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Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF PROBABLE ACETYLTRANSFERASE

Authors :   J. S. Brunzelle, S. V. Korolev, R. Wu, A. Joachimiak, W. F. Anderson, Mid Center For Structural Genomics (Mcsg)

Date :   27 Jan 03 (Deposition) - 29 Jul 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

Chains :   Asym./Biol. Unit : A,B,C,D,E,F

Keywords :   Structural Genomics, Hexamer, Alpha-Beta, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. S. Brunzelle, R. Wu, S. V. Korolev, F. R. Collart, A. Joachimiak, W. F. Anderson
Crystal Structure Of Bacillus Subtilis Ydaf Protein: A Putative Ribosomal N-Acetyltransferase
Proteins V. 57 850 2004
PubMed-ID: 15468321 | Reference-DOI: 10.1002/PROT.10601

Molecule 1 - PROBABLE ACETYLTRANSFERASE
	Chains	:	A, B, C, D, E, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	YDAF
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423

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

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 24)

No.	Name	Count	Type	Full Name
1	CL	6	Ligand/Ion	CHLORIDE ION
2	MSE	18	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY B:108 , ILE B:109 , ILE B:110	BINDING SITE FOR RESIDUE CL B 184
2	AC2	SOFTWARE	GLY A:108 , THR A:111	BINDING SITE FOR RESIDUE CL A 184
3	AC3	SOFTWARE	GLY C:108 , THR C:111	BINDING SITE FOR RESIDUE CL C 184
4	AC4	SOFTWARE	GLY F:108 , THR F:111	BINDING SITE FOR RESIDUE CL F 184
5	AC5	SOFTWARE	GLY E:108 , ILE E:109 , ILE E:110 , THR E:111	BINDING SITE FOR RESIDUE CL E 184

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

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

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

Asymmetric/Biological Unit (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GNAT	PS51186	Gcn5-related N-acetyltransferase (GNAT) domain profile.	YDAF_BACSU	10-176	6	A:10-176 B:10-176 C:10-176 D:10-176 E:10-176 F:10-176

(no "Exon" information available for 1NSL)

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
	(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:176
 aligned with YDAF_BACSU | P96579 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:180
                             1                                                                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179
           YDAF_BACSU     - -MFTCKVNEHITIRLLEPKDAERLAELIIQNQQRLGKWLFFAENPSSADTYRETIIPDWRRQYADLNGIEAGLLYDGSLCGMISLHNLDQVNRKAEIGYWIAKEFEGKGIITAACRKLITYAFEELELNRVAICAAVGNEKSRAVPERIGFLEEGKARDGLYVNGMHHDLVYYSLLKREW 179
               SCOP domains d1nsla_ A: Probable acetyltransferase Yda    F                                                                                                                                       SCOP domains
               CATH domains 1nslA00 A:0-179  [code=3.40.630.30, no na    me defined]                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee....eeee..hhhhhhhhhhhhhh...........----.hhhhhhhhhhhhhhhhhhh...eeeeeee..eeeeeeeeeeee....eeeeeeee.hhhh..hhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhh.eeeeeeeeeeee..eeeeeeeeeee.hhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------GNAT  PDB: A:10-176 UniProt: 10-176                                                                                                                                    --- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1nsl A   0 GmFTCKVNEHITIRLLEPKDAERLAELIIQNQQRLGKWLFF----SSADTYRETIIPDWRRQYADLNGIEAGLLYDGSLCGmISLHNLDQVNRKAEIGYWIAKEFEGKGIITAACRKLITYAFEELELNRVAICAAVGNEKSRAVPERIGFLEEGKARDGLYVNGmHHDLVYYSLLKREW 179
                             |       9        19        29        39|    |  49        59        69        79 |      89        99       109       119       129       139       149       159     | 169       179
                             |                                     40   45                                  81-MSE                                                                             165-MSE          
                             1-MSE

Chain B from PDB  Type:PROTEIN  Length:176
 aligned with YDAF_BACSU | P96579 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:180
                             1                                                                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179
           YDAF_BACSU     - -MFTCKVNEHITIRLLEPKDAERLAELIIQNQQRLGKWLFFAENPSSADTYRETIIPDWRRQYADLNGIEAGLLYDGSLCGMISLHNLDQVNRKAEIGYWIAKEFEGKGIITAACRKLITYAFEELELNRVAICAAVGNEKSRAVPERIGFLEEGKARDGLYVNGMHHDLVYYSLLKREW 179
               SCOP domains d1nslb_ B: Probable acetyltransferase Yda    F                                                                                                                                       SCOP domains
               CATH domains 1nslB00 B:0-179  [code=3.40.630.30, no na    me defined]                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee..eeeee.hhhhhhhhhhhhhh...........----.hhhhhhhhhhhhhhhhhhh...eeeeeee..eeeeeeeeeeee....eeeeeeee.hhhh..hhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhh.eeeeeeeeeeee..eeeeeeeeeee.hhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------GNAT  PDB: B:10-176 UniProt: 10-176                                                                                                                                    --- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1nsl B   0 GmFTCKVNEHITIRLLEPKDAERLAELIIQNQQRLGKWLFF----SSADTYRETIIPDWRRQYADLNGIEAGLLYDGSLCGmISLHNLDQVNRKAEIGYWIAKEFEGKGIITAACRKLITYAFEELELNRVAICAAVGNEKSRAVPERIGFLEEGKARDGLYVNGmHHDLVYYSLLKREW 179
                             |       9        19        29        39|    |  49        59        69        79 |      89        99       109       119       129       139       149       159     | 169       179
                             1-MSE                                 40   45                                  81-MSE                                                                             165-MSE

