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Asym./Biol. Unit (Jmol Viewer)

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

Title :   GLUTAMINASE DOMAIN OF GLUCOSAMINE 6-PHOSPHATE SYNTHASE COMPLEXED WITH L-GLU HYDROXAMATE

Authors :   M. N. Isupov, A. Teplyakov

Date :   14 Sep 04 (Deposition) - 28 Sep 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

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

Keywords :   Glutamine Amidotransferase; N-Terminal Nucleophile (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. N. Isupov, G. Obmolova, S. Butterworth, M. -A. Badet-Denisot, B. Badet, I. Polikarpov, J. A. Littlechild, A. Teplyakov
Substrate Binding Is Required For Assembly Of The Active Conformation Of The Catalytic Site In Ntn Amidotransferases: Evidence From The 1. 8 Angstrom Crystal Structure Of The Glutaminase Domain Of Glucosamine 6-Phosphate Synthase
Structure V. 4 801 1996
PubMed-ID: 8805567 | Reference-DOI: 10.1016/S0969-2126(96)00087-1
(for further references see the PDB file header)

Molecule 1 - GLUCOSAMINE--FRUCTOSE-6-PHOSPHATE AMINOTRANSFERASE [ISOMERIZING]
	Atcc	:	25257
	Chains	:	A, B
	EC Number	:	2.6.1.16
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGM10A
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	GLUTAMINASE DOMAIN
	Gene	:	GLMS
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Other Details	:	INHIBITED BY L-GLUTAMATE
	Strain	:	3000HFR
	Synonym	:	HEXOSEPHOSPHATE AMINOTRANSFERASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 5)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	HGA	2	Ligand/Ion	GLUTAMINE HYDROXAMATE
3	NA	2	Ligand/Ion	SODIUM ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:154 , SER A:174 , HOH A:5356 , HOH A:5397	BINDING SITE FOR RESIDUE NA A 5301
2	AC2	SOFTWARE	GLY B:154 , TYR B:156 , SER B:174 , HOH B:9359 , HOH B:9385	BINDING SITE FOR RESIDUE NA B 9301
3	AC3	SOFTWARE	HOH A:5333 , HOH A:5334 , HOH A:5432 , HOH A:5436 , ARG B:173 , PRO B:177 , SER B:191	BINDING SITE FOR RESIDUE ACT A 5302
4	AC4	SOFTWARE	CYS A:1 , ARG A:73 , TRP A:74 , THR A:76 , HIS A:77 , HIS A:86 , HIS A:97 , ASN A:98 , GLY A:99 , ASP A:123 , THR A:124 , HOH A:5359	BINDING SITE FOR RESIDUE HGA A 5300
5	AC5	SOFTWARE	CYS B:1 , ARG B:73 , TRP B:74 , THR B:76 , HIS B:77 , HIS B:86 , HIS B:97 , ASN B:98 , GLY B:99 , ASP B:123 , THR B:124 , HOH B:9326	BINDING SITE FOR RESIDUE HGA B 9300

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

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

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

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GATASE_TYPE_2	PS51278	Glutamine amidotransferase type 2 domain profile.	GLMS_ECOLI	2-218	2	A:1-217 B:1-217

(no "Exon" information available for 1XFG)

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:238
 aligned with GLMS_ECOLI | P17169 from UniProtKB/Swiss-Prot  Length:609

    Alignment length:238
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231        
           GLMS_ECOLI     2 CGIVGAIAQRDVAEILLEGLRRLEYRGYDSAGLAVVDAEGHMTRLRRLGKVQMLAQAAEEHPLHGGTGIAHTRWATHGEPSEVNAHPHVSEHIVVVHNGIIENHEPLREELKARGYTFVSETDTEVIAHLVNWELKQGGTLREAVLRAIPQLRGAYGTVIMDSRHPDTLLAARSGSPLVIGLGMGENFIASDQLALLPVTRRFIFLEEGDIAEITRRSVNIFDKTGAEVKRQDIESNL 239
               SCOP domains d1xfga_ A: Glucosamine 6-phosphate synthase, N-terminal domain                                                                                                                                                                                 SCOP domains
               CATH domains 1xfgA00 A:1-238 Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1                                                                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhh..eeeeeee.....eeeeeee.hhhhhhhhhh.......eeeeeee..............eee..eeeeeee...hhhhhhhhhhhh........hhhhhhhhhhhhhhh..hhhhhhhhhhhhh...eeeeeee......eeeee.....eeee....eeee.hhhhhh....eeee.....eeee....eeee.....ee...eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE GATASE_TYPE_2  PDB: A:1-217 UniProt: 2-218                                                                                                                                                                               --------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xfg A   1 CGIVGAIAQRDVAEILLEGLRRLEYRGYDSAGLAVVDAEGHMTRLRRLGKVQMLAQAAEEHPLHGGTGIAHTRWATHGEPSEVNAHPHVSEHIVVVHNGIIENHEPLREELKARGYTFVSETDTEVIAHLVNWELKQGGTLREAVLRAIPQLRGAYGTVIMDSRHPDTLLAARSGSPLVIGLGMGENFIASDQLALLPVTRRFIFLEEGDIAEITRRSVNIFDKTGAEVKRQDIESNL 238
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230

