1I1D - JenaLib

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Title :   CRYSTAL STRUCTURE OF YEAST GNA1 BOUND TO COA AND GLNAC-6P

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

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

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Alpha/Beta, Domain Swapping, Gnat Conserved Core, 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, C, D
	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
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A			D
Biological Unit 2 (1x)	:		B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	16G	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE-6-PHOSPHATE
2	COA	2	Ligand/Ion	COENZYME A
3	IMD	1	Ligand/Ion	IMIDAZOLE

Biological Unit 1 (3, 4)

No.	Name	Count	Type	Full Name
1	16G	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE-6-PHOSPHATE
2	COA	1	Ligand/Ion	COENZYME A
3	IMD	1	Ligand/Ion	IMIDAZOLE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	16G	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE-6-PHOSPHATE
2	COA	1	Ligand/Ion	COENZYME A
3	IMD	-1	Ligand/Ion	IMIDAZOLE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:28 , GLU A:98 , ASP A:99 , ILE A:100 , ASP A:134 , TYR A:143 , ARG A:158 , HOH A:942 , HOH A:1016 , HOH A:1017 , HOH A:1039 , LYS D:86 , ILE D:88 , HIS D:89 , TYR D:129 , LYS D:130	BINDING SITE FOR RESIDUE 16G A 905
2	AC2	SOFTWARE	LEU B:27 , THR B:28 , GLU B:98 , ASP B:99 , ILE B:100 , LEU B:133 , ASP B:134 , TYR B:143 , ARG B:158 , HOH B:921 , HOH B:1017 , LYS C:86 , ILE C:88 , HIS C:89 , TYR C:129 , LYS C:130 , HOH C:262	BINDING SITE FOR RESIDUE 16G B 906
3	AC3	SOFTWARE	LYS A:86 , ILE A:88 , HIS A:89 , TYR A:129 , LYS A:130 , LEU D:27 , THR D:28 , GLU D:98 , ASP D:99 , ILE D:100 , ASP D:134 , TYR D:143 , ARG D:158 , HOH D:914 , HOH D:928 , HOH D:955 , HOH D:1004 , HOH D:1006	BINDING SITE FOR RESIDUE 16G D 908
4	AC4	SOFTWARE	VAL A:26 , ILE A:100 , ALA A:101 , VAL A:102 , GLN A:107 , GLY A:108 , GLN A:109 , GLY A:110 , LEU A:111 , GLY A:112 , LYS A:113 , ASN A:139 , PHE A:142 , LYS A:145 , HOH A:911 , HOH A:919 , HOH A:933 , HOH A:948 , HOH A:954 , HOH A:957 , HOH A:959 , HOH A:960 , HOH A:970 , HOH A:976 , HOH A:1020 , HOH A:1034 , LYS B:141 , COA B:901 , THR D:29	BINDING SITE FOR RESIDUE COA A 900
5	AC5	SOFTWARE	LYS A:141 , COA A:900 , VAL B:26 , ALA B:101 , VAL B:102 , GLN B:107 , GLY B:108 , GLN B:109 , GLY B:110 , LEU B:111 , GLY B:112 , LYS B:113 , LYS B:138 , ASN B:139 , LYS B:141 , PHE B:142 , LYS B:145 , HOH B:907 , HOH B:929 , HOH B:947 , HOH B:960 , HOH B:962 , HOH B:980 , HOH B:990 , HOH B:992 , HOH B:1004 , HOH B:1057 , HOH B:1074 , HOH B:1075	BINDING SITE FOR RESIDUE COA B 901
6	AC6	SOFTWARE	ASP A:117 , VAL A:120 , HOH A:969 , LYS D:159	BINDING SITE FOR RESIDUE IMD A 910

(no "SS Bond" information available for 1I1D)

(no "Cis Peptide Bond" information available for 1I1D)

(no "SAP(SNP)/Variant" information available for 1I1D)

Asymmetric Unit (1, 4)

	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	4	A:28-159 B:28-159 C:28-159 D:28-159

