1I21 - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF YEAST GNA1

Authors :   C. Peneff, D. Mengin-Lecreulx, Y. Bourne

Date :   05 Feb 01 (Deposition) - 16 May 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym. Unit : A,B,M,N,X,Y
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: M,N  (1x)
Biol. Unit 3: X,Y  (1x)

Keywords :   Alpha/Beta, Domain Swapping, Gnat, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Peneff, D. Mengin-Lecreulx, Y. Bourne
The Crystal Structures Of Apo And Complexed Saccharomyces Cerevisiae Gna1 Shed Light On The Catalytic Mechanism Of An Amino-Sugar N-Acetyltransferase.
J. Biol. Chem. V. 276 16328 2001
PubMed-ID: 11278591 | Reference-DOI: 10.1074/JBC.M009988200
(for further references see the PDB file header)

Molecule 1 - GLUCOSAMINE-PHOSPHATE N-ACETYLTRANSFERASE
	Chains	:	A, B, M, N, X, Y
	EC Number	:	2.3.1.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PQE30
	Expression System Strain	:	M15 (PREP 4)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	YFL017C
	Mutation	:	YES
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	PHOSPHOGLUCOSAMINE TRANSACETYLASE

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	M	N	X	Y
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			M	N
Biological Unit 3 (1x)	:					X	Y

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 27)

No.	Name	Count	Type	Full Name
1	MSE	27	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 10)

No.	Name	Count	Type	Full Name
1	MSE	10	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 9)

No.	Name	Count	Type	Full Name
1	MSE	9	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 3 (1, 8)

No.	Name	Count	Type	Full Name
1	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 1I21)

(no "SS Bond" information available for 1I21)

(no "Cis Peptide Bond" information available for 1I21)

(no "SAP(SNP)/Variant" information available for 1I21)

Asymmetric Unit (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GNAT	PS51186	Gcn5-related N-acetyltransferase (GNAT) domain profile.	GNA1_YEAST	28-159	6	A:28-158 B:28-158 M:28-158 N:28-159 X:28-158 Y:28-158

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GNAT	PS51186	Gcn5-related N-acetyltransferase (GNAT) domain profile.	GNA1_YEAST	28-159	2	A:28-158 B:28-158 - - - -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GNAT	PS51186	Gcn5-related N-acetyltransferase (GNAT) domain profile.	GNA1_YEAST	28-159	2	- - M:28-158 N:28-159 - -

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GNAT	PS51186	Gcn5-related N-acetyltransferase (GNAT) domain profile.	GNA1_YEAST	28-159	2	- - - - X:28-158 Y:28-158

Asymmetric Unit (1, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YFL017C	1	YFL017C.1	VI:104456-103977	480	GNA1_YEAST	1-159	159	6	A:1-158 (gaps) B:1-158 (gaps) M:1-158 (gaps) N:6-159 (gaps) X:6-158 (gaps) Y:3-158	158 158 158 154 153 156

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:155
 aligned with GNA1_YEAST | P43577 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150        
           GNA1_YEAST     1 MSLPDGFYIRRMEEGDLEQVTETLKVLTTVGTITPESFSKLIKYWNEATVWNDNEDKKIMQYNPMVIVDKRTETVAATGNIIIERKIIHELGLCGHIEDIAVNSKYQGQGLGKLLIDQLVTIGFDYGCYKIILDCDEKNVKFYEKCGFSNAGVEMQIR 158
               SCOP domains d1i21a_ A: Glucosamine-phosphate N-acetyltransferase    GNA1                                                                                                   SCOP domains
               CATH domains -1i21A00 A:2-158  [code=3.40.630.30, no name defined   ]                                                                                                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...eeeee.hhhhhhhhhhhhh........hhhhhhhhhhhhhhh....---.........eeeee....eeeeeeeeeeee.hhhhhheeeeeeeeee.hhhh..hhhhhhhhhhhhhhhhhheeeeeeeehhhhhhhhhhh..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------GNAT  PDB: A:28-158 UniProt: 28-159                                                                                                 PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-158 (gaps) UniProt: 1-159 [INCOMPLETE]                                                                                                      Transcript 1
                 1i21 A   1 mSLPDGFYIRRmEEGDLEQVTETLKVLTTVGTITPESFCKLIKYWNEATVWN---DKKImQYNPmVIVDKRTETVAATGNIIIERKIIHELGLCGHIEDIAVNSKYQGQGLGKLLIDQLVTIGFDYGCYKIILDCDEKNVKFYEKCGFSNAGVEmQIR 158
                            |       10 |      20        30        40        50 |   |  60    |   70        80        90       100       110       120       130       140       150    |   
                            |         12-MSE                                  52  56   |    |                                                                                       155-MSE
                            1-MSE                                                     60-MSE|                                                                                             
                                                                                           65-MSE

