3IU1 - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN TYPE-I N-MYRISTOYLTRANSFERASE WITH BOUND MYRISTOYL-COA

Authors :   W. Qiu, A. Hutchinson, A. Wernimont, Y. -H. Lin, A. Kania, M. Ravichandr I. Kozieradzki, D. Cossar, M. Schapira, C. H. Arrowsmith, C. Bountra, J. Weigelt, A. M. Edwards, P. G. Wyatt, M. A. J. Ferguson, J. A. Frearson S. Y. Brand, D. A. Robinson, A. Bochkarev, R. Hui, Structural Genomic Consortium (Sgc)

Date :   29 Aug 09 (Deposition) - 15 Sep 09 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.42

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

Keywords :   Transferase, N-Myristoyltransferase, Nmt1, Acyltransferase, Phosphoprotein, Structural Genomics, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. Qiu, A. Hutchinson, A. Wernimont, Y. -H. Lin, A. Kania, M. Ravichandran, I. Kozieradzki, D. Cossar, M. Schapira, C. H. Arrowsmith, C. Bountra, J. Weigelt, A. M. Edwards, P. G. Wyatt, M. A. J. Ferguson, J. A. Frearson, S. Y. Brand, D. A. Robinson, A. Bochkarev, R. Hui
Crystal Structure Of Human Type-I N-Myristoyltransferase With Bound Myristoyl-Coa
To Be Published
PubMed: search

Molecule 1 - GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE 1
	Chains	:	A, B
	EC Number	:	2.3.1.97
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	NMT, NMT1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		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	TYR A:117 , GLN A:118 , PHE A:119 , TRP A:120 , ASN A:179 , TYR A:180 , VAL A:181 , ASN A:246 , PHE A:247 , LEU A:248 , CYS A:249 , VAL A:250 , ARG A:255 , SER A:256 , LYS A:257 , ARG A:258 , VAL A:259 , ALA A:260 , PRO A:261 , THR A:268 , VAL A:271 , PHE A:277 , TYR A:281 , THR A:282 , LEU A:287 , TYR A:479 , HOH A:532 , HOH A:587 , HOH A:601 , HOH A:607 , HOH A:649 , HOH A:653 , HOH A:663 , HOH A:696 , HOH A:720 , HOH A:822	BINDING SITE FOR RESIDUE MYA A 1001
2	AC2	SOFTWARE	HOH B:7 , TYR B:117 , GLN B:118 , PHE B:119 , TRP B:120 , ASN B:179 , TYR B:180 , VAL B:181 , ASN B:246 , PHE B:247 , LEU B:248 , CYS B:249 , VAL B:250 , ARG B:255 , SER B:256 , LYS B:257 , ARG B:258 , VAL B:259 , ALA B:260 , PRO B:261 , THR B:268 , VAL B:271 , PHE B:277 , TYR B:281 , THR B:282 , LEU B:287 , TYR B:479 , HOH B:531 , HOH B:534 , HOH B:545 , HOH B:565 , HOH B:640 , HOH B:729 , HOH B:734 , HOH B:741 , HOH B:806	BINDING SITE FOR RESIDUE MYA B 2001

(no "SS Bond" information available for 3IU1)

Asymmetric Unit

No.	Residues
1	Pro A:288	-	Lys A:289
2	Pro B:288	-	Lys B:289

(no "SAP(SNP)/Variant" information available for 3IU1)

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.	NMT1_HUMAN	244-252	2	A:244-252 B:244-252
2	NMT_2	PS00976	Myristoyl-CoA:protein N-myristoyltransferase signature 2.	NMT1_HUMAN	466-472	2	A:466-472 B:466-472

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.	NMT1_HUMAN	244-252	1	A:244-252 -
2	NMT_2	PS00976	Myristoyl-CoA:protein N-myristoyltransferase signature 2.	NMT1_HUMAN	466-472	1	A:466-472 -

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.	NMT1_HUMAN	244-252	1	- B:244-252
2	NMT_2	PS00976	Myristoyl-CoA:protein N-myristoyltransferase signature 2.	NMT1_HUMAN	466-472	1	- B:466-472

Asymmetric Unit (10, 20)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000258960	1	ENSE00001324312	chr17:43138680-43138828	149	NMT1_HUMAN	1-44	44	0	-	-
1.2	ENST00000258960	2	ENSE00001134100	chr17:43159012-43159120	109	NMT1_HUMAN	44-80	37	0	-	-
1.3	ENST00000258960	3	ENSE00000924941	chr17:43163876-43164020	145	NMT1_HUMAN	81-129	49	2	A:115-129 B:115-129	15 15
1.4	ENST00000258960	4	ENSE00000924940	chr17:43171053-43171171	119	NMT1_HUMAN	129-168	40	2	A:129-168 B:129-168	40 40
1.5	ENST00000258960	5	ENSE00000924939	chr17:43173562-43173653	92	NMT1_HUMAN	169-199	31	2	A:169-199 B:169-199	31 31
1.6	ENST00000258960	6	ENSE00000924938	chr17:43174496-43174612	117	NMT1_HUMAN	199-238	40	2	A:199-238 B:199-238	40 40
1.7	ENST00000258960	7	ENSE00000924937	chr17:43175750-43175920	171	NMT1_HUMAN	238-295	58	2	A:238-295 B:238-295	58 58
1.8	ENST00000258960	8	ENSE00000924936	chr17:43176773-43176881	109	NMT1_HUMAN	295-331	37	2	A:295-331 (gaps) B:295-331	37 37
1.9	ENST00000258960	9	ENSE00000924935	chr17:43180319-43180489	171	NMT1_HUMAN	332-388	57	2	A:332-388 B:332-388	57 57
1.10	ENST00000258960	10	ENSE00000924934	chr17:43181077-43181244	168	NMT1_HUMAN	389-444	56	2	A:389-444 B:389-444	56 56
1.11	ENST00000258960	11	ENSE00000924933	chr17:43182227-43182364	138	NMT1_HUMAN	445-490	46	2	A:445-490 B:445-490	46 46
1.12	ENST00000258960	12	ENSE00001110185	chr17:43182987-43186377	3391	NMT1_HUMAN	491-496	6	2	A:491-496 B:491-496	6 6

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:380
 aligned with NMT1_HUMAN | P30419 from UniProtKB/Swiss-Prot  Length:496

    Alignment length:382
                                   124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494  
           NMT1_HUMAN   115 RSYQFWDTQPVPKLGEVVNTHGPVEPDKDNIRQEPYTLPQGFTWDALDLGDRGVLKELYTLLNENYVEDDDNMFRFDYSPEFLLWALRPPGWLPQWHCGVRVVSSRKLVGFISAIPANIHIYDTEKKMVEINFLCVHKKLRSKRVAPVLIREITRRVHLEGIFQAVYTAGVVLPKPVGTCRYWHRSLNPRKLIEVKFSHLSRNMTMQRTMKLYRLPETPKTAGLRPMETKDIPVVHQLLTRYLKQFHLTPVMSQEEVEHWFYPQENIIDTFVVENANGEVTDFLSFYTLPSTIMNHPTHKSLKAAYSFYNVHTQTPLLDLMSDALVLAKMKGFDVFNALDLMENKTFLEKLKFGIGDGNLQYYLYNWKCPSMGAEKVGLVLQ 496
               SCOP domains d3iu1a1 A:115-295 automated matches                                                                                                                                                  d3iu1a2 A:296-496 a  utomated matches                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh................................eeeee....hhhhhhhhhhhhhhhh.......eee..hhhhhhhhhh....hhh.eeeeee.....eeeeeeeeeeeeee..eeeeeeeeeeeee.hhhh..hhhhhhhhhhhhhhhh.....eeeee........eeeeeeeee.hhhhhhhh.....--..hhhhhhhhhh.........eee.hhhhhhhhhhhhhhhhhhh.eeee.hhhhhhhhhh.....eeeeeee.....eeeeeeeee..eee.......ee.eeee........hhhhhhhhhhhhhhhh...eeeee...hhhhh......eeeeeeeeeeee.......hhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------NMT_1    ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NMT_2  ------------------------ PROSITE
           Transcript 1 (1) Exon 1.3       ---------------------------------------Exon 1.5  PDB: A:169-199       --------------------------------------Exon 1.7  PDB: A:238-295 UniProt: 238-295                 ------------------------------------Exon 1.9  PDB: A:332-388 UniProt: 332-388                Exon 1.10  PDB: A:389-444 UniProt: 389-444              Exon 1.11  PDB: A:445-490 UniProt: 445-490    1.12   Transcript 1 (1)
           Transcript 1 (2) --------------Exon 1.4  PDB: A:129-168                ------------------------------Exon 1.6  PDB: A:199-238                --------------------------------------------------------Exon 1.8  PDB: A:295-331 (gaps)      --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3iu1 A 115 RSYQFWDTQPVPKLGEVVNTHGPVEPDKDNIRQEPYTLPQGFTWDALDLGDRGVLKELYTLLNENYVEDDDNMFRFDYSPEFLLWALRPPGWLPQWHCGVRVVSSRKLVGFISAIPANIHIYDTEKKMVEINFLCVHKKLRSKRVAPVLIREITRRVHLEGIFQAVYTAGVVLPKPVGTCRYWHRSLNPRKLIEVKFSHL--NMTMQRTMKLYRLPETPKTAGLRPMETKDIPVVHQLLTRYLKQFHLTPVMSQEEVEHWFYPQENIIDTFVVENANGEVTDFLSFYTLPSTIMNHPTHKSLKAAYSFYNVHTQTPLLDLMSDALVLAKMKGFDVFNALDLMENKTFLEKLKFGIGDGNLQYYLYNWKCPSMGAEKVGLVLQ 496
                                   124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314  |    324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494  
                                                                                                                                                                                                                                 314  |                                                                                                                                                                                   
                                                                                                                                                                                                                                    317

Chain B from PDB  Type:PROTEIN  Length:382
 aligned with NMT1_HUMAN | P30419 from UniProtKB/Swiss-Prot  Length:496

    Alignment length:382
                                   124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494  
           NMT1_HUMAN   115 RSYQFWDTQPVPKLGEVVNTHGPVEPDKDNIRQEPYTLPQGFTWDALDLGDRGVLKELYTLLNENYVEDDDNMFRFDYSPEFLLWALRPPGWLPQWHCGVRVVSSRKLVGFISAIPANIHIYDTEKKMVEINFLCVHKKLRSKRVAPVLIREITRRVHLEGIFQAVYTAGVVLPKPVGTCRYWHRSLNPRKLIEVKFSHLSRNMTMQRTMKLYRLPETPKTAGLRPMETKDIPVVHQLLTRYLKQFHLTPVMSQEEVEHWFYPQENIIDTFVVENANGEVTDFLSFYTLPSTIMNHPTHKSLKAAYSFYNVHTQTPLLDLMSDALVLAKMKGFDVFNALDLMENKTFLEKLKFGIGDGNLQYYLYNWKCPSMGAEKVGLVLQ 496
               SCOP domains d3iu1b1 B:115-295 automated matches                                                                                                                                                  d3iu1b2 B:296-496 automated matches                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh................................eeeee....hhhhhhhhhhhhhhhh.......eee..hhhhhhhhhh....hhh.eeeeee.....eeeeeeeeeeeeee..eeeeeeeeeeeee.hhhh..hhhhhhhhhhhhhhhh.....eeeee........eee.eeeee.hhhhhhhh.........hhhhhhhhhh.........eee.hhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhh.....eeeeeee.....eeeeeeeee..eee..........eeee...ee...hhhhhhhhhhhhhhhh...eeeee...hhhhh......ee....eeeeee.......hhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------NMT_1    ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NMT_2  ------------------------ PROSITE
           Transcript 1 (1) Exon 1.3       ---------------------------------------Exon 1.5  PDB: B:169-199       --------------------------------------Exon 1.7  PDB: B:238-295 UniProt: 238-295                 ------------------------------------Exon 1.9  PDB: B:332-388 UniProt: 332-388                Exon 1.10  PDB: B:389-444 UniProt: 389-444              Exon 1.11  PDB: B:445-490 UniProt: 445-490    1.12   Transcript 1 (1)
           Transcript 1 (2) --------------Exon 1.4  PDB: B:129-168                ------------------------------Exon 1.6  PDB: B:199-238                --------------------------------------------------------Exon 1.8  PDB: B:295-331             --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3iu1 B 115 RSYQFWDTQPVPKLGEVVNTHGPVEPDKDNIRQEPYTLPQGFTWDALDLGDRGVLKELYTLLNENYVEDDDNMFRFDYSPEFLLWALRPPGWLPQWHCGVRVVSSRKLVGFISAIPANIHIYDTEKKMVEINFLCVHKKLRSKRVAPVLIREITRRVHLEGIFQAVYTAGVVLPKPVGTCRYWHRSLNPRKLIEVKFSHLSRNMTMQRTMKLYRLPETPKTAGLRPMETKDIPVVHQLLTRYLKQFHLTPVMSQEEVEHWFYPQENIIDTFVVENANGEVTDFLSFYTLPSTIMNHPTHKSLKAAYSFYNVHTQTPLLDLMSDALVLAKMKGFDVFNALDLMENKTFLEKLKFGIGDGNLQYYLYNWKCPSMGAEKVGLVLQ 496
                                   124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494

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: automated matches (63)

Protein domain: automated matches (63)

Human (Homo sapiens) [TaxId: 9606] (11)

1a	d3iu1a1	A:115-295
1b	d3iu1a2	A:296-496
1c	d3iu1b1	B:115-295
1d	d3iu1b2	B:296-496

(no "CATH Domain" information available for 3IU1)

(no "Pfam Domain" information available for 3IU1)

Asymmetric Unit(hide GO term definitions)

Chain A,B (NMT1_HUMAN | P30419)

molecular function
	GO:0004379	glycylpeptide N-tetradecanoyltransferase activity	Catalysis of the reaction: tetradecanoyl-CoA + glycyl-peptide = CoA + N-tetradecanoylglycyl-peptide.
	GO:0019107	myristoyltransferase activity	Catalysis of the transfer of a myristoyl (CH3-[CH2]12-CO-) group to an acceptor molecule.
	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:0001701	in utero embryonic development	The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus.
	GO:1900740	positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway	Any process that activates or increases the frequency, rate or extent of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway.
	GO:0022400	regulation of rhodopsin mediated signaling pathway	Any process that modulates the frequency, rate or extent of rhodopsin-mediated signaling.
cellular component
	GO:0015629	actin cytoskeleton	The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
	GO:0030054	cell junction	A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
	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.
	GO:0019898	extrinsic component of membrane	The component of a membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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	3iu1
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	2.3.1.97
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	NMT1_HUMAN \| P30419
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	NMT1_HUMAN \| P30419	:	1rxt 3iu2 3iwe 3jtk 4c2y 4c2z

1rxt	SAME PROTEIN WITH SHORTER TRUNCATION
3iu2

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (10, 20)

Sequences/Alignments

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SCOP Domains (1, 4)

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Gene Ontology (17, 17)

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Related Entries Specified in the PDB File