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:28-159 - - D:28-159

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	- B:28-159 C:28-159 -

Asymmetric Unit (1, 4)

	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	4	A:1-159 (gaps) B:3-159 (gaps) C:1-159 (gaps) D:1-159	159 157 159 159

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:156
 aligned with GNA1_YEAST | P43577 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:159
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150         
           GNA1_YEAST     1 MSLPDGFYIRRMEEGDLEQVTETLKVLTTVGTITPESFSKLIKYWNEATVWNDNEDKKIMQYNPMVIVDKRTETVAATGNIIIERKIIHELGLCGHIEDIAVNSKYQGQGLGKLLIDQLVTIGFDYGCYKIILDCDEKNVKFYEKCGFSNAGVEMQIRK 159
               SCOP domains d1i1da_ A: Glucosamine-phosphate N-acetyltransferase    GNA1                                                                                                    SCOP domains
               CATH domains 1i1dA00 A:1-159  [code=3.40.630.30, no name defined]                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee.hhhhhhhhhhhhh........hhhhhhhhhhhhhhhee...---..ee....eeeee....eeeeeeeeeeee.hhhhhheeeeeeeeee.hhhh..hhhhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhh..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------GNAT  PDB: A:28-159 UniProt: 28-159                                                                                                  PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-159 (gaps) UniProt: 1-159                                                                                                                    Transcript 1
                 1i1d A   1 MSLPDGFYIRRMEEGDLEQVTETLKVLTTVGTITPESFCKLIKYWNEATVWND---KKIMQYNPMVIVDKRTETVAATGNIIIERKIIHELGLCGHIEDIAVNSKYQGQGLGKLLIDQLVTIGFDYGCYKIILDCDEKNVKFYEKCGFSNAGVEMQIRK 159
                                    10        20        30        40        50  |   | 60        70        80        90       100       110       120       130       140       150         
                                                                               53  57

Chain B from PDB  Type:PROTEIN  Length:154
 aligned with GNA1_YEAST | P43577 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:157
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       
           GNA1_YEAST     3 LPDGFYIRRMEEGDLEQVTETLKVLTTVGTITPESFSKLIKYWNEATVWNDNEDKKIMQYNPMVIVDKRTETVAATGNIIIERKIIHELGLCGHIEDIAVNSKYQGQGLGKLLIDQLVTIGFDYGCYKIILDCDEKNVKFYEKCGFSNAGVEMQIRK 159
               SCOP domains d1i1db_ B: Glucosamine-phosphate N-acetyltransferas   e GNA1                                                                                                  SCOP domains
               CATH domains 1i1dB00 B:3-159  [code=3.40.630.30, no name defined   ]                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.hhhhhhhhhhhhh........hhhhhhhhhhhhhhhee...---..ee.eeeeeeee....eeeeeeeeeeee.hhhhhheeeeeeeeee.hhhh..hhhhhhhhhhhhhhhhhheeeeeeeehhhhhhhhhhh..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------GNAT  PDB: B:28-159 UniProt: 28-159                                                                                                  PROSITE
               Transcript 1 Exon 1.1  PDB: B:3-159 (gaps) UniProt: 1-159 [INCOMPLETE]                                                                                                     Transcript 1
                 1i1d B   3 LPDGFYIRRMEEGDLEQVTETLKVLTTVGTITPESFCKLIKYWNEATVWND---KKIMQYNPMVIVDKRTETVAATGNIIIERKIIHELGLCGHIEDIAVNSKYQGQGLGKLLIDQLVTIGFDYGCYKIILDCDEKNVKFYEKCGFSNAGVEMQIRK 159
                                    12        22        32        42        52|   |   62        72        82        92       102       112       122       132       142       152       
                                                                             53  57

