4F9J - JenaLib

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Biological Unit 2 (Jmol Viewer)

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

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 :   2.10

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

Keywords :   Family 4 Carbohydrate Esterase, Tim Barrel, Carbohydrate/Sugar Binding, Hydrolase, Deacetylase (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 (5, 32)

No.	Name	Count	Type	Full Name
1	ACY	2	Ligand/Ion	ACETIC ACID
2	CA	2	Ligand/Ion	CALCIUM ION
3	FE	2	Ligand/Ion	FE (III) ION
4	MES	2	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
5	MSE	24	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (3, 14)

No.	Name	Count	Type	Full Name
1	ACY	1	Ligand/Ion	ACETIC ACID
2	CA	-1	Ligand/Ion	CALCIUM ION
3	FE	-1	Ligand/Ion	FE (III) ION
4	MES	1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
5	MSE	12	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (3, 14)

No.	Name	Count	Type	Full Name
1	ACY	1	Ligand/Ion	ACETIC ACID
2	CA	-1	Ligand/Ion	CALCIUM ION
3	FE	-1	Ligand/Ion	FE (III) ION
4	MES	1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
5	MSE	12	Mod. Amino Acid	SELENOMETHIONINE

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:919	BINDING SITE FOR RESIDUE FE 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 , FE 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:954 , HOH A:955	BINDING SITE FOR RESIDUE CA A 703
4	AC4	SOFTWARE	HIS A:465 , ASP A:466 , PHE A:540 , MSE A:570 , MSE A:572 , PRO A:573 , TYR A:645 , HOH A:807 , HOH A:969 , HOH A:1129 , ARG B:215 , HOH B:948	BINDING SITE FOR RESIDUE MES A 704
5	AC5	SOFTWARE	ASP B:115 , HIS B:184 , HIS B:189 , ACY B:702	BINDING SITE FOR RESIDUE FE 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 , FE 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:923 , HOH B:954	BINDING SITE FOR RESIDUE CA B 703
8	AC8	SOFTWARE	ARG A:215 , HOH A:930 , HOH A:1017 , HIS B:465 , ASP B:466 , PHE B:540 , MSE B:570 , MSE B:572 , PRO B:573 , TYR B:645 , HOH B:808 , HOH B:968 , HOH B:1127	BINDING SITE FOR RESIDUE MES B 704

(no "SS Bond" information available for 4F9J)

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 4F9J)

(no "PROSITE Motif" information available for 4F9J)

(no "Exon" information available for 4F9J)

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:599
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               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............hhhhhhhhhhhhhh.eeeeee................hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh...eeee............hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeehhhhhh..hhhhhh.hhhhhhhhh.eeeee.hhhhh..hhhhhhhhhhhhhhhhhhh.hhhhheeeeee...hhhhhhhhhhhhhhhhhhhh....eeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f9j A  43 PWPHNGFVAISWHNVEDEQRFmSVRTSALREQFAWLRENGYQPVSIAQIREAHRGGKPLPEKAVVLTFDDGYQSFYTRVFPILQAFQWPAVWAPVGSWVDTPADKQVKFGDELVDREYFATWQQVREVARSRLVELASHTWNSHYGIQANATGSLLPVYVNRAYFTDHARYETAAEYRERIRLDAVKmTEYLRTKVEVNPHVFVWPYGEANGIAIEELKKLGYDmFFTLESGLANASQLDSIPRVLIANNPSLKEFAQQIITVQEKSPQRImHIDLDYVYDENLQQmDRNIDVLIQRVKDmQISTVYLQAFADPDGDGLVKEVWFPNRLLPmKADIFSRVAWQLRTRSGVNIYAWmPVLSWDLDPTLTRVKYLPTGEKKAQIHPEQYHRLSPFDDRVRAQVGmLYEDLAGHAAFDGILFHDDALLSDYEDASAPAITAYQQAGFSGSLSEIRQNPEQFKQWARFKSRALTDFTLELSARVKAIRGPHIKTARNIFALPVIQPESEAWFAQNYADFLKSYDWTAImAmPYLEGVAEKSADQWLIQLTNQIKNIPQAKDKSILELQAQGQHQAISSQQLAHWmSLLQLNGVKNYGYYPDNF 649
                                    52       |65 |      75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265    |  275       285       295       305       315 |     325      |335       345|      355       365       375 |     385       395     | 405       415       425       435       445  |    455       465       475       485       495       505       515       525       535       545       555       565    | |575       585       595       605     ||620       630|      640         
                                            60|  |                                                                                                                                                                   233-MSE                              270-MSE                                        317-MSE        332-MSE       346-MSE                        377-MSE                 401-MSE                                        448-MSE                                                                                                                   570-MSE                                  611|           631-MSE              
                                             64  |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      572-MSE                                 617                                
                                                67-MSE