Chain C from PDB  Type:PROTEIN  Length:180
 aligned with YDAF_BACSU | P96579 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:180
                             1                                                                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179
           YDAF_BACSU     - -MFTCKVNEHITIRLLEPKDAERLAELIIQNQQRLGKWLFFAENPSSADTYRETIIPDWRRQYADLNGIEAGLLYDGSLCGMISLHNLDQVNRKAEIGYWIAKEFEGKGIITAACRKLITYAFEELELNRVAICAAVGNEKSRAVPERIGFLEEGKARDGLYVNGMHHDLVYYSLLKREW 179
               SCOP domains d1nslc_ C: Probable acetyltransferase YdaF                                                                                                                                           SCOP domains
               CATH domains 1nslC00 C:0-179  [code=3.40.630.30, no name defined]                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee....eeeee.hhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhh..eeeeeee..eeeeeeeeeeee....eeeeeeee.hhhh..hhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhh.eeeeeeeeeeee..eeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------GNAT  PDB: C:10-176 UniProt: 10-176                                                                                                                                    --- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1nsl C   0 GmFTCKVNEHITIRLLEPKDAERLAELIIQNQQRLGKWLFFAENPSSADTYRETIIPDWRRQYADLNGIEAGLLYDGSLCGmISLHNLDQVNRKAEIGYWIAKEFEGKGIITAACRKLITYAFEELELNRVAICAAVGNEKSRAVPERIGFLEEGKARDGLYVNGmHHDLVYYSLLKREW 179
                             |       9        19        29        39        49        59        69        79 |      89        99       109       119       129       139       149       159     | 169       179
                             1-MSE                                                                          81-MSE                                                                             165-MSE

Chain D from PDB  Type:PROTEIN  Length:180
 aligned with YDAF_BACSU | P96579 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:180
                             1                                                                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179
           YDAF_BACSU     - -MFTCKVNEHITIRLLEPKDAERLAELIIQNQQRLGKWLFFAENPSSADTYRETIIPDWRRQYADLNGIEAGLLYDGSLCGMISLHNLDQVNRKAEIGYWIAKEFEGKGIITAACRKLITYAFEELELNRVAICAAVGNEKSRAVPERIGFLEEGKARDGLYVNGMHHDLVYYSLLKREW 179
               SCOP domains d1nsld_ D: Probable acetyltransferase YdaF                                                                                                                                           SCOP domains
               CATH domains 1nslD00 D:0-179  [code=3.40.630.30, no name defined]                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee....eeeee.hhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhh..eeeeeee..eeeeeeeeeeee....eeeeeeee.hhhh..hhhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhhhh.eeeeeeeeeeee..eeeeeeeeeee.hhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------GNAT  PDB: D:10-176 UniProt: 10-176                                                                                                                                    --- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1nsl D   0 GmFTCKVNEHITIRLLEPKDAERLAELIIQNQQRLGKWLFFAENPSSADTYRETIIPDWRRQYADLNGIEAGLLYDGSLCGmISLHNLDQVNRKAEIGYWIAKEFEGKGIITAACRKLITYAFEELELNRVAICAAVGNEKSRAVPERIGFLEEGKARDGLYVNGmHHDLVYYSLLKREW 179
                             |       9        19        29        39        49        59        69        79 |      89        99       109       119       129       139       149       159     | 169       179
                             1-MSE                                                                          81-MSE                                                                             165-MSE

Chain E from PDB  Type:PROTEIN  Length:179
 aligned with YDAF_BACSU | P96579 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:180
                             1                                                                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179
           YDAF_BACSU     - -MFTCKVNEHITIRLLEPKDAERLAELIIQNQQRLGKWLFFAENPSSADTYRETIIPDWRRQYADLNGIEAGLLYDGSLCGMISLHNLDQVNRKAEIGYWIAKEFEGKGIITAACRKLITYAFEELELNRVAICAAVGNEKSRAVPERIGFLEEGKARDGLYVNGMHHDLVYYSLLKREW 179
               SCOP domains d1nsle_ E: Probable acetyltransferase Yda F                                                                                                                                          SCOP domains
               CATH domains 1nslE00 E:0-179  [code=3.40.630.30, no na me defined]                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....ee....eeee..hhhhhhhhhhhhhh...........-....hhhhhhhhhhhhhhhhhhhh..eeeeeee..eeeeeeeeeeee....eeeeeeee.......hhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhh.eeeeeeeeeee....eeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------GNAT  PDB: E:10-176 UniProt: 10-176                                                                                                                                    --- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1nsl E   0 GmFTCKVNEHITIRLLEPKDAERLAELIIQNQQRLGKWLFF-ENPSSADTYRETIIPDWRRQYADLNGIEAGLLYDGSLCGmISLHNLDQVNRKAEIGYWIAKEFEGKGIITAACRKLITYAFEELELNRVAICAAVGNEKSRAVPERIGFLEEGKARDGLYVNGmHHDLVYYSLLKREW 179
                             |       9        19        29        39| |     49        59        69        79 |      89        99       109       119       129       139       149       159     | 169       179
                             1-MSE                                 40 |                                     81-MSE                                                                             165-MSE          
                                                                     42

