2Y4F - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   X-RAY CRYSTALLOGRAPHIC STRUCTURE OF E. COLI HEME-EFEB

Authors :   V. A. Bamford, S. C. Andrews, K. A. Watson

Date :   05 Jan 11 (Deposition) - 26 Jan 11 (Release) - 26 Jan 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

Chains :   Asym./Biol. Unit : A,B

Keywords :   Iron Uptake, Oxidoreductase, Dyp-Peroxidase-Like, Deferrochelatase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. A. Bamford, S. C. Andrews, K. A. Watson
Efeb, The Peroxidase Component Of The Efeuob Bacterial Fe(Ii) Transport System, Also Shows Novel Removal Of Iron From Heme
To Be Published
PubMed: search

Molecule 1 - PEROXIDASE YCDB
	Chains	:	A, B
	EC Number	:	1.11.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PEHISTEV
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K-12
	Synonym	:	EFEB

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 13)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	SO4	10	Ligand/Ion	SULFATE ION

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN A:194 , LEU A:196 , LYS A:199 , ASP A:200 , GLY A:201 , THR A:202 , ALA A:203 , ILE A:240 , PHE A:242 , PHE A:259 , HIS A:294 , ILE A:295 , ASN A:299 , ARG A:301 , MET A:310 , ARG A:312 , LEU A:331 , PHE A:333 , PHE A:344 , GLN A:348 , LEU A:351 , HOH A:2076 , HOH A:2103 , HOH A:2104	BINDING SITE FOR RESIDUE HEM A 389
02	AC2	SOFTWARE	LEU A:137 , ARG A:175 , HOH A:2049 , HOH A:2050 , HOH A:2105 , GLY B:320 , VAL B:321	BINDING SITE FOR RESIDUE SO4 A 400
03	AC3	SOFTWARE	ARG A:243 , LYS A:361	BINDING SITE FOR RESIDUE SO4 A 401
04	AC4	SOFTWARE	GLN A:241 , THR A:322 , ASN A:323	BINDING SITE FOR RESIDUE SO4 A 402
05	AC5	SOFTWARE	ARG A:15 , ASN A:16 , THR A:126 , ARG A:127 , HOH A:2106	BINDING SITE FOR RESIDUE SO4 A 403
06	AC6	SOFTWARE	ARG A:172	BINDING SITE FOR RESIDUE SO4 A 404
07	AC7	SOFTWARE	LYS A:120 , HOH A:2107 , ASP B:222	BINDING SITE FOR RESIDUE SO4 A 405
08	AC8	SOFTWARE	HIS A:105 , SER A:106 , LYS A:124	BINDING SITE FOR RESIDUE SO4 A 406
09	AC9	SOFTWARE	ALA A:136 , HOH A:2109 , ASN B:323	BINDING SITE FOR RESIDUE GOL A 407
10	BC1	SOFTWARE	ASN B:194 , LYS B:199 , ASP B:200 , GLY B:201 , THR B:202 , ALA B:203 , PHE B:259 , HIS B:294 , ILE B:295 , ASN B:299 , ARG B:301 , ARG B:312 , PHE B:333 , VAL B:347 , GLN B:348 , LEU B:351 , HOH B:2090	BINDING SITE FOR RESIDUE HEM B 389
11	BC2	SOFTWARE	GLY A:320 , VAL A:321 , HOH A:2092 , LEU B:137 , ARG B:175 , HOH B:2042	BINDING SITE FOR RESIDUE SO4 B 400
12	BC3	SOFTWARE	ARG B:172 , HOH B:2091	BINDING SITE FOR RESIDUE SO4 B 401
13	BC4	SOFTWARE	ARG B:243 , LYS B:361 , HOH B:2092 , HOH B:2093	BINDING SITE FOR RESIDUE SO4 B 402

(no "SS Bond" information available for 2Y4F)

Asymmetric/Biological Unit

No.	Residues
1	Ala A:6	-	Pro A:7
2	Ala B:6	-	Pro B:7

(no "SAP(SNP)/Variant" information available for 2Y4F)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DYP_PEROXIDASE	PS51404	DyP-type peroxidase family.	EFEB_ECOLI	58-415	2	A:23-380 B:23-380

(no "Exon" information available for 2Y4F)

Asymmetric/Biological 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:384
 aligned with EFEB_ECOLI | P31545 from UniProtKB/Swiss-Prot  Length:423

