2CNM - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   RIMI - RIBOSOMAL S18 N-ALPHA-PROTEIN ACETYLTRANSFERASE IN COMPLEX WITH A BISUBSTRATE INHIBITOR (CTERM-ARG-ARG-PHE-TYR-ARG-ALA-N-ALPHA-ACETYL-S-COA).

Authors :   M. W. Vetting, M. Yu, D. C. Bareich, J. S. Blanchard

Date :   22 May 06 (Deposition) - 22 May 07 (Release) - 15 Feb 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,D  (1x)
Biol. Unit 2: B,E  (1x)
Biol. Unit 3: C,F  (1x)

Keywords :   N-Alpha Acetylation, Gcn5-N-Acetyltransferase, Ribosomal Protein, Acetyltransferase, Gnat, Transferase, Acyltransferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. W. Vetting, D. C. Bareich, M. Yu, J. S. Blanchard
Crystal Structure Of Rimi From Salmonella Typhimurium Lt2, The Gnat Responsible For N{Alpha}- Acetylation Of Ribosomal Protein S18.
Protein Sci. V. 17 1781 2008
PubMed-ID: 18596200 | Reference-DOI: 10.1110/PS.035899.108

Molecule 1 - MODIFICATION OF 30S RIBOSOMAL SUBUNIT PROTEIN S18
	Chains	:	A, B, C
	EC Number	:	2.3.1.128
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	SALMONELLA TYPHIMURIUM LT2
	Organism Taxid	:	99287
	Synonym	:	RIBOSOMAL-N-ALPHA-ACETYLTRANSFERASE

Molecule 2 - 30S RIBOSOMAL PROTEIN S18
	Chains	:	D, E, F
	Organism Scientific	:	SALMONELLA TYPHIMURIUM LT2
	Organism Taxid	:	99287
	Synonym	:	CTERM-ARG-ARG-PHE-TYR-ARG-ALA-N-ALPHA-ACETYL
	Synthetic	:	YES

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:	A			D
Biological Unit 2 (1x)	:		B			E
Biological Unit 3 (1x)	:			C			F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	ACE	3	Mod. Amino Acid	ACETYL GROUP
2	COA	3	Ligand/Ion	COENZYME A

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	ACE	1	Mod. Amino Acid	ACETYL GROUP
2	COA	1	Ligand/Ion	COENZYME A

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	ACE	1	Mod. Amino Acid	ACETYL GROUP
2	COA	1	Ligand/Ion	COENZYME A

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	ACE	1	Mod. Amino Acid	ACETYL GROUP
2	COA	1	Ligand/Ion	COENZYME A

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:22 , HIS A:23 , ILE A:69 , ALA A:70 , VAL A:71 , GLN A:76 , ARG A:77 , ARG A:78 , GLY A:79 , GLY A:81 , ARG A:82 , GLU A:103 , VAL A:104 , ASN A:108 , ALA A:110 , ALA A:113 , LEU A:114 , TYR A:115 , HOH A:2013 , ACE D:1 , ALA D:2	BINDING SITE FOR RESIDUE COA D 0
2	AC2	SOFTWARE	ALA A:133 , GLN A:134 , ALA B:22 , HIS B:23 , ILE B:69 , ALA B:70 , VAL B:71 , GLN B:76 , ARG B:77 , ARG B:78 , GLY B:79 , LEU B:80 , GLY B:81 , ARG B:82 , GLU B:103 , ASN B:108 , ALA B:110 , ALA B:113 , TYR B:115 , ACE E:1 , ALA E:2 , HOH E:2001	BINDING SITE FOR RESIDUE COA E 0
3	AC3	SOFTWARE	ALA C:22 , HIS C:23 , ILE C:69 , ALA C:70 , VAL C:71 , GLN C:76 , ARG C:77 , ARG C:78 , GLY C:79 , LEU C:80 , GLY C:81 , ARG C:82 , ASP C:90 , GLU C:103 , ASN C:108 , ALA C:110 , ALA C:111 , LEU C:114 , TYR C:115 , LYS C:149 , ACE F:1 , ALA F:2	BINDING SITE FOR RESIDUE COA F 0

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

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

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

(no "PROSITE Motif" information available for 2CNM)

(no "Exon" information available for 2CNM)

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:151
 aligned with Q8ZJW4_SALTY | Q8ZJW4 from UniProtKB/TrEMBL  Length:148

    Alignment length:151
                                                                                                                                                                             148   
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       | - 
         Q8ZJW4_SALTY     1 MNTISILSTTDLPAAWQIEQRAHAFPWSEKTFFGNQGERYLNLKLTADDRMAAFAITQVVLDEATLFNIAVDPDFQRRGLGRMLLEHLIDELETRGVVTLWLEVRASNAAAIALYESLGFNEATIRRNYYPTAQGHEDAIIMALPISM---   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhhhhhh....hhhhhhhh.......eeeee..eeeeeeeeeee..eeeeeeeee.hhhh..hhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhh.eeeeeeeeeeee..eeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cnm A   1 MNTISILSTTDLPAAWQIEQRAHAFPWSEKTFFGNQGERYLNLKLTADDRMAAFAITQVVLDEATLFNIAVDPDFQRRGLGRMLLEHLIDELETRGVVTLWLEVRASNAAAIALYESLGFNEATIRRNYYPTAQGHEDAIIMALPISMKLH 151
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain B from PDB  Type:PROTEIN  Length:151
 aligned with Q8ZJW4_SALTY | Q8ZJW4 from UniProtKB/TrEMBL  Length:148

