2O28 - JenaLib

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Title :   CRYSTAL STRUCTURE OF GNPNAT1

Authors :   J. Min, H. Wu, H. Zeng, P. Loppnau, J. Weigelt, M. Sundstrom, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, A. N. Plotnikov, Structural Genomics Consortium (Sgc)

Date :   29 Nov 06 (Deposition) - 12 Dec 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym./Biol. Unit : A,B

Keywords :   Acetyltransferase, Structural Genomics, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Wu, J. Min, H. Zeng, P. Loppnau, J. Weigelt, M. Sundstrom, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, A. N. Plotnikov
Crystal Structure Of Glucosamine-Phosphate N-Acetyltransferase 1
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - GLUCOSAMINE 6-PHOSPHATE N-ACETYLTRANSFERASE
	Chains	:	A, B
	EC Number	:	2.3.1.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	GNPNAT1, GNA1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PHOSPHOGLUCOSAMINE TRANSACETYLASE, PHOSPHOGLUCOSAMINE ACETYLASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

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

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:61 , GLU A:120 , ASP A:121 , VAL A:122 , GLU A:156 , TYR A:165 , ARG A:181 , COA A:401 , HOH A:516 , HOH A:525 , HOH A:641 , LYS B:108 , ILE B:110 , HIS B:111 , TYR B:151 , LYS B:152 , GLU B:175 , HOH B:472	BINDING SITE FOR RESIDUE 16G A 501
2	AC2	SOFTWARE	LEU A:60 , VAL A:122 , VAL A:123 , VAL A:124 , ARG A:129 , GLY A:130 , LYS A:131 , GLN A:132 , LEU A:133 , GLY A:134 , LYS A:135 , CYS A:157 , GLN A:160 , ASN A:161 , GLY A:163 , PHE A:164 , TYR A:165 , LYS A:167 , 16G A:501 , HOH A:511 , HOH A:512 , HOH A:518 , HOH A:537 , HOH A:545 , HOH A:624 , HOH A:652 , HOH A:653	BINDING SITE FOR RESIDUE COA A 401
3	AC3	SOFTWARE	VAL B:122 , VAL B:123 , VAL B:124 , ARG B:129 , GLY B:130 , LYS B:131 , GLN B:132 , LEU B:133 , GLY B:134 , LYS B:135 , CYS B:157 , GLN B:160 , ASN B:161 , GLY B:163 , PHE B:164 , TYR B:165 , LYS B:167 , HOH B:405 , HOH B:422 , HOH B:441 , HOH B:454 , HOH B:456 , HOH B:466 , HOH B:475 , HOH B:545	BINDING SITE FOR RESIDUE COA B 401

(no "SS Bond" information available for 2O28)

Asymmetric/Biological Unit

No.	Residues
1	Ser A:27	-	Pro A:28
2	Ser B:27	-	Pro B:28

(no "SAP(SNP)/Variant" information available for 2O28)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GNAT	PS51186	Gcn5-related N-acetyltransferase (GNAT) domain profile.	GNA1_HUMAN	39-184	2	A:39-184 B:39-182

Asymmetric/Biological Unit (5, 10)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000216410	1	ENSE00001255425	chr14:53258319-53258146	174	GNA1_HUMAN	-	0	0	-	-
1.2	ENST00000216410	2	ENSE00001147742	chr14:53251382-53251215	168	GNA1_HUMAN	1-52	52	2	A:3-52 B:3-52	50 50
1.3	ENST00000216410	3	ENSE00001002747	chr14:53250203-53250141	63	GNA1_HUMAN	52-73	22	2	A:52-73 B:52-73	22 22
1.4	ENST00000216410	4	ENSE00000657482	chr14:53248629-53248502	128	GNA1_HUMAN	73-115	43	2	A:73-115 B:73-115	43 43
1.5	ENST00000216410	5	ENSE00000657480	chr14:53247458-53247397	62	GNA1_HUMAN	116-136	21	2	A:116-136 B:116-136	21 21
1.6	ENST00000216410	6	ENSE00001255438	chr14:53245176-53241912	3265	GNA1_HUMAN	136-184	49	2	A:136-184 B:136-182	49 47

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:182
 aligned with GNA1_HUMAN | Q96EK6 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:182
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182  
           GNA1_HUMAN     3 PDETPMFDPSLLKEVDWSQNTATFSPAISPTHPGEGLVLRPLCTADLNRGFFKVLGQLTETGVVSPEQFMKSFEHMKKSGDYYVTVVEDVTLGQIVATATLIIEHKFIHSCAKRGRVEDVVVSDECRGKQLGKLLLSTLTLLSKKLNCYKITLECLPQNVGFYKKFGYTVSEENYMCRRFLK 184
               SCOP domains d2o28a_ A: automated matches                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhh................eeeee.hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhh.eeeeeeee....eeeeeeeeeeee.hhhhhheeeeeeeeee.hhhh..hhhhhhhhhhhhhhhhh.eeeeeeeehhhhhhhhhh...ee...eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------GNAT  PDB: A:39-184 UniProt: 39-184                                                                                                                PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:3-52 UniProt: 1-52 [INCOMPLETE]  --------------------Exon 1.4  PDB: A:73-115 UniProt: 73-115    Exon 1.5             ------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------Exon 1.3  PDB: A:52-73--------------------------------------------------------------Exon 1.6  PDB: A:136-184 UniProt: 136-184         Transcript 1 (2)
                 2o28 A   3 PDETPMFDPSLLKEVDWSQNTATFSPAISPTHPGEGLVLRPLCTADLNRGFFKVLGQLTETGVVSPEQFMKSFEHMKKSGDYYVTVVEDVTLGQIVATATLIIEHKFIHSCAKRGRVEDVVVSDECRGKQLGKLLLSTLTLLSKKLNCYKITLECLPQNVGFYKKFGYTVSEENYMCRRFLK 184
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182

Chain B from PDB  Type:PROTEIN  Length:180
 aligned with GNA1_HUMAN | Q96EK6 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:180
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182
           GNA1_HUMAN     3 PDETPMFDPSLLKEVDWSQNTATFSPAISPTHPGEGLVLRPLCTADLNRGFFKVLGQLTETGVVSPEQFMKSFEHMKKSGDYYVTVVEDVTLGQIVATATLIIEHKFIHSCAKRGRVEDVVVSDECRGKQLGKLLLSTLTLLSKKLNCYKITLECLPQNVGFYKKFGYTVSEENYMCRRF 182
               SCOP domains d2o28b_ B: automated matches                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------Acetyltransf_1-2o28B01 B:92-171                                                 ----------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------Acetyltransf_1-2o28B02 B:92-171                                                 ----------- Pfam domains (2)
         Sec.struct. author ........hhhhhh.hhhhh................eeeee.hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhh.eeeeeeee....eeeeeeeeeeee.hhhhhheeeeeeeeee.hhhh..hhhhhhhhhhhhhhhhh.eeeeeeeehhhhhhhhhhhh.ee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------GNAT  PDB: B:39-182 UniProt: 39-184                                                                                                              PROSITE
           Transcript 1 (1) Exon 1.2  PDB: B:3-52 UniProt: 1-52 [INCOMPLETE]  --------------------Exon 1.4  PDB: B:73-115 UniProt: 73-115    Exon 1.5             ---------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------Exon 1.3  PDB: B:52-73--------------------------------------------------------------Exon 1.6  PDB: B:136-182 UniProt: 136-184       Transcript 1 (2)
                 2o28 B   3 PDETPMFDPSLLKEVDWSQNTATFSPAISPTHPGEGLVLRPLCTADLNRGFFKVLGQLTETGVVSPEQFMKSFEHMKKSGDYYVTVVEDVTLGQIVATATLIIEHKFIHSCAKRGRVEDVVVSDECRGKQLGKLLLSTLTLLSKKLNCYKITLECLPQNVGFYKKFGYTVSEENYMCRRF 182
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182

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: automated matches (63)

Protein domain: automated matches (63)

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

1a	d2o28a_	A:
1b	d2o28b_	B:

(no "CATH Domain" information available for 2O28)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Acetyltrans (109)

Family: Acetyltransf_1 (58)

Homo sapiens (Human) (6)

1a	Acetyltransf_1-2o28B01	B:92-171
1b	Acetyltransf_1-2o28B02	B:92-171

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (GNA1_HUMAN | Q96EK6)

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:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0048029	monosaccharide binding	Interacting selectively and non-covalently with any monosaccharide. Monosaccharides are the simplest carbohydrates; they are polyhydroxy aldehydes H[CH(OH)]nC(=O)H or polyhydroxy ketones H[CHOH]nC(=O)[CHOH]mH with three or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides.
	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:0006044	N-acetylglucosamine metabolic process	The chemical reactions and pathways involving N-acetylglucosamine. The D isomer is a common structural unit of glycoproteins in plants, bacteria and animals; it is often the terminal sugar of an oligosaccharide group of a glycoprotein.
	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.
	GO:0006041	glucosamine metabolic process	The chemical reactions and pathways involving glucosamine (2-amino-2-deoxyglucopyranose), an aminodeoxysugar that occurs in combined form in chitin.
	GO:0001889	liver development	The process whose specific outcome is the progression of the liver over time, from its formation to the mature structure. The liver is an exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes.
cellular component
	GO:0005794	Golgi apparatus	A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
	GO:0000139	Golgi membrane	The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
	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:0005793	endoplasmic reticulum-Golgi intermediate compartment	A complex system of membrane-bounded compartments located between endoplasmic reticulum (ER) and the Golgi complex, with a distinctive membrane protein composition; involved in ER-to-Golgi and Golgi-to-ER transport.
	GO:0005768	endosome	A vacuole to which materials ingested by endocytosis are delivered.
	GO:0010008	endosome membrane	The lipid bilayer surrounding an endosome.
	GO:0005770	late endosome	A prelysosomal endocytic organelle differentiated from early endosomes by lower lumenal pH and different protein composition. Late endosomes are more spherical than early endosomes and are mostly juxtanuclear, being concentrated near the microtubule organizing center.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Asymmetric/Biological Unit
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		Ser A:27 - Pro A:28	[ RasMol ]
		Ser B:27 - Pro B:28	[ RasMol ]

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	2o28
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	GNA1_HUMAN \| Q96EK6	:	2huz 3cxp 3cxq 3cxs

(no "Related Entries Specified in the PDB File" available for 2O28)

Description

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Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

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Exons (5, 10)

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