1DEA - JenaLib

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Asymmetric Unit (Jmol Viewer)

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Biological Unit 3 (Jmol Viewer)

Title :   STRUCTURE AND CATALYTIC MECHANISM OF GLUCOSAMINE 6-PHOSPHATE DEAMINASE FROM ESCHERICHIA COLI AT 2.1 ANGSTROMS RESOLUTION

Authors :   G. Oliva, M. R. M. Fontes, R. C. Garratt, M. M. Altamirano, M. L. Calcagno E. Horjales

Date :   13 Sep 95 (Deposition) - 29 Jan 96 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (3x)
Biol. Unit 2: A  (3x)
Biol. Unit 3: B  (3x)

Keywords :   Intramolecular Oxidoreductase Deaminase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Oliva, M. R. Fontes, R. C. Garratt, M. M. Altamirano, M. L. Calcagno, E. Horjales
Structure And Catalytic Mechanism Of Glucosamine 6-Phosphat Deaminase From Escherichia Coli At 2. 1 A Resolution.
Structure V. 3 1323 1995
PubMed-ID: 8747459 | Reference-DOI: 10.1016/S0969-2126(01)00270-2
(for further references see the PDB file header)

Molecule 1 - GLUCOSAMINE 6-PHOSPHATE DEAMINASE
	Chains	:	A, B
	EC Number	:	5.3.1.10
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (3x)	:	A	B
Biological Unit 2 (3x)	:	A
Biological Unit 3 (3x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	PO4	4	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (1, 12)

No.	Name	Count	Type	Full Name
1	PO4	12	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (1, 6)

No.	Name	Count	Type	Full Name
1	PO4	6	Ligand/Ion	PHOSPHATE ION

Biological Unit 3 (1, 6)

No.	Name	Count	Type	Full Name
1	PO4	6	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	MET A:1 , SER A:151 , SER A:152 , ARG A:158 , LYS A:160 , HOH A:338 , HOH A:362 , HOH A:364	BINDING SITE FOR RESIDUE PO4 A 267
2	AC2	SOFTWARE	GLY A:42 , GLY A:43 , THR A:44 , ARG A:172 , LYS A:208 , HOH A:323 , HOH A:348 , HOH A:386	BINDING SITE FOR RESIDUE PO4 A 268
3	AC3	SOFTWARE	MET B:1 , SER B:151 , SER B:152 , ARG B:158 , LYS B:160 , HOH B:299 , HOH B:352 , HOH B:402 , HOH B:406	BINDING SITE FOR RESIDUE PO4 B 267
4	AC4	SOFTWARE	GLY B:42 , GLY B:43 , THR B:44 , ARG B:172 , LYS B:208 , HOH B:328 , HOH B:332 , HOH B:377 , HOH B:395	BINDING SITE FOR RESIDUE PO4 B 268

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

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

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLC_GALNAC_ISOMERASE	PS01161	Glucosamine/galactosamine-6-phosphate isomerases signature.	NAGB_ECOLI	125-143	2	A:125-143 B:125-143

Biological Unit 1 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLC_GALNAC_ISOMERASE	PS01161	Glucosamine/galactosamine-6-phosphate isomerases signature.	NAGB_ECOLI	125-143	6	A:125-143 B:125-143

Biological Unit 2 (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLC_GALNAC_ISOMERASE	PS01161	Glucosamine/galactosamine-6-phosphate isomerases signature.	NAGB_ECOLI	125-143	3	A:125-143 -

Biological Unit 3 (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLC_GALNAC_ISOMERASE	PS01161	Glucosamine/galactosamine-6-phosphate isomerases signature.	NAGB_ECOLI	125-143	3	- B:125-143

(no "Exon" information available for 1DEA)