Chain B from PDB  Type:PROTEIN  Length:599
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               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......ee....ee.hhhhhhhhhhhhhhhhhhhhhhhh.....eee.hhhh.hhhhhhhhhh....eee......ee.........ee.....hhhhhhhhhhhhhh....eeeeehhhhhh..hhhhhhhhhhhhhhhhhhh...eeeee.ee.........ee............hhhhhhhhhhhhhh.eeeeee................hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh...eeee............hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeehhhhhh..hhhhhh.hhhhhhhhh.eeeee.hhhhh..hhhhhhhhhhhhhhhhhhh.hhhhheeeeee...hhhhhhhhhhhhhhhhhhhh...eeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f9j B  43 PWPHNGFVAISWHNVEDEQRFmSVRTSALREQFAWLRENGYQPVSIAQIREAHRGGKPLPEKAVVLTFDDGYQSFYTRVFPILQAFQWPAVWAPVGSWVDTPADKQVKFGDELVDREYFATWQQVREVARSRLVELASHTWNSHYGIQANATGSLLPVYVNRAYFTDHARYETAAEYRERIRLDAVKmTEYLRTKVEVNPHVFVWPYGEANGIAIEELKKLGYDmFFTLESGLANASQLDSIPRVLIANNPSLKEFAQQIITVQEKSPQRImHIDLDYVYDENLQQmDRNIDVLIQRVKDmQISTVYLQAFADPDGDGLVKEVWFPNRLLPmKADIFSRVAWQLRTRSGVNIYAWmPVLSWDLDPTLTRVKYLPTGEKKAQIHPEQYHRLSPFDDRVRAQVGmLYEDLAGHAAFDGILFHDDALLSDYEDASAPAITAYQQAGFSGSLSEIRQNPEQFKQWARFKSRALTDFTLELSARVKAIRGPHIKTARNIFALPVIQPESEAWFAQNYADFLKSYDWTAImAmPYLEGVAEKSADQWLIQLTNQIKNIPQAKDKSILELQAQGQHQAISSQQLAHWmSLLQLNGVKNYGYYPDNF 649
                                    52       |65 |      75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265    |  275       285       295       305       315 |     325      |335       345|      355       365       375 |     385       395     | 405       415       425       435       445  |    455       465       475       485       495       505       515       525       535       545       555       565    | |575       585       595       605     ||620       630|      640         
                                            60|  |                                                                                                                                                                   233-MSE                              270-MSE                                        317-MSE        332-MSE       346-MSE                        377-MSE                 401-MSE                                        448-MSE                                                                                                                   570-MSE                                  611|           631-MSE              
                                             64  |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      572-MSE                                 617                                
                                                67-MSE

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 4F9J)

(no "CATH Domain" information available for 4F9J)

(no "Pfam Domain" information available for 4F9J)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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		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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	4f9j
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	PGAB_ECOLI \| P75906	:	3vus 4f9d 4p7l 4p7n 4p7o 4p7q 4p7r

4f9d	THE SAME PROTEIN IN COMPLEX WITH NICKEL

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 32)

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)

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Gene Ontology (9, 9)

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