4F9D - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF ESCHERICHIA COLI PGAB 42-655 IN COMPLEX WITH NICKEL

Authors :   D. J. Little, J. Poloczek, J. C. Whitney, H. Robinson, M. Nitz, P. L. Howe

Date :   18 May 12 (Deposition) - 25 Jul 12 (Release) - 26 Jun 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Family 4 Carbohydrate Esterase, Tim Barrel, Hydrolase, Deacetylase, Carbohydrate/Sugar Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. J. Little, J. Poloczek, J. C. Whitney, H. Robinson, M. Nitz, P. L. Howell
The Structure And Metal Dependent Activity Of Escherichia Coli Pgab Provides Insight Into The Partial De-N-Acetylatio Of Poly-B-1, 6-N-Acetyl-D-Glucosamine
J. Biol. Chem. V. 287 31126 2012
PubMed-ID: 22810235 | Reference-DOI: 10.1074/JBC.M112.390005

Molecule 1 - POLY-BETA-1,6-N-ACETYL-D-GLUCOSAMINE N-DEACETYLASE
	Chains	:	A, B
	EC Number	:	3.5.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 42-655
	Gene	:	PGAB, YCDR, B1023, JW5142
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12
	Synonym	:	PGA N-DEACETYLASE, POLY-BETA-1,6-GLCNAC N-DEACETYLASE

		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 (4, 8)

No.	Name	Count	Type	Full Name
1	ACY	2	Ligand/Ion	ACETIC ACID
2	CA	2	Ligand/Ion	CALCIUM ION
3	MES	2	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4	NI	2	Ligand/Ion	NICKEL (II) ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	ACY	1	Ligand/Ion	ACETIC ACID
2	CA	-1	Ligand/Ion	CALCIUM ION
3	MES	1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4	NI	-1	Ligand/Ion	NICKEL (II) ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	ACY	1	Ligand/Ion	ACETIC ACID
2	CA	-1	Ligand/Ion	CALCIUM ION
3	MES	1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4	NI	-1	Ligand/Ion	NICKEL (II) ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:115 , HIS A:184 , HIS A:189 , ACY A:702 , HOH A:1139	BINDING SITE FOR RESIDUE NI A 701
2	AC2	SOFTWARE	HIS A:55 , ASP A:114 , ASP A:115 , HIS A:184 , HIS A:189 , PRO A:251 , TYR A:252 , LEU A:274 , NI A:701	BINDING SITE FOR RESIDUE ACY A 702
3	AC3	SOFTWARE	ASP A:358 , ASP A:360 , ASP A:362 , LEU A:364 , HOH A:1140 , HOH A:1141	BINDING SITE FOR RESIDUE CA A 703
4	AC4	SOFTWARE	HIS A:465 , ASP A:466 , PHE A:540 , MET A:570 , PRO A:573 , TYR A:645 , HOH A:807 , HOH A:958 , HOH A:961 , ARG B:215 , HOH B:1078	BINDING SITE FOR RESIDUE MES A 704
5	AC5	SOFTWARE	ASP B:115 , HIS B:184 , HIS B:189 , ACY B:702 , HOH B:1081	BINDING SITE FOR RESIDUE NI B 701
6	AC6	SOFTWARE	HIS B:55 , ASP B:114 , ASP B:115 , HIS B:184 , HIS B:189 , PRO B:251 , TYR B:252 , LEU B:274 , NI B:701	BINDING SITE FOR RESIDUE ACY B 702
7	AC7	SOFTWARE	ASP B:358 , ASP B:360 , ASP B:362 , LEU B:364 , HOH B:1083 , HOH B:1085	BINDING SITE FOR RESIDUE CA B 703
8	AC8	SOFTWARE	ARG A:215 , HOH A:928 , HIS B:465 , ASP B:466 , PHE B:540 , MET B:570 , MET B:572 , PRO B:573 , TYR B:645 , HOH B:808 , HOH B:942 , HOH B:1018	BINDING SITE FOR RESIDUE MES B 704

(no "SS Bond" information available for 4F9D)

Asymmetric Unit

No.	Residues
1	Glu A:474	-	Asp A:475
2	Glu B:474	-	Asp B:475

(no "SAP(SNP)/Variant" information available for 4F9D)

(no "PROSITE Motif" information available for 4F9D)

(no "Exon" information available for 4F9D)