Chain B from PDB  Type:PROTEIN  Length:157
 aligned with GNA1_YEAST | P43577 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150        
           GNA1_YEAST     1 MSLPDGFYIRRMEEGDLEQVTETLKVLTTVGTITPESFSKLIKYWNEATVWNDNEDKKIMQYNPMVIVDKRTETVAATGNIIIERKIIHELGLCGHIEDIAVNSKYQGQGLGKLLIDQLVTIGFDYGCYKIILDCDEKNVKFYEKCGFSNAGVEMQIR 158
               SCOP domains d1i21b_ B: Glucosamine-phosphate N-acetyltransferase G NA1                                                                                                     SCOP domains
               CATH domains -1i21B00 B:2-158  [code=3.40.630.30, no name defined]                                                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhh.eeeee.hhhhhhhhhhhhh........hhhhhhhhhhhhhhhee....-...ee....eeeee....eeeeeeeeeeee.hhhhhheeeeeeeeee.hhhh..hhhhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhh..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------GNAT  PDB: B:28-158 UniProt: 28-159                                                                                                 PROSITE
               Transcript 1 Exon 1.1  PDB: B:1-158 (gaps) UniProt: 1-159 [INCOMPLETE]                                                                                                      Transcript 1
                 1i21 B   1 mSLPDGFYIRRmEEGDLEQVTETLKVLTTVGTITPESFCKLIKYWNEATVWNDN-DKKImQYNPmVIVDKRTETVAATGNIIIERKIIHELGLCGHIEDIAVNSKYQGQGLGKLLIDQLVTIGFDYGCYKIILDCDEKNVKFYEKCGFSNAGVEmQIR 158
                            |       10 |      20        30        40        50   | |  60    |   70        80        90       100       110       120       130       140       150    |   
                            |         12-MSE                                    54 |   |    |                                                                                       155-MSE
                            1-MSE                                                 56   |    |                                                                                             
                                                                                      60-MSE|                                                                                             
                                                                                           65-MSE

Chain M from PDB  Type:PROTEIN  Length:156
 aligned with GNA1_YEAST | P43577 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150        
           GNA1_YEAST     1 MSLPDGFYIRRMEEGDLEQVTETLKVLTTVGTITPESFSKLIKYWNEATVWNDNEDKKIMQYNPMVIVDKRTETVAATGNIIIERKIIHELGLCGHIEDIAVNSKYQGQGLGKLLIDQLVTIGFDYGCYKIILDCDEKNVKFYEKCGFSNAGVEMQIR 158
               SCOP domains d1i21m_ M: Glucosamine-phosphate N-acetyltransferase G  NA1                                                                                                    SCOP domains
               CATH domains -1i21M00 M:2-158  [code=3.40.630.30, no name defined]                                                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...eeeee.hhhhhhhhhhhhh........hhhhhhhhhhhhh........--.......eeeeee.....eeeeeeeeeee.hhhhhheeeeeeeeee.hhhh..hhhhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhh..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------GNAT  PDB: M:28-158 UniProt: 28-159                                                                                                 PROSITE
               Transcript 1 Exon 1.1  PDB: M:1-158 (gaps) UniProt: 1-159 [INCOMPLETE]                                                                                                      Transcript 1
                 1i21 M   1 mSLPDGFYIRRmEEGDLEQVTETLKVLTTVGTITPESFCKLIKYWNEATVWNDN--KKImQYNPmVIVDKRTETVAATGNIIIERKIIHELGLCGHIEDIAVNSKYQGQGLGKLLIDQLVTIGFDYGCYKIILDCDEKNVKFYEKCGFSNAGVEmQIR 158
                            |       10 |      20        30        40        50   |  | 60    |   70        80        90       100       110       120       130       140       150    |   
                            |         12-MSE                                    54 57  |    |                                                                                       155-MSE
                            1-MSE                                                     60-MSE|                                                                                             
                                                                                           65-MSE