Chain F from PDB  Type:PROTEIN  Length:177
 aligned with YDAF_BACSU | P96579 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:180
                             1                                                                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179
           YDAF_BACSU     - -MFTCKVNEHITIRLLEPKDAERLAELIIQNQQRLGKWLFFAENPSSADTYRETIIPDWRRQYADLNGIEAGLLYDGSLCGMISLHNLDQVNRKAEIGYWIAKEFEGKGIITAACRKLITYAFEELELNRVAICAAVGNEKSRAVPERIGFLEEGKARDGLYVNGMHHDLVYYSLLKREW 179
               SCOP domains d1nslf_ F: Probable acetyltransferase Yda   F                                                                                                                                        SCOP domains
               CATH domains 1nslF00 F:0-179  [code=3.40.630.30, no na   me defined]                                                                                                                              CATH domains
           Pfam domains (1) ------------------------------------------------------------------------Acetyltransf_1-1nslF01 F:72-151                                                 ---------------------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------Acetyltransf_1-1nslF02 F:72-151                                                 ---------------------------- Pfam domains (2)
           Pfam domains (3) ------------------------------------------------------------------------Acetyltransf_1-1nslF03 F:72-151                                                 ---------------------------- Pfam domains (3)
           Pfam domains (4) ------------------------------------------------------------------------Acetyltransf_1-1nslF04 F:72-151                                                 ---------------------------- Pfam domains (4)
           Pfam domains (5) ------------------------------------------------------------------------Acetyltransf_1-1nslF05 F:72-151                                                 ---------------------------- Pfam domains (5)
           Pfam domains (6) ------------------------------------------------------------------------Acetyltransf_1-1nslF06 F:72-151                                                 ---------------------------- Pfam domains (6)
         Sec.struct. author ....eeee..eeeee.hhhhhhhhhhhhhh...........---..hhhhhhhhhhhhhhhhhhh...eeeeeee..eeeeeeeeeeee....eeeeeeee.hhhh..hhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhh.eeeeeeeeeeee..eeeeeeeeeee.hhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------GNAT  PDB: F:10-176 UniProt: 10-176                                                                                                                                    --- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1nsl F   0 GmFTCKVNEHITIRLLEPKDAERLAELIIQNQQRLGKWLFF---PSSADTYRETIIPDWRRQYADLNGIEAGLLYDGSLCGmISLHNLDQVNRKAEIGYWIAKEFEGKGIITAACRKLITYAFEELELNRVAICAAVGNEKSRAVPERIGFLEEGKARDGLYVNGmHHDLVYYSLLKREW 179
                             |       9        19        29        39|   |   49        59        69        79 |      89        99       109       119       129       139       149       159     | 169       179
                             1-MSE                                 40  44                                   81-MSE                                                                             165-MSE

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( (-)

)

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

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

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

Family: N-acetyl transferase, NAT (154)

Protein domain: Probable acetyltransferase YdaF (1)

Bacillus subtilis [TaxId: 1423] (1)

1a	d1nsla_	A:
1b	d1nslb_	B:
1c	d1nslc_	C:
1d	d1nsld_	D:
1e	d1nsle_	E:
1f	d1nslf_	F:

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)

Bacillus subtilis. Organism_taxid: 1423. (4)

1a	1nslA00	A:0-179
1b	1nslF00	F:0-179
1c	1nslE00	E:0-179
1d	1nslC00	C:0-179
1e	1nslD00	D:0-179
1f	1nslB00	B:0-179

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Acetyltrans (109)

Family: Acetyltransf_1 (58)

Bacillus subtilis (9)

1a	Acetyltransf_1-1nslF01	F:72-151
1b	Acetyltransf_1-1nslF02	F:72-151
1c	Acetyltransf_1-1nslF03	F:72-151
1d	Acetyltransf_1-1nslF04	F:72-151
1e	Acetyltransf_1-1nslF05	F:72-151
1f	Acetyltransf_1-1nslF06	F:72-151

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D,E,F (YDAF_BACSU | P96579)

molecular function
	GO:0008080	N-acetyltransferase activity	Catalysis of the transfer of an acetyl group to a nitrogen atom on the 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:0017198	N-terminal peptidyl-serine acetylation	The acetylation of the N-terminal serine of proteins to form the derivative N-acetyl-L-serine.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 24)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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