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:592
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee.eee........eeehhhhhhhhhhhhhh..ee.hhhhhhhhhh........eeeeeeee.hhhhhhhhhhhhhhhh..eeeeehhhhhh......eee..eeehhhhh.hhhhhhhhhhhh.eee.........eee......eee.hhh..ee....ee.hhhhhhhhhhhhhhhhhhhhhhhhh....eee.hhhh.hhhhhhhhhhh...eee......ee.........ee.....hhhhhhhhhhh.......eeeeehhhhhh..hhhhhhhhhhhhhhhhhhh...eeeee.ee.........ee............hhhhhhhhhhhhhh.eeeeee................hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh...eeee............hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeehhhhhhhhhhhhh..hhhhhhhhh.eeeee.hhhhh..hhhhhhhhhhhhhhhhhh..hhhhheeeee..hhhhhhhhhhhhhhh....eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f9d A  43 PWPHNGFVAISWHNVEDEADQRFMSVRTSALREQFAWLRENGYQPVSIAQIREAHRGGKPLPEKAVVLTFDDGYQSFYTRVFPILQAFQWPAVWAPVGSWVDTPADKQVKFGDELVDREYFATWQQVREVARSRLVELASHTWNSHYGIQANATGSLLPVYVNRAYFTDHARYETAAEYRERIRLDAVKMTEYLRTKVEVNPHVFVWPYGEANGIAIEELKKLGYDMFFTLESGLANASQLDSIPRVLIANNPSLKEFAQQIITVQEKSPQRIMHIDLDYVYDENLQQMDRNIDVLIQRVKDMQISTVYLQAFADPDGDGLVKEVWFPNRLLPMKADIFSRVAWQLRTRSGVNIYAWMPVLSWDLDPTLTRVKYLPTGEKKAQIHPEQYHRLSPFDDRVRAQVGMLYEDLAGHAAFDGILFHDDALLSDYEDASAPAITAYQQAGFSGSLSEIRQNPEQFKQWARFKSRALTDFTLELSARVKAIRGPHIKTARNIFALPVIQPESEAWFAQNYADFLKSYDWTAIMAMPYLEGVAEKSADQWLIQLTNQIKNIPQAKDKSILELQAISSQQLAHWMSLLQLNGVKNYGYYP 646
                                    52        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603     ||624       634       644  
                                             61|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               609|                         
                                              63                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                621

Chain B from PDB  Type:PROTEIN  Length:592
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee.eee........eeehhhhhhhhhhhhhh..ee.hhhhhhhhhh........eeeeeeee.hhhhhhhhhhhhhhhh..eeeeehhhhhh......eee..eeehhhhh.hhhhhhhhhhh..eee.........eee......eee.hhh..ee....ee.hhhhhhhhhhhhhhhhhhhhhhhh.....eee.hhhh.hhhhhhhhhhh...eee......ee.........ee.....hhhhhhhhhhh.......eeeeehhhhhh..hhhhhhhhhhhhhhhhhhh...eeeee.ee.........ee............hhhhhhhhhhhhh..eeeeee................hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh...eeee............hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeehhhhhhhhhhhhh..hhhhhhhhh.eeeee.hhhhh..hhhhhhhhhhhhhhhhhh..hhhhheeeee..hhhhhhhhhhhhhhh....eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f9d B  43 PWPHNGFVAISWHNVEDEADQRFMSVRTSALREQFAWLRENGYQPVSIAQIREAHRGGKPLPEKAVVLTFDDGYQSFYTRVFPILQAFQWPAVWAPVGSWVDTPADKQVKFGDELVDREYFATWQQVREVARSRLVELASHTWNSHYGIQANATGSLLPVYVNRAYFTDHARYETAAEYRERIRLDAVKMTEYLRTKVEVNPHVFVWPYGEANGIAIEELKKLGYDMFFTLESGLANASQLDSIPRVLIANNPSLKEFAQQIITVQEKSPQRIMHIDLDYVYDENLQQMDRNIDVLIQRVKDMQISTVYLQAFADPDGDGLVKEVWFPNRLLPMKADIFSRVAWQLRTRSGVNIYAWMPVLSWDLDPTLTRVKYLPTGEKKAQIHPEQYHRLSPFDDRVRAQVGMLYEDLAGHAAFDGILFHDDALLSDYEDASAPAITAYQQAGFSGSLSEIRQNPEQFKQWARFKSRALTDFTLELSARVKAIRGPHIKTARNIFALPVIQPESEAWFAQNYADFLKSYDWTAIMAMPYLEGVAEKSADQWLIQLTNQIKNIPQAKDKSILELQAISSQQLAHWMSLLQLNGVKNYGYYP 646
                                    52        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603     ||624       634       644  
                                             61|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               609|                         
                                              63                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                621

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 4F9D)

(no "CATH Domain" information available for 4F9D)

(no "Pfam Domain" information available for 4F9D)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
		ACY	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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		NI	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
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		AC2	[ RasMol ]	+environment [ RasMol ]
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		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Glu A:474 - Asp A:475	[ RasMol ]
		Glu B:474 - Asp B:475	[ RasMol ]

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

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Access by PDB/NDB ID
	4f9d
		Family and Domain Information	:	ProDom \| SYSTERS
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	PGAB_ECOLI \| P75906
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	3.5.1.-
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		Interatomic Contacts of Structural Units	:	CSU
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	PGAB_ECOLI \| P75906	:	3vus 4f9j 4p7l 4p7n 4p7o 4p7q 4p7r

4f9j	THE SAME PROTEIN IN COMPLEX WITH IRON

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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Gene Ontology (9, 9)

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