2RI0 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF GLUCOSAMINE 6-PHOSPHATE DEAMINASE (NAGB) FROM S. MUTANS

Authors :   D. Li, C. Liu, L. F. Li, X. D. Su

Date :   10 Oct 07 (Deposition) - 25 Mar 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

Keywords :   Glucosamine 6-Phosphate Deaminase, Carbohydrate Metabolism, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Liu, D. Li, Y. H. Liang, L. F. Li, X. D. Su
Ring-Opening Mechanism Revealed By Crystal Structures Of Nagb And Its Es Intermediate Complex
J. Mol. Biol. V. 379 73 2008
PubMed-ID: 18436239 | Reference-DOI: 10.1016/J.JMB.2008.03.031

Molecule 1 - GLUCOSAMINE-6-PHOSPHATE DEAMINASE
	Chains	:	A, B
	EC Number	:	3.5.99.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	SMU.636
	Organism Scientific	:	STREPTOCOCCUS MUTANS
	Organism Taxid	:	1309
	Synonym	:	NAGB, GLUCOSAMINE-6-PHOSPHATE ISOMERASE, GNPDA, GLCN6P DEAMINASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	BTB	2	Ligand/Ion	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2	NA	2	Ligand/Ion	SODIUM ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	BTB	1	Ligand/Ion	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	BTB	1	Ligand/Ion	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA B:99 , ALA B:100 , HOH B:498 , HOH B:589	BINDING SITE FOR RESIDUE NA B 234
2	AC2	SOFTWARE	LEU B:94 , ASN B:96 , GLU B:105 , TYR B:108 , HOH B:433	BINDING SITE FOR RESIDUE NA B 235
3	AC3	SOFTWARE	GLU A:22 , GLU A:23 , PHE A:26 , LYS A:220 , GLU B:22 , GLU B:23 , PHE B:26 , LYS B:220	BINDING SITE FOR RESIDUE BTB A 234
4	AC4	SOFTWARE	HOH A:513 , ASN B:96 , GLU B:105 , HOH B:400 , HOH B:436	BINDING SITE FOR RESIDUE BTB B 236

(no "SS Bond" information available for 2RI0)

Asymmetric Unit

No.	Residues
1	Glu A:162	-	Lys A:163

(no "SAP(SNP)/Variant" information available for 2RI0)

(no "PROSITE Motif" information available for 2RI0)

(no "Exon" information available for 2RI0)

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:234
 aligned with NAGB_STRMU | Q8DV70 from UniProtKB/Swiss-Prot  Length:233

    Alignment length:234
                             1                                                                                                                                                                                                                                        
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229    
           NAGB_STRMU     - -MKTIKVKNKTEGSKVAFRMLEEEITFGAKTLGLATGSTPLELYKEIRESHLDFSDMVSINLDEYVGLSADDKQSYAYFMKQNLFAAKPFKKSYLPNGLAADLAKETEYYDQILAQYPIDLQILGIGRNAHIGFNEPGTAFSSQTHLVDLTPSTIAANSRFFEKAEDVPKQAISMGLASIMSAKMILLMAFGEEKAEAVAAMVKGPVTEEIPASILQTHPKVILIVDEKAGAGI 233
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2ri0A00 A:0-233  [code=3.40.50.1360, no name defined]                                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee.hhhhhhhhhhhhhhhhhhh...eeee.....hhhhhhhhhh........eeee.eee.........hhhhhhhhhh.......eee.......hhhhhhhhhhhhhhhh...eeee.....................eeee.hhhhhhhhhh...hhhhh..eeee.hhhhhhh..eeeeee.hhhhhhhhhhhhhh.....hhhhhhhhh..eeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ri0 A   0 SMKTIKVKNKTEGSKVAFRMLEEEITFGAKTLGLATGSTPLELYKEIRESHLDFSDMVSINLDEYVGLSADDKQSYAYFMKQNLFAAKPFKKSYLPNGLAADLAKETEYYDQILAQYPIDLQILGIGRNAHIGFNEPGTAFSSQTHLVDLTPSTIAANSRFFEKAEDVPKQAISMGLASIMSAKMILLMAFGEEKAEAVAAMVKGPVTEEIPASILQTHPKVILIVDEKAGAGI 233
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229

Chain B from PDB  Type:PROTEIN  Length:234
 aligned with NAGB_STRMU | Q8DV70 from UniProtKB/Swiss-Prot  Length:233

    Alignment length:234
                             1                                                                                                                                                                                                                                        
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229    
           NAGB_STRMU     - -MKTIKVKNKTEGSKVAFRMLEEEITFGAKTLGLATGSTPLELYKEIRESHLDFSDMVSINLDEYVGLSADDKQSYAYFMKQNLFAAKPFKKSYLPNGLAADLAKETEYYDQILAQYPIDLQILGIGRNAHIGFNEPGTAFSSQTHLVDLTPSTIAANSRFFEKAEDVPKQAISMGLASIMSAKMILLMAFGEEKAEAVAAMVKGPVTEEIPASILQTHPKVILIVDEKAGAGI 233
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2ri0B00 B:0-233  [code=3.40.50.1360, no name defined]                                                                                                                                                                                      CATH domains
           Pfam domains (1) ------------Glucosamine_iso-2ri0B01 B:12-203                                                                                                                                                                ------------------------------ Pfam domains (1)
           Pfam domains (2) ------------Glucosamine_iso-2ri0B02 B:12-203                                                                                                                                                                ------------------------------ Pfam domains (2)
         Sec.struct. author .eeeeee.hhhhhhhhhhhhhhhhhhh...eeee.....hhhhhhhhhh........eeee.eee.........hhhhhhhhhh.......eee.......hhhhhhhhhhhhhhhh...eeee.....................eeee.hhhhhhhhhhhh.hhhhh..eeee.hhhhhhh..eeeeee.hhhhhhhhhhhhhh.....hhhhhhhhh..eeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ri0 B   0 SMKTIKVKNKTEGSKVAFRMLEEEITFGAKTLGLATGSTPLELYKEIRESHLDFSDMVSINLDEYVGLSADDKQSYAYFMKQNLFAAKPFKKSYLPNGLAADLAKETEYYDQILAQYPIDLQILGIGRNAHIGFNEPGTAFSSQTHLVDLTPSTIAANSRFFEKAEDVPKQAISMGLASIMSAKMILLMAFGEEKAEAVAAMVKGPVTEEIPASILQTHPKVILIVDEKAGAGI 233
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229

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 '\|'

(no "SCOP Domain" information available for 2RI0)

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)

Streptococcus mutans. Organism_taxid: 1309. (2)

1a	2ri0A00	A:0-233
1b	2ri0B00	B:0-233

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: ISOCOT_Fold (53)

Family: Glucosamine_iso (12)

Streptococcus mutans (2)

1a	Glucosamine_iso-2ri0B01	B:12-203
1b	Glucosamine_iso-2ri0B02	B:12-203

Asymmetric Unit(hide GO term definitions)

Chain A,B (NAGB_STRMU | Q8DV70)

molecular function
	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.
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: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:0006040	amino sugar metabolic process	The chemical reactions and pathways involving any amino sugar, sugars containing an amino group in place of a hydroxyl group.
	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.

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		Glu A:162 - Lys A:163	[ RasMol ]

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Description

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Cis Peptide Bonds (1, 1)

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