1NT4 - JenaLib

Asym.Unit - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF ESCHERICHIA COLI PERIPLASMIC GLUCOSE-1-PHOSPHATASE H18A MUTANT COMPLEXED WITH GLUCOSE-1-PHOSPHATE

Authors :   D. C. Lee, M. A. Cottrill, C. W. Forsberg, Z. Jia, Montreal-Kingston Bacterial Structural Genomics Initiative (Bsgi)

Date :   28 Jan 03 (Deposition) - 13 Jan 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Alpha Domain, Alpha-Beta Domain, Occluded Active Site, Enzyme-Substrate Complex, Montreal-Kingston Bacterial Structural Genomics Initiative, Bsgi, Structural Genomics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. C. Lee, M. A. Cottrill, C. W. Forsberg, Z. Jia
Functional Insights Revealed By The Crystal Structures Of Escherichia Coli Glucose-1-Phosphatase.
J. Biol. Chem. V. 278 31412 2003
PubMed-ID: 12782623 | Reference-DOI: 10.1074/JBC.M213154200
(for further references see the PDB file header)

Molecule 1 - GLUCOSE-1-PHOSPHATASE
	Chains	:	A, B
	EC Number	:	3.1.3.10
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PBR322
	Expression System Strain	:	SBS1572
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	AGP OR B1002
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	G1PASE

		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 (1, 2)

No.	Name	Count	Type	Full Name
1	G1P	2	Ligand/Ion	ALPHA-D-GLUCOSE-1-PHOSPHATE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	G1P	1	Ligand/Ion	ALPHA-D-GLUCOSE-1-PHOSPHATE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	G1P	1	Ligand/Ion	ALPHA-D-GLUCOSE-1-PHOSPHATE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:17 , ARG A:21 , ARG A:94 , GLU A:196 , HIS A:289 , ASP A:290 , SER A:291 , HOH A:3102 , HOH A:3181	BINDING SITE FOR RESIDUE G1P A 2000
2	AC2	SOFTWARE	ARG B:1017 , ARG B:1021 , ARG B:1094 , GLU B:1196 , HIS B:1289 , ASP B:1290 , SER B:1291 , HOH B:3210 , HOH B:3211	BINDING SITE FOR RESIDUE G1P B 2001

Asymmetric Unit

No.	Residues
1	A:79	-	A:110
2	A:174	-	A:180
3	A:369	-	A:377
4	B:1079	-	B:1110
5	B:1174	-	B:1180
6	B:1369	-	B:1377

(no "Cis Peptide Bond" information available for 1NT4)

(no "SAP(SNP)/Variant" information available for 1NT4)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HIS_ACID_PHOSPHAT_1	PS00616	Histidine acid phosphatases phosphohistidine signature.	AGP_ECOLI	31-45	2	A:9-23 B:1009-1023
2	HIS_ACID_PHOSPHAT_2	PS00778	Histidine acid phosphatases active site signature.	AGP_ECOLI	305-321	2	A:283-299 B:1283-1299

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HIS_ACID_PHOSPHAT_1	PS00616	Histidine acid phosphatases phosphohistidine signature.	AGP_ECOLI	31-45	1	A:9-23 -
2	HIS_ACID_PHOSPHAT_2	PS00778	Histidine acid phosphatases active site signature.	AGP_ECOLI	305-321	1	A:283-299 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HIS_ACID_PHOSPHAT_1	PS00616	Histidine acid phosphatases phosphohistidine signature.	AGP_ECOLI	31-45	1	- B:1009-1023
2	HIS_ACID_PHOSPHAT_2	PS00778	Histidine acid phosphatases active site signature.	AGP_ECOLI	305-321	1	- B:1283-1299

(no "Exon" information available for 1NT4)

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:391
 aligned with AGP_ECOLI | P19926 from UniProtKB/Swiss-Prot  Length:413