    Alignment length:151
                                                                                                                                                                             148   
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       | - 
         Q8ZJW4_SALTY     1 MNTISILSTTDLPAAWQIEQRAHAFPWSEKTFFGNQGERYLNLKLTADDRMAAFAITQVVLDEATLFNIAVDPDFQRRGLGRMLLEHLIDELETRGVVTLWLEVRASNAAAIALYESLGFNEATIRRNYYPTAQGHEDAIIMALPISM---   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhhhhhh....hhhhhhhh....eeeeeeee..eeeeeeeeeee..eeeeeeeee.hhhh..hhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhh.eeeeeeeeeee....eeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cnm B   1 MNTISILSTTDLPAAWQIEQRAHAFPWSEKTFFGNQGERYLNLKLTADDRMAAFAITQVVLDEATLFNIAVDPDFQRRGLGRMLLEHLIDELETRGVVTLWLEVRASNAAAIALYESLGFNEATIRRNYYPTAQGHEDAIIMALPISMKLH 151
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain C from PDB  Type:PROTEIN  Length:151
 aligned with Q8ZJW4_SALTY | Q8ZJW4 from UniProtKB/TrEMBL  Length:148

    Alignment length:151
                                                                                                                                                                             148   
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       | - 
         Q8ZJW4_SALTY     1 MNTISILSTTDLPAAWQIEQRAHAFPWSEKTFFGNQGERYLNLKLTADDRMAAFAITQVVLDEATLFNIAVDPDFQRRGLGRMLLEHLIDELETRGVVTLWLEVRASNAAAIALYESLGFNEATIRRNYYPTAQGHEDAIIMALPISM---   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhhhhhh....hhhhhhhh.......eeeee...eeeeeeeeee..eeeeeeeee.hhhh..hhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhh..eeeeeeeeeee....eeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cnm C   1 MNTISILSTTDLPAAWQIEQRAHAFPWSEKTFFGNQGERYLNLKLTADDRMAAFAITQVVLDEATLFNIAVDPDFQRRGLGRMLLEHLIDELETRGVVTLWLEVRASNAAAIALYESLGFNEATIRRNYYPTAQGHEDAIIMALPISMKLH 151
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain D from PDB  Type:PROTEIN  Length:7
 aligned with RS18_SALTY | Q8ZK81 from UniProtKB/Swiss-Prot  Length:75

    Alignment length:7
           RS18_SALTY     1 MARYFRR   7
               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
                 2cnm D   1 xARYFRR   7
                            |      
                            1-ACE

Chain E from PDB  Type:PROTEIN  Length:7
 aligned with RS18_SALTY | Q8ZK81 from UniProtKB/Swiss-Prot  Length:75

    Alignment length:7
           RS18_SALTY     1 MARYFRR   7
               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
                 2cnm E   1 xARYFRR   7
                            |      
                            1-ACE

Chain F from PDB  Type:PROTEIN  Length:7
 aligned with RS18_SALTY | Q8ZK81 from UniProtKB/Swiss-Prot  Length:75

    Alignment length:7
           RS18_SALTY     1 MARYFRR   7
               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
                 2cnm F   1 xARYFRR   7
                            |      
                            1-ACE

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 '\|'

(no "SCOP Domain" information available for 2CNM)

(no "CATH Domain" information available for 2CNM)

(no "Pfam Domain" information available for 2CNM)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (Q8ZJW4_SALTY | Q8ZJW4)

molecular function
	GO:0008080	N-acetyltransferase activity	Catalysis of the transfer of an acetyl group to a nitrogen atom on the acceptor molecule.
	GO:0016407	acetyltransferase activity	Catalysis of the transfer of an acetyl group to an acceptor molecule.
	GO:0004596	peptide alpha-N-acetyltransferase activity	Catalysis of the reaction: acetyl-CoA + peptide = CoA + N-alpha-acetylpeptide. This reaction is the acetylation of the N-terminal amino acid residue of a peptide or protein.
	GO:0008999	ribosomal-protein-alanine N-acetyltransferase activity	Catalysis of the reaction: acetyl-CoA + ribosomal-protein L-alanine = CoA + ribosomal-protein N-acetyl-L-alanine.
	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:0017189	N-terminal peptidyl-alanine acetylation	The acetylation of the N-terminal alanine of proteins; catalyzed by peptide alpha-N-acetyltransferase or other enzymes of this class, such as ribosomal-protein-alanine N-acetyltransferase.
	GO:0006474	N-terminal protein amino acid acetylation	The acetylation of the N-terminal amino acid of proteins.
cellular component
	GO:0031248	protein acetyltransferase complex	A complex that catalyzes the transfer of an acetyl group to a protein acceptor molecule.

Chain D,E,F (RS18_SALTY | Q8ZK81)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0019843	rRNA binding	Interacting selectively and non-covalently with ribosomal RNA.
	GO:0003735	structural constituent of ribosome	The action of a molecule that contributes to the structural integrity of the ribosome.
biological process
	GO:0006412	translation	The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
cellular component
	GO:0022627	cytosolic small ribosomal subunit	The small subunit of a ribosome located in the cytosol.
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
	GO:0030529	intracellular ribonucleoprotein complex	An intracellular macromolecular complex containing both protein and RNA molecules.
	GO:0005840	ribosome	An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.

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	2cnm
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	Q8ZJW4_SALTY \| Q8ZJW4
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	RS18_SALTY \| Q8ZK81
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	2.3.1.128
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UniProtKB/TrEMBL
	Q8ZJW4_SALTY \| Q8ZJW4	:	2cns 2cnt

2cns	RIMI - RIBOSOMAL S18 N-ALPHA-PROTEIN ACETYLTRANSFERASE IN COMPLEX WITH ACETYLCOA.
2cnt	RIMI - RIBOSOMAL S18 N-ALPHA-PROTEIN ACETYLTRANSFERASE IN COMPLEX WITH COENZYMEA.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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Exons (0, 0)

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Gene Ontology (17, 17)

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