Chain N from PDB  Type:PROTEIN  Length:147
 aligned with GNA1_YEAST | P43577 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:154
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155    
           GNA1_YEAST     6 GFYIRRMEEGDLEQVTETLKVLTTVGTITPESFSKLIKYWNEATVWNDNEDKKIMQYNPMVIVDKRTETVAATGNIIIERKIIHELGLCGHIEDIAVNSKYQGQGLGKLLIDQLVTIGFDYGCYKIILDCDEKNVKFYEKCGFSNAGVEMQIRK 159
               SCOP domains d1i21n_ N: Glucosamine-p    hosphate N-acetyltran   sferase GNA1                                                                                           SCOP domains
               CATH domains 1i21N00 N:6-159  [code=3    .40.630.30, no name d   efined]                                                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhhh....----hhhhhhhhhhhhh........---......eeeeee.....eeeeeeeeeee.hhhhhheeeeeeeeee.hhhh..hhhhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhh..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------GNAT  PDB: N:28-159 UniProt: 28-159                                                                                                  PROSITE
               Transcript 1 Exon 1.1  PDB: N:6-159 (gaps) UniProt: 1-159 [INCOMPLETE]                                                                                                  Transcript 1
                 1i21 N   6 GFYIRRmEEGDLEQVTETLKVLTT----TPESFCKLIKYWNEATVWNDN---KImQYNPmVIVDKRTETVAATGNIIIERKIIHELGLCGHIEDIAVNSKYQGQGLGKLLIDQLVTIGFDYGCYKIILDCDEKNVKFYEKCGFSNAGVEmQIRK 159
                                  | 15        25   |    35        45        |-  | |   65        75        85        95       105       115       125       135       145       155    
                                 12-MSE           29   34                  54  58 |    |                                                                                       155-MSE
                                                                                 60-MSE|                                                                                              
                                                                                      65-MSE

Chain X from PDB  Type:PROTEIN  Length:150
 aligned with GNA1_YEAST | P43577 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:153
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155   
           GNA1_YEAST     6 GFYIRRMEEGDLEQVTETLKVLTTVGTITPESFSKLIKYWNEATVWNDNEDKKIMQYNPMVIVDKRTETVAATGNIIIERKIIHELGLCGHIEDIAVNSKYQGQGLGKLLIDQLVTIGFDYGCYKIILDCDEKNVKFYEKCGFSNAGVEMQIR 158
               SCOP domains d1i21x_ X: Glucosamine-phosphate N-acetyltransferase GNA1                                                                                                 SCOP domains
               CATH domains 1i21X00 X:6-158  [code=3.40.630.30, no name defined]                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.hhhhhhhhhhhhh........hhhhhhhhhhhhhhh................eeee......eeeeeeeeeee.hhhhhheeeeeeeeee.---....hhhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhh...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------GNAT  PDB: X:28-158 UniProt: 28-159                                                                                                 PROSITE
               Transcript 1 Exon 1.1  PDB: X:6-158 (gaps) UniProt: 1-159 [INCOMPLETE]                                                                                                 Transcript 1
                 1i21 X   6 GFYIRRmEEGDLEQVTETLKVLTTVGTITPESFCKLIKYWNEATVWNDNEDKKImQYNPmVIVDKRTETVAATGNIIIERKIIHELGLCGHIEDIAVN---QGQGLGKLLIDQLVTIGFDYGCYKIILDCDEKNVKFYEKCGFSNAGVEmQIR 158
                                  | 15        25        35        45        55    |   65        75        85        95       | - |     115       125       135       145       155   
                                 12-MSE                                          60-MSE|                                   103 107                                             155-MSE
                                                                                      65-MSE