    Alignment length:384
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419    
           EFEB_ECOLI    40 SAPGTLSPDARNEKQPFYGEHQAGILTPQQAAMMLVAFDVLASDKADLERLFRLLTQRFAFLTQGGAAPETPNPRLPPLDSGILGGYIAPDNLTITLSVGHSLFDERFGLAPQMPKKLQKMTRFPNDSLDAALCHGDVLLQICANTQDTVIHALRDIIKHTPDLLSVRWKREGFISDHAARSKGKETPINLLGFKDGTANPDSQNDKLMQKVVWVTADQQEPAWTIGGSYQAVRLIQFRVEFWDRTPLKEQQTIFGRDKQTGAPLGMQHEHDVPDYASDPEGKVIALDSHIRLANPRTAESESSLMLRRGYSYSLGVTNSGQLDMGLLFVCYQHDLEKGFLTVQKRLNGEALEEYVKPIGGGYFFALPGVKDANDYFGSALLRV 423
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...............................eeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhee...................ee.....eeeeeee.hhhh....hhhhh...............hhhh....eeeeeee.hhhhhhhhhhhhhhh....eeeeeeeeee.hhhhhhh......................hhhhhhhhh........hhhhh..eeeeeeeeeehhhhhhh.hhhhhhhhhh................................hhhhhhh....hhhhhh.....eeeeeee.....eeeeeeeeeee.....hhhhhhhhhh.hhhhh.eeeeeeeeeee...........hhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------DYP_PEROXIDASE  PDB: A:23-380 UniProt: 58-415                                                                                                                                                                                                                                                                                                                         -------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2y4f A   5 SAPGTLSPDARNEKQPFYGEHQAGILTPQQAAMMLVAFDVLASDKADLERLFRLLTQRFAFLTQGGAAPETPNPRLPPLDSGILGGYIAPDNLTITLSVGHSLFDERFGLAPQMPKKLQKMTRFPNDSLDAALCHGDVLLQICANTQDTVIHALRDIIKHTPDLLSVRWKREGFISDHAARSKGKETPINLLGFKDGTANPDSQNDKLMQKVVWVTADQQEPAWTIGGSYQAVRLIQFRVEFWDRTPLKEQQTIFGRDKQTGAPLGMQHEHDVPDYASDPEGKVIALDSHIRLANPRTAESESSLMLRRGYSYSLGVTNSGQLDMGLLFVCYQHDLEKGFLTVQKRLNGEALEEYVKPIGGGYFFALPGVKDANDYFGSALLRV 388
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384

Chain B from PDB  Type:PROTEIN  Length:384
 aligned with EFEB_ECOLI | P31545 from UniProtKB/Swiss-Prot  Length:423

    Alignment length:384
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419    
           EFEB_ECOLI    40 SAPGTLSPDARNEKQPFYGEHQAGILTPQQAAMMLVAFDVLASDKADLERLFRLLTQRFAFLTQGGAAPETPNPRLPPLDSGILGGYIAPDNLTITLSVGHSLFDERFGLAPQMPKKLQKMTRFPNDSLDAALCHGDVLLQICANTQDTVIHALRDIIKHTPDLLSVRWKREGFISDHAARSKGKETPINLLGFKDGTANPDSQNDKLMQKVVWVTADQQEPAWTIGGSYQAVRLIQFRVEFWDRTPLKEQQTIFGRDKQTGAPLGMQHEHDVPDYASDPEGKVIALDSHIRLANPRTAESESSLMLRRGYSYSLGVTNSGQLDMGLLFVCYQHDLEKGFLTVQKRLNGEALEEYVKPIGGGYFFALPGVKDANDYFGSALLRV 423
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...............................eeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhee...................ee.....eeeeeee.hhhh....hhhhh...............hhhh....eeeeeee.hhhhhhhhhhhhhhhh...eeeeeeeeee.hhhhhhh......................hhhhhhhhh...............eeeeeeeeeehhhhhhh.hhhhhhhhhh..................hhhhh.........hhhhhhh.....hhhhh.....eeeeeee.....eeeeeeeeeee.....hhhhhhhhhh.hhhhh.eeeeeeeeeee...........hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------DYP_PEROXIDASE  PDB: B:23-380 UniProt: 58-415                                                                                                                                                                                                                                                                                                                         -------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2y4f B   5 SAPGTLSPDARNEKQPFYGEHQAGILTPQQAAMMLVAFDVLASDKADLERLFRLLTQRFAFLTQGGAAPETPNPRLPPLDSGILGGYIAPDNLTITLSVGHSLFDERFGLAPQMPKKLQKMTRFPNDSLDAALCHGDVLLQICANTQDTVIHALRDIIKHTPDLLSVRWKREGFISDHAARSKGKETPINLLGFKDGTANPDSQNDKLMQKVVWVTADQQEPAWTIGGSYQAVRLIQFRVEFWDRTPLKEQQTIFGRDKQTGAPLGMQHEHDVPDYASDPEGKVIALDSHIRLANPRTAESESSLMLRRGYSYSLGVTNSGQLDMGLLFVCYQHDLEKGFLTVQKRLNGEALEEYVKPIGGGYFFALPGVKDANDYFGSALLRV 388
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384

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 2Y4F)

(no "CATH Domain" information available for 2Y4F)

(no "Pfam Domain" information available for 2Y4F)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (EFEB_ECOLI | P31545)

molecular function
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0016675	oxidoreductase activity, acting on a heme group of donors	Catalysis of an oxidation-reduction (redox) reaction in which a heme group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
	GO:0004601	peroxidase activity	Catalysis of the reaction: donor + hydrogen peroxide = oxidized donor + 2 H2O.
biological process
	GO:0098869	cellular oxidant detoxification	Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
	GO:0006974	cellular response to DNA damage stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
	GO:0015684	ferrous iron transport	The directed movement of ferrous iron (Fe(II) or Fe2+) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0033212	iron assimilation	A process in which iron is solubilized and transported into a cell.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
	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/Biological Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Ala A:6 - Pro A:7	[ RasMol ]
		Ala B:6 - Pro B:7	[ RasMol ]

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Access by PDB/NDB ID
	2y4f
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	EFEB_ECOLI \| P31545
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	1.11.1.-
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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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	EFEB_ECOLI \| P31545
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UniProtKB/Swiss-Prot
	EFEB_ECOLI \| P31545	:	2y4d 2y4e

2y4d	X-RAY CRYSTALLOGRAPHIC STRUCTURE OF E. COLI APO-EFEB
2y4e	X-RAY CRYSTALLOGRAPHIC STRUCTURE OF E. COLI PPIX-EFEB

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 13)

Sites (13, 13)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (11, 11)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File