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:266
 aligned with NAGB_ECOLI | P0A759 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:266
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260      
           NAGB_ECOLI     1 MRLIPLTTAEQVGKWAARHIVNRINAFKPTADRPFVLGLPTGGTPMTTYKALVEMHKAGQVSFKHVVTFNMDEYVGLPKEHPESYYSFMHRNFFDHVDIPAENINLLNGNAPDIDAECRQYEEKIRSYGKIHLFMGGVGNDGHIAFNEPASSLASRTRIKTLTHDTRVANSRFFDNDVNQVPKYALTVGVGTLLDAEEVMILVLGSQKALALQAAVEGCVNHMWTISCLQLHPKAIMVCDEPSTMELKVKTLRYFNELEAENIKGL 266
               SCOP domains d1deaa_ A: Glucosamine 6-phosphate deaminase/isomerase NagB                                                                                                                                                                                                                SCOP domains
               CATH domains 1deaA00 A:1-266  [code=3.40.50.1360, no name defined]                                                                                                                                                                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...hhhhhhhhhhhhhhhhhhh.......eeeee....hhhhhhhhhhhhhh........eeeee.eee..........hhhhhhhh.hhh....hhh..........hhhhhhhhhhhhhhh.....eee.....................eeee..hhhhhhhhhhh...hhh...eeee..hhhhh....eeeee..hhhhhhhhhhhh.......hhhhhhh...eeeee..hhh....hhhhhhhhhhh.hhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------GLC_GALNAC_ISOMERAS--------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dea A   1 MRLIPLTTAEQVGKWAARHIVNRINAFKPTADRPFVLGLPTGGTPMTTYKALVEMHKAGQVSFKHVVTFNMDEYVGLPKEHPESYYSFMHRNFFDHVDIPAENINLLNGNAPDIDAECRQYEEKIRSYGKIHLFMGGVGNDGHIAFNEPASSLASRTRIKTLTHDTRVANSRFFDNDVNQVPKYALTVGVGTLLDAEEVMILVLGSQKALALQAAVEGCVNHMWTISCLQLHPKAIMVCDEPSTMELKVKTLRYFNELEAENIKGL 266
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260

Chain B from PDB  Type:PROTEIN  Length:266
 aligned with NAGB_ECOLI | P0A759 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:266
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260      
           NAGB_ECOLI     1 MRLIPLTTAEQVGKWAARHIVNRINAFKPTADRPFVLGLPTGGTPMTTYKALVEMHKAGQVSFKHVVTFNMDEYVGLPKEHPESYYSFMHRNFFDHVDIPAENINLLNGNAPDIDAECRQYEEKIRSYGKIHLFMGGVGNDGHIAFNEPASSLASRTRIKTLTHDTRVANSRFFDNDVNQVPKYALTVGVGTLLDAEEVMILVLGSQKALALQAAVEGCVNHMWTISCLQLHPKAIMVCDEPSTMELKVKTLRYFNELEAENIKGL 266
               SCOP domains d1deab_ B: Glucosamine 6-phosphate deaminase/isomerase NagB                                                                                                                                                                                                                SCOP domains
               CATH domains 1deaB00 B:1-266  [code=3.40.50.1360, no name defined]                                                                                                                                                                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...hhhhhhhhhhhhhhhhhhh.......eeeee....hhhhhhhhhhhhhh........eeeee.eee..........hhhhhhhh.hhh....hhh..........hhhhhhhhhhhhhhh.....eee.....................eeee..hhhhhhhhhhh...hhh...eeee..hhhhh....eeeee..hhhhhhhhhhhh.......hhhhhhh...eeeee..hhh....hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------GLC_GALNAC_ISOMERAS--------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dea B   1 MRLIPLTTAEQVGKWAARHIVNRINAFKPTADRPFVLGLPTGGTPMTTYKALVEMHKAGQVSFKHVVTFNMDEYVGLPKEHPESYYSFMHRNFFDHVDIPAENINLLNGNAPDIDAECRQYEEKIRSYGKIHLFMGGVGNDGHIAFNEPASSLASRTRIKTLTHDTRVANSRFFDNDVNQVPKYALTVGVGTLLDAEEVMILVLGSQKALALQAAVEGCVNHMWTISCLQLHPKAIMVCDEPSTMELKVKTLRYFNELEAENIKGL 266
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260

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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

)

Organisms( (-)

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Class: Alpha and beta proteins (a/b) (23833)

Fold: NagB/RpiA/CoA transferase-like (94)

Superfamily: NagB/RpiA/CoA transferase-like (94)

Family: NagB-like (14)

Protein domain: Glucosamine 6-phosphate deaminase/isomerase NagB (11)

Escherichia coli [TaxId: 562] (10)

1a	d1deaa_	A:
1b	d1deab_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.1360, no name defined] (40)

Escherichia coli. Organism_taxid: 562. (10)

1a	1deaA00	A:1-266
1b	1deaB00	B:1-266

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (NAGB_ECOLI | P0A759)

molecular function
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0004342	glucosamine-6-phosphate deaminase activity	Catalysis of the reaction: D-glucosamine 6-phosphate + H(2)O = beta-D-fructose 6-phosphate + NH(4)(+).
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
biological process
	GO:0006046	N-acetylglucosamine catabolic process	The chemical reactions and pathways resulting in the breakdown of 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: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:0019262	N-acetylneuraminate catabolic process	The chemical reactions and pathways resulting in the breakdown of N-acetylneuraminate, the anion of 5-(acetylamino)-3,5-dideoxy-D-glycero-D-galacto-non-3-ulosonic acid.
	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: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:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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(no "Related Entries Specified in the PDB File" available for 1DEA)

Description

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Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

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