Chain Y from PDB  Type:PROTEIN  Length:156
 aligned with GNA1_YEAST | P43577 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:156
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152      
           GNA1_YEAST     3 LPDGFYIRRMEEGDLEQVTETLKVLTTVGTITPESFSKLIKYWNEATVWNDNEDKKIMQYNPMVIVDKRTETVAATGNIIIERKIIHELGLCGHIEDIAVNSKYQGQGLGKLLIDQLVTIGFDYGCYKIILDCDEKNVKFYEKCGFSNAGVEMQIR 158
               SCOP domains d1i21y_ Y: Glucosamine-phosphate N-acetyltransferase GNA1                                                                                                    SCOP domains
               CATH domains 1i21Y00 Y:3-158  [code=3.40.630.30, no name defined]                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeee.hhhhhhhhhhhhh........hhhhhhhhhhhhhhh................eeeee....eeeeeeeeeeee.hhhhhheeeeeeeeee.hhhh...hhhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhh...eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------GNAT  PDB: Y:28-158 UniProt: 28-159                                                                                                 PROSITE
               Transcript 1 Exon 1.1  PDB: Y:3-158 UniProt: 1-159 [INCOMPLETE]                                                                                                           Transcript 1
                 1i21 Y   3 LPDGFYIRRmEEGDLEQVTETLKVLTTVGTITPESFCKLIKYWNEATVWNDNEDKKImQYNPmVIVDKRTETVAATGNIIIERKIIHELGLCGHIEDIAVNSKYQGQGLGKLLIDQLVTIGFDYGCYKIILDCDEKNVKFYEKCGFSNAGVEmQIR 158
                                    12        22        32        42        52       |62  |     72        82        92       102       112       122       132       142       152  |   
                                    12-MSE                                          60-MSE|                                                                                       155-MSE
                                                                                         65-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 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: Glucosamine-phosphate N-acetyltransferase GNA1 (3)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (3)

1a	d1i21a_	A:
1b	d1i21m_	M:
1c	d1i21n_	N:
1d	d1i21x_	X:
1e	d1i21y_	Y:
1f	d1i21b_	B:

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	1i21B00	B:2-158
1b	1i21M00	M:2-158
1c	1i21A00	A:2-158
1d	1i21X00	X:6-158
1e	1i21N00	N:6-159
1f	1i21Y00	Y:3-158

(no "Pfam Domain" information available for 1I21)

Asymmetric Unit(hide GO term definitions)

Chain A,B,M,N,X,Y (GNA1_YEAST | P43577)

molecular function
	GO:0008080	N-acetyltransferase activity	Catalysis of the transfer of an acetyl group to a nitrogen atom on the acceptor molecule.
	GO:0004343	glucosamine 6-phosphate N-acetyltransferase activity	Catalysis of the reaction: D-glucosamine 6-phosphate + acetyl-CoA = N-acetyl-D-glucosamine 6-phosphate + CoA + H(+).
	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:0006048	UDP-N-acetylglucosamine biosynthetic process	The chemical reactions and pathways resulting in the formation of UDP-N-acetylglucosamine, a substance composed of N-acetylglucosamine, a common structural unit of oligosaccharides, in glycosidic linkage with uridine diphosphate.

Asymmetric Unit
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	Sites
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(no "Cis Peptide Bonds" information available for 1i21)

Biological Units
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	1i21
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	GNA1_YEAST \| P43577
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UniProtKB/Swiss-Prot
	GNA1_YEAST \| P43577	:	1i12 1i1d

1i12	CRYSTAL STRUCTURE OF SACCHAROMYCES CEREVISIAE GNA1 COMPLEXED WITH ACCOA
1i1d	CRYSTAL STRUCTURE OF YEAST GNA1 BOUND TO COA AND GLNAC-6P

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 27)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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Exons (1, 6)

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