharomyces cerevisiae) (10)

1a	2nmtA01	A:34-206
1b	2nmtA02	A:207-454

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (NMT_YEAST | P14743)

molecular function
	GO:0004379	glycylpeptide N-tetradecanoyltransferase activity	Catalysis of the reaction: tetradecanoyl-CoA + glycyl-peptide = CoA + N-tetradecanoylglycyl-peptide.
	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.
	GO:0016746	transferase activity, transferring acyl groups	Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
biological process
	GO:0018008	N-terminal peptidyl-glycine N-myristoylation	The myristoylation of the N-terminal glycine of proteins to form the derivative N-myristoyl-glycine.
	GO:0006499	N-terminal protein myristoylation	The covalent attachment of a myristoyl group to the N-terminal amino acid residue of a protein.
	GO:0001302	replicative cell aging	The process associated with progression of the cell from its inception to the end of its lifespan that occurs as the cell continues cycles of growth and division.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric/Biological Unit
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	NMT_YEAST \| P14743	:	1iic 1iid 2p6e 2p6f 2p6g

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 14)

Sites (14, 14)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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Exons (1, 1)

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