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Title :   CRYSTAL STRUCTURE OF SACCHAROMYCES CEREVISIAE N-MYRISTOYLTRANSFERASE WITH BOUND S-(2-OXO)PENTADECYLCOA AND THE OCTAPEPTIDE GLYASKLA

Authors :   T. A. Farazi, J. I. Gordon, G. Waksman

Date :   22 Apr 01 (Deposition) - 02 May 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym./Biol. Unit : A,O

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

Reference :   T. A. Farazi, G. Waksman, J. I. Gordon
Structures Of Saccharomyces Cerevisiae N-Myristoyltransferase With Bound Myristoylcoa And Peptide Provide Insights About Substrate Recognition And Catalysis.
Biochemistry V. 40 6335 2001
PubMed-ID: 11371195 | Reference-DOI: 10.1021/BI0101401
(for further references see the PDB file header)

Molecule 1 - PEPTIDE N-MYRISTOYLTRANSFERASE
	Chains	:	A
	EC Number	:	2.3.1.97
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PBB502
	Expression System Strain	:	JM101
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	N-MYRISTOYLTRANSFERASE (N-TERMINAL 33 RESIDUES DELETED)
	Gene	:	NMT
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE

Molecule 2 - OCTAPEPTIDE GLYASKLA
	Chains	:	O
	Engineered	:	YES
	Other Details	:	THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED.
	Synthetic	:	YES

		1	2
Asymmetric/Biological Unit	:	A	O

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	NHM	1	Ligand/Ion	S-(2-OXO)PENTADECYLCOA
2	NI	2	Ligand/Ion	NICKEL (II) ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:34 , ASP A:37 , HIS A:38	BINDING SITE FOR RESIDUE NI A 1
2	AC2	SOFTWARE	HIS A:296 , HOH A:534 , HOH A:552	BINDING SITE FOR RESIDUE NI A 2
3	AC3	SOFTWARE	HIS A:38 , LYS A:39 , PHE A:40 , TRP A:41 , ASN A:102 , TYR A:103 , GLU A:105 , ILE A:168 , ASN A:169 , PHE A:170 , LEU A:171 , CYS A:172 , VAL A:173 , ARG A:178 , SER A:179 , LYS A:180 , ARG A:181 , LEU A:182 , THR A:183 , PRO A:184 , ILE A:187 , THR A:191 , VAL A:194 , TYR A:204 , THR A:205 , ILE A:208 , LEU A:210 , PHE A:425 , HOH A:510 , HOH A:549	BINDING SITE FOR RESIDUE NHM A 500

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

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

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

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 d1iida1 A:34-218 N-myristoyl transferase, NMT                                                                                                                                            d1iida2 A:219-455 N-myristoyl transferase, NMT                                                                                                                                                                                                SCOP domains
               CATH domains 1iidA01 A:34-206  [code=3.40.630.30, no name defined]                                                                                                                        1iidA02 A:207-454  [code=3.40.630.30, no name defined]                                                                                                                                                                                                  - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh............ee.....hhhhh..........eeee.....hhhhhhhhhhhhhhhh........ee..hhhhhhhhh.........eeeeee.....eeeeeeeeeeeeee..eeeeeeeeeeeee.hhhh...hhhhhhhhhhhhhhh.....eeeee........eeeeeeeee.hhhhhhhhh....hhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhh...eee..hhhhhhhhhh...........eeeeeee.....eeeeeeeee..ee........ee.eeeeeeeee.hhhhh......hhhhhhhhhhhhhhhhhhhhhhhh...eeee....hhhhhhh....eeeeeeeeeeee.ee........................... Sec.struct. author
                 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
                 1iid 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

Chain O from PDB  Type:PROTEIN  Length:8
                                        
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ........ Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 1iid O 697 GLYASKLA 704

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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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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	d1iida1	A:34-218
1b	d1iida2	A:219-455

Asymmetric/Biological Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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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	1iidA01	A:34-206
1b	1iidA02	A:207-454

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

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 2nmt 2p6e 2p6f 2p6g

2nmt	2NMT CONTAINS THE SAME PROTEIN COMPLEXED WITH S-(2-OXO) PENTADECYLCOA AND THE PEPTIDOMIMETIC SC-58272

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