Chain B from PDB  Type:PROTEIN  Length:239
 aligned with GLMS_ECOLI | P17169 from UniProtKB/Swiss-Prot  Length:609

    Alignment length:239
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231         
           GLMS_ECOLI     2 CGIVGAIAQRDVAEILLEGLRRLEYRGYDSAGLAVVDAEGHMTRLRRLGKVQMLAQAAEEHPLHGGTGIAHTRWATHGEPSEVNAHPHVSEHIVVVHNGIIENHEPLREELKARGYTFVSETDTEVIAHLVNWELKQGGTLREAVLRAIPQLRGAYGTVIMDSRHPDTLLAARSGSPLVIGLGMGENFIASDQLALLPVTRRFIFLEEGDIAEITRRSVNIFDKTGAEVKRQDIESNLQ 240
               SCOP domains d1xfgb_ B: Glucosamine 6-phosphate synthase, N-terminal domain                                                                                                                                                                                  SCOP domains
               CATH domains 1xfgB00 B:1-239 Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1                                                                                                                                                                      CATH domains
           Pfam domains (1) ------------------------------------------------GATase_2-1xfgB01 B:49-159                                                                                      -------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------GATase_2-1xfgB02 B:49-159                                                                                      -------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) ------------------------------------------------GATase_2-1xfgB03 B:49-159                                                                                      -------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) ------------------------------------------------GATase_2-1xfgB04 B:49-159                                                                                      -------------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhh..eeeeeee.....eeeeeee.hhhhhhhhhhh......eeeeeee..............eee..eeeeeee...hhhhhhhhhhhhh.......hhhhhhhhhhhhhhh..hhhhhhhhhhhhh...eeeeeee......eeeee.....eeee....eeee.hhhhh.....eeee.....eeee....eeee.....ee....ee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE GATASE_TYPE_2  PDB: B:1-217 UniProt: 2-218                                                                                                                                                                               ---------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xfg B   1 CGIVGAIAQRDVAEILLEGLRRLEYRGYDSAGLAVVDAEGHMTRLRRLGKVQMLAQAAEEHPLHGGTGIAHTRWATHGEPSEVNAHPHVSEHIVVVHNGIIENHEPLREELKARGYTFVSETDTEVIAHLVNWELKQGGTLREAVLRAIPQLRGAYGTVIMDSRHPDTLLAARSGSPLVIGLGMGENFIASDQLALLPVTRRFIFLEEGDIAEITRRSVNIFDKTGAEVKRQDIESNLQ 239
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230

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: Ntn hydrolase-like (356)

Superfamily: N-terminal nucleophile aminohydrolases (Ntn hydrolases) (352)

Family: Class II glutamine amidotransferases (27)

Protein domain: Glucosamine 6-phosphate synthase, N-terminal domain (4)

Escherichia coli [TaxId: 562] (4)

1a	d1xfga_	A:
1b	d1xfgb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 4-Layer Sandwich (459)

Topology: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 (128)

Homologous Superfamily: Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 (124)

Escherichia coli. Organism_taxid: 562. Strain: 3000hfr. (2)

1a	1xfgA00	A:1-238
1b	1xfgB00	B:1-239

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NTN (93)

Family: GATase_2 (9)

Escherichia coli (strain K12) (3)

1a	GATase_2-1xfgB01	B:49-159
1b	GATase_2-1xfgB02	B:49-159
1c	GATase_2-1xfgB03	B:49-159
1d	GATase_2-1xfgB04	B:49-159

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (GLMS_ECOLI | P17169)

molecular function
	GO:0030246	carbohydrate binding	Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
	GO:0004360	glutamine-fructose-6-phosphate transaminase (isomerizing) activity	Catalysis of the reaction: beta-D-fructose 6-phosphate + L-glutamine = D-glucosamine 6-phosphate + L-glutamate.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0008483	transaminase activity	Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid.
	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.
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.
	GO:1901137	carbohydrate derivative biosynthetic process	The chemical reactions and pathways resulting in the formation of carbohydrate derivative.
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	GO:0006002	fructose 6-phosphate metabolic process	The chemical reactions and pathways involving fructose 6-phosphate, also known as F6P. The D-enantiomer is an important intermediate in glycolysis, gluconeogenesis, and fructose metabolism.
	GO:0006541	glutamine metabolic process	The chemical reactions and pathways involving glutamine, 2-amino-4-carbamoylbutanoic acid.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
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	1xfg
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UniProtKB/Swiss-Prot
	GLMS_ECOLI \| P17169	:	1jxa 1moq 1mor 1mos 1xff 2j6h 2vf4 2vf5 3ooj 4amv

1jxa	INTACT GLUCOSAMINE-6P SYNTHASE WITH GLUCOSE-6P
1moq	IOSMERASE DOMAIN OF GLUCOSAMINE-6P SYNTHASE WITH GLUCOSAMINE-6P
1mor	IOSMERASE DOMAIN OF GLUCOSAMINE-6P SYNTHASE WITH GLUCOSE-6P
1mos	IOSMERASE DOMAIN OF GLUCOSAMINE-6P SYNTHASE WITH 2-AMINO-2- DEOXYGLUCITOL-6P
1xff	GLUTAMINASE DOMAIN OF GLUCOSAMINE-6P SYNTHASE WITH L-GLU

Description

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Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

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