    Alignment length:391
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412 
           AGP_ECOLI     23 QTVPEGYQLQQVLMMSRHNLRAPLANNGSVLEQSTPNKWPEWDVPGGQLTTKGGVLEVYMGHYMREWLAEQGMVKSGECPPPYTVYAYANSLQRTVATAQFFITGAFPGCDIPVHHQEKMGTMDPTFNPVITDDSAAFSEQAVAAMEKELSKLQLTDSYQLLEKIVNYKDSPACKEKQQCSLVDGKNTFSAKYQQEPGVSGPLKVGNSLVDAFTLQYYEGFPMDQVAWGEIKSDQQWKVLSKLKNGYQDSLFTSPEVARNVAKPLVSYIDKALVTDRTSAPKITVLVGHDSNIASLLTALDFKPYQLHDQNERTPIGGKIVFQRWHDSKANRDLMKIEYVYQSAEQLRNADALTLQAPAQRVTLELSGCPIDADGFCPMDKFDSVLNEAVK  413
               SCOP domains d1nt4a_ A: Glucose-1-phosphatase                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1nt4A01              1nt4A02 A:22-48,A:133-252  1nt4A01 A:1-21,A:49-132,A:253-391 Phosphoglycerate mutase-like                      1nt4A02 A:22-48,A:133-252 Phosphoglycerate mutase-like                                                                  1nt4A01 A:1-21,A:49-132,A:253-391 Phosphoglycerate mutase-like                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeee.......hhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhh.............eeeee..hhhhhhhhhhhhhhhh......ee....................hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh................eee.......eeehhhhhhhhhhhhhhhhhhh.....hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeee.hhhhhhhhhhhh..................eeeeeeeee....eeeeeeeeee.hhhhhhhh.........eeee.............eehhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------HIS_ACID_PHOSPH-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HIS_ACID_PHOSPHAT-------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1nt4 A    1 QTVPEGYQLQQVLMMSRANLRAPLANNGSVLEQSTPNKWPEWDVPGGQLTTKGGVLEVYMGHYMREWLAEQGMVKSGECPPPYTVYAYANSLQRTVATAQFFITGAFPGCDIPVHHQEKMGTMDPTFNPVITDDSAAFSEQAVAAMEKELSKLQLTDSYQLLEKIVNYKDSPACKEKQQCSLVDGKNTFSAKYQQEPGVSGPLKVGNSLVDAFTLQYYEGFPMDQVAWGEIKSDQQWKVLSKLKNGYQDSLFTSPEVARNVAKPLVSYIDKALVTDRTSAPKITVLVGHDSNIASLLTALDFKPYQLHDQNERTPIGGKIVFQRWHDSKANRDLMKIEYVYQSAEQLRNADALTLQAPAQRVTLELSGCPIDADGFCPMDKFDSVLNEAVK  391
                                    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       270       280       290       300       310       320       330       340       350       360       370       380       390

Chain B from PDB  Type:PROTEIN  Length:391
 aligned with AGP_ECOLI | P19926 from UniProtKB/Swiss-Prot  Length:413

    Alignment length:391
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412 
           AGP_ECOLI     23 QTVPEGYQLQQVLMMSRHNLRAPLANNGSVLEQSTPNKWPEWDVPGGQLTTKGGVLEVYMGHYMREWLAEQGMVKSGECPPPYTVYAYANSLQRTVATAQFFITGAFPGCDIPVHHQEKMGTMDPTFNPVITDDSAAFSEQAVAAMEKELSKLQLTDSYQLLEKIVNYKDSPACKEKQQCSLVDGKNTFSAKYQQEPGVSGPLKVGNSLVDAFTLQYYEGFPMDQVAWGEIKSDQQWKVLSKLKNGYQDSLFTSPEVARNVAKPLVSYIDKALVTDRTSAPKITVLVGHDSNIASLLTALDFKPYQLHDQNERTPIGGKIVFQRWHDSKANRDLMKIEYVYQSAEQLRNADALTLQAPAQRVTLELSGCPIDADGFCPMDKFDSVLNEAVK  413
               SCOP domains d1nt4b_ B: Glucose-1-phosphatase                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1nt4B01              1nt4B02                    1nt4B01 B:1001-1021,B:1049-1132,B:1253-1391 Phosphoglycerate mutase-like            1nt4B02 B:1022-1048,B:1133-1252 Phosphoglycerate mutase-like                                                            1nt4B01 B:1001-1021,B:1049-1132,B:1253-1391 Phosphoglycerate mutase-like                                                                    CATH domains
           Pfam domains (1) -------His_Phos_2-1nt4B01 B:1008-1342                                                                                                                                                                                                                                                                                                                 ------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -------His_Phos_2-1nt4B02 B:1008-1342                                                                                                                                                                                                                                                                                                                 ------------------------------------------------- Pfam domains (2)
         Sec.struct. author ........eeeeeeeee......hhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhh.............eee....hhhhhhhhhhhhhhhh............................hhhhhhhhhhhhhhhh.....hhhhhhhhhhh....................ee.........eehhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeeehhhhhhhhhhhh..................eeeeeeeee....eeeeeeeeee.hhhhhhh..........eeee.............eehhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------HIS_ACID_PHOSPH-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HIS_ACID_PHOSPHAT-------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1nt4 B 1001 QTVPEGYQLQQVLMMSRANLRAPLANNGSVLEQSTPNKWPEWDVPGGQLTTKGGVLEVYMGHYMREWLAEQGMVKSGECPPPYTVYAYANSLQRTVATAQFFITGAFPGCDIPVHHQEKMGTMDPTFNPVITDDSAAFSEQAVAAMEKELSKLQLTDSYQLLEKIVNYKDSPACKEKQQCSLVDGKNTFSAKYQQEPGVSGPLKVGNSLVDAFTLQYYEGFPMDQVAWGEIKSDQQWKVLSKLKNGYQDSLFTSPEVARNVAKPLVSYIDKALVTDRTSAPKITVLVGHDSNIASLLTALDFKPYQLHDQNERTPIGGKIVFQRWHDSKANRDLMKIEYVYQSAEQLRNADALTLQAPAQRVTLELSGCPIDADGFCPMDKFDSVLNEAVK 1391
                                  1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190      1200      1210      1220      1230      1240      1250      1260      1270      1280      1290      1300      1310      1320      1330      1340      1350      1360      1370      1380      1390

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Phosphoglycerate mutase-like (103)

Superfamily: Phosphoglycerate mutase-like (103)

Family: Histidine acid phosphatase (24)

Protein domain: Glucose-1-phosphatase (1)

Escherichia coli [TaxId: 562] (1)

1a	d1nt4a_	A:
1b	d1nt4b_	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: Phosphoglycerate mutase-like (91)

Escherichia coli. Organism_taxid: 562. (1)

1a	1nt4A01	A:1-21,A:49-132,A:253-391
1b	1nt4B01	B:1001-1021,B:1049-1132,B:1253-1391
1c	1nt4A02	A:22-48,A:133-252
1d	1nt4B02	B:1022-1048,B:1133-1252

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PGM (50)

Family: His_Phos_2 (19)

Escherichia coli (strain K12) (1)

1a	His_Phos_2-1nt4B01	B:1008-1342
1b	His_Phos_2-1nt4B02	B:1008-1342

Asymmetric Unit(hide GO term definitions)

Chain A,B (AGP_ECOLI | P19926)

molecular function
	GO:0016158	3-phytase activity	Catalysis of the reaction: myo-inositol hexakisphosphate + H2O = D-myo-inositol 1,2,4,5,6-pentakisphosphate + phosphate.
	GO:0003993	acid phosphatase activity	Catalysis of the reaction: an orthophosphoric monoester + H2O = an alcohol + phosphate, with an acid pH optimum.
	GO:0008877	glucose-1-phosphatase activity	Catalysis of the reaction: alpha-D-glucose 1-phosphate + H2O = D-glucose + phosphate.
	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:0016311	dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
	GO:0006007	glucose catabolic process	The chemical reactions and pathways resulting in the breakdown of glucose, the aldohexose gluco-hexose.
cellular component
	GO:0030288	outer membrane-bounded periplasmic space	The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
	GO:0042597	periplasmic space	The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		G1P	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1nt4)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1nt4
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	AGP_ECOLI \| P19926
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	3.1.3.10
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	AGP_ECOLI \| P19926
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 1NT4)

(no "Related Entries Specified in the PDB File" available for 1NT4)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (6, 6)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 4)

Pfam Domains (1, 2)

Gene Ontology (8, 8)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File