Chain C from PDB  Type:PROTEIN  Length:155
 aligned with GNA1_YEAST | P43577 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:160
                             1                                                                                                                                                              
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159
           GNA1_YEAST     - -MSLPDGFYIRRMEEGDLEQVTETLKVLTTVGTITPESFSKLIKYWNEATVWNDNEDKKIMQYNPMVIVDKRTETVAATGNIIIERKIIHELGLCGHIEDIAVNSKYQGQGLGKLLIDQLVTIGFDYGCYKIILDCDEKNVKFYEKCGFSNAGVEMQIRK 159
               SCOP domains d1i1dc_ C: Glucosamine-phosphate N-acetyltransferase      GNA1                                                                                                   SCOP domains
               CATH domains 1i1dC00 C:0-159  [code=3.40.630.30, no name defined]                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...eeeee.hhhhhhhhhhhhh........hhhhhhhhhhhhhhh....-----....eeeeeeee....eeeeeeeeeeee.hhhhhheeeeeeeeee.hhhh..hhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhh..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------GNAT  PDB: C:28-159 UniProt: 28-159                                                                                                  PROSITE
               Transcript 1 -Exon 1.1  PDB: C:1-159 (gaps) UniProt: 1-159                                                                                                                    Transcript 1
                 1i1d C   0 SMSLPDGFYIRRMEEGDLEQVTETLKVLTTVGTITPESFCKLIKYWNEATVWN-----KIMQYNPMVIVDKRTETVAATGNIIIERKIIHELGLCGHIEDIAVNSKYQGQGLGKLLIDQLVTIGFDYGCYKIILDCDEKNVKFYEKCGFSNAGVEMQIRK 159
                                     9        19        29        39        49  |     59        69        79        89        99       109       119       129       139       149       159
                                                                               52    58

Chain D from PDB  Type:PROTEIN  Length:161
 aligned with GNA1_YEAST | P43577 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:161
                              1                                                                                                                                                              
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158 
           GNA1_YEAST     - --MSLPDGFYIRRMEEGDLEQVTETLKVLTTVGTITPESFSKLIKYWNEATVWNDNEDKKIMQYNPMVIVDKRTETVAATGNIIIERKIIHELGLCGHIEDIAVNSKYQGQGLGKLLIDQLVTIGFDYGCYKIILDCDEKNVKFYEKCGFSNAGVEMQIRK 159
               SCOP domains d1i1dd_ D: Glucosamine-phosphate N-acetyltransferase GNA1                                                                                                         SCOP domains
               CATH domains 1i1dD00 D:-1-159  [code=3.40.630.30, no name defined]                                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...eeeee.hhhhhhhhhhhhh........hhhhhhhhhhhhhhhee........ee....eeeee....eeeeeeeeeeee.hhhhhheeeeeeeeee.hhhh..hhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhh..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------GNAT  PDB: D:28-159 UniProt: 28-159                                                                                                  PROSITE
               Transcript 1 --Exon 1.1  PDB: D:1-159 UniProt: 1-159                                                                                                                           Transcript 1
                 1i1d D  -1 GSMSLPDGFYIRRMEEGDLEQVTETLKVLTTVGTITPESFCKLIKYWNEATVWNDNEDKKIMQYNPMVIVDKRTETVAATGNIIIERKIIHELGLCGHIEDIAVNSKYQGQGLGKLLIDQLVTIGFDYGCYKIILDCDEKNVKFYEKCGFSNAGVEMQIRK 159
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158

Legend:		→ Mismatch	(orange background)
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	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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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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	d1i1da_	A:
1b	d1i1db_	B:
1c	d1i1dc_	C:
1d	d1i1dd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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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	1i1dA00	A:1-159
1b	1i1dC00	C:0-159
1c	1i1dB00	B:3-159
1d	1i1dD00	D:-1-159

(no "Pfam Domain" information available for 1I1D)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (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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	Cis Peptide Bonds
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	1i1d
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	GNA1_YEAST \| P43577	:	1i12 1i21

1i12	CRYSTAL STRUCTURE OF SACCHAROMYCES CEREVISIAE GNA1 COMPLEXED WITH ACCOA
1i21	CRYSTAL STRUCTURE OF YEAST GNA1

Description

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Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

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