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(-) Description

Title :  X-RAY CRYSTALLOGRAPHIC STRUCTURE OF E. COLI APO-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 :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
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

(-) Compounds

Molecule 1 - PEROXIDASE YCDB
    Chains: A, B
    EC Number: 1.11.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-46 EK/LIC
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K-12
    Synonym: EFEB

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 23)

Asymmetric Unit (4, 23)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL6Ligand/IonGLYCEROL
3PG43Ligand/IonTETRAETHYLENE GLYCOL
4SO413Ligand/IonSULFATE ION
Biological Unit 1 (4, 23)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL6Ligand/IonGLYCEROL
3PG43Ligand/IonTETRAETHYLENE GLYCOL
4SO413Ligand/IonSULFATE ION

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:203 , ARG A:261 , ARG A:312 , HOH A:2297 , HOH A:2298BINDING SITE FOR RESIDUE SO4 A1389
02AC2SOFTWAREARG A:243 , LYS A:361 , HOH A:2299BINDING SITE FOR RESIDUE SO4 A1390
03AC3SOFTWAREARG A:175 , HOH A:2301 , HOH A:2303 , GLY B:320 , VAL B:321 , HOH B:2220BINDING SITE FOR RESIDUE SO4 A1391
04AC4SOFTWAREHIS A:105 , SER A:106 , LYS A:124 , HOH A:2304 , HOH A:2305 , HOH A:2306BINDING SITE FOR RESIDUE SO4 A1392
05AC5SOFTWAREARG A:15 , ASN A:16 , THR A:126 , ARG A:127 , HOH A:2007 , HOH A:2129 , HOH A:2307BINDING SITE FOR RESIDUE SO4 A1393
06AC6SOFTWAREGLN A:241 , THR A:322 , ASN A:323 , HOH A:2257 , HOH A:2308 , HOH A:2309 , HOH A:2310 , HOH A:2311BINDING SITE FOR RESIDUE SO4 A1394
07AC7SOFTWAREGLU A:17 , ALA A:135 , ALA A:136 , ARG A:172 , LYS A:187 , HOH A:2312 , ASN B:323BINDING SITE FOR RESIDUE PG4 A1395
08AC8SOFTWAREALA A:298 , ARG A:312 , PHE A:333 , LEU A:351 , HOH A:2263 , HOH A:2315BINDING SITE FOR RESIDUE PG4 A1396
09AC9SOFTWAREPRO A:32 , GLN A:33 , ALA A:183 , ALA A:184 , LYS A:187 , GLY A:188 , GOL A:1398 , HOH A:2316 , HOH A:2317BINDING SITE FOR RESIDUE ACT A1397
10BC1SOFTWAREGLN A:19 , THR A:31 , PRO A:32 , ALA A:184 , LYS A:187 , ACT A:1397 , HOH A:2182 , HOH A:2318BINDING SITE FOR RESIDUE GOL A1398
11BC2SOFTWAREALA A:72 , PRO A:73 , GLU A:74 , GLY A:90 , HOH A:2319 , HOH A:2320 , HOH A:2321 , GLN B:264 , HOH B:2185BINDING SITE FOR RESIDUE GOL A1399
12BC3SOFTWAREHIS A:273 , HIS A:275BINDING SITE FOR RESIDUE GOL A1400
13BC4SOFTWARELEU A:83 , HIS A:164 , HOH A:2322BINDING SITE FOR RESIDUE GOL A1401
14BC5SOFTWAREGLY B:201 , THR B:202 , ALA B:203 , ARG B:261 , ARG B:312 , HOH B:2255BINDING SITE FOR RESIDUE SO4 B1389
15BC6SOFTWAREARG B:243 , LYS B:361 , HOH B:2212BINDING SITE FOR RESIDUE SO4 B1390
16BC7SOFTWAREGLY A:320 , VAL A:321 , ARG B:175 , HOH B:2256BINDING SITE FOR RESIDUE SO4 B1391
17BC8SOFTWAREHIS B:105 , SER B:106 , LYS B:124 , HOH B:2081 , HOH B:2257 , HOH B:2258BINDING SITE FOR RESIDUE SO4 B1392
18BC9SOFTWARELYS A:375 , ARG B:172 , HOH B:2259 , HOH B:2260BINDING SITE FOR RESIDUE SO4 B1393
19CC1SOFTWAREARG B:79 , THR B:346 , ARG B:350 , HOH B:2261 , