1IIC - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF SACCHAROMYCES CEREVISIAE N-MYRISTOYLTRANSFERASE WITH BOUND MYRISTOYLCOA

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

Date :   22 Apr 01 (Deposition) - 02 May 01 (Release) - 02 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

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

Molecule 1 - PEPTIDE N-MYRISTOYLTRANSFERASE
	Chains	:	A, B
	EC Number	:	2.3.1.97
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PBB501
	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

		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 (1, 2)

No.	Name	Count	Type	Full Name
1	MYA	2	Ligand/Ion	TETRADECANOYL-COA

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	MYA	1	Ligand/Ion	TETRADECANOYL-COA

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	MYA	1	Ligand/Ion	TETRADECANOYL-COA

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:38 , LYS A:39 , PHE A:40 , TRP A:41 , TYR A:103 , 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 , THR A:191 , TRP A:200 , HIS A:201 , TYR A:204 , THR A:205 , ILE A:208 , LEU A:210 , PHE A:425 , HOH A:558 , HOH A:575	BINDING SITE FOR RESIDUE MYA A 500
2	AC2	SOFTWARE	HIS B:38 , LYS B:39 , PHE B:40 , TRP B:41 , ASN B:102 , TYR B:103 , GLU B:105 , ILE B:168 , PHE B:170 , LEU B:171 , VAL B:173 , ARG B:178 , SER B:179 , LYS B:180 , ARG B:181 , LEU B:182 , THR B:183 , PRO B:184 , ILE B:187 , THR B:191 , TRP B:200 , HIS B:201 , ALA B:202 , TYR B:204 , THR B:205 , ILE B:208 , LEU B:210 , PHE B:425 , HOH B:607 , HOH B:718	BINDING SITE FOR RESIDUE MYA B 600

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

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

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

Asymmetric Unit (2, 4)

	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	2	A:167-175 B:167-175
2	NMT_2	PS00976	Myristoyl-CoA:protein N-myristoyltransferase signature 2.	NMT_YEAST	412-418	2	A:412-418 B:412-418

Biological Unit 1 (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 -

Biological Unit 2 (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	- B:167-175
2	NMT_2	PS00976	Myristoyl-CoA:protein N-myristoyltransferase signature 2.	NMT_YEAST	412-418	1	- B:412-418

Asymmetric Unit (1, 2)

	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	2	A:34-455 B:34-455	422 422

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: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 d1iica1 A:34-218 N-myristoyl transferase, NMT                                                                                                                                            d1iica2 A:219-455 N-myristoyl transferase, NMT                                                                                                                                                                                                SCOP domains
               CATH domains 1iicA01 A:34-206  [code=3.40.630.30, no name defined]                                                                                                                        1iicA02 A:207-454  [code=3.40.630.30, no name defined]                                                                                                                                                                                                  - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh............ee.....hhhhh..........eeeee....hhhhhhhhhhhhhhhh..hhhh.eee..hhhhhhhhhh....hhh.eeeeee.....eeeeeeeeeeeeee..eeeeeeeeeeeee.hhhh...hhhhhhhhhhhhhhh.....eeeee........eeeeeeeee.hhhhhhhh.........hhhhhhhhhh.........eee.hhhhhhhhhhhhhhhhh...eee..hhhhhhhhhh.....hhhhh.eeeeeee.....eeeeeeeee..eee.......ee.eeeeeeeee..........hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhh......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
                 1iic 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 B 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 d1iicb1 B:34-218 N-myristoyl transferase, NMT                                                                                                                                            d1iicb2 B:219-455 N-myristoyl transferase, NMT                                                                                                                                                                                                SCOP domains
               CATH domains 1iicB01 B:34-206  [code=3.40.630.30, no name defined]                                                                                                                        1iicB02 B:207-454  [code=3.40.630.30, no name defined]                                                                                                                                                                                                  - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh............ee.....hhhhh..........eeeee....hhhhhhhhhhhhhhhh.......eee..hhhhhhhhh.....hhh.eeeeee.....eeeeeeeeeeeeee..eeeeeeeeeeeee.hhhh...hhhhhhhhhhhhhhhh....eeeee........eeeeeeeee.hhhhhhhh.........hhhhhhhhhh.........eee.hhhhhhhhhhhhhhhhh...eee..hhhhhhhhhh...........eeeeeee.....eeeeeeeee..eee.......ee.eeeeeeeee..........hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhh......eeeeeeeeeeee.ee........................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------NMT_1    --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NMT_2  ------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:34-455 UniProt: 1-455 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                    Transcript 1
                 1iic B  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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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	d1iica1	A:34-218
1b	d1iica2	A:219-455
1c	d1iicb1	B:34-218
1d	d1iicb2	B:219-455

Asymmetric 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	1iicA01	A:34-206
1b	1iicB01	B:34-206
1c	1iicA02	A:207-454
1d	1iicB02	B:207-454

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (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 Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		MYA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1iic)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1iic
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	NMT_YEAST \| P14743
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	2.3.1.97
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	NMT_YEAST \| P14743
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	NMT_YEAST \| P14743	:	1iid 2nmt 2p6e 2p6f 2p6g

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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (1, 2)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (1, 4)

Pfam Domains (0, 0)

Gene Ontology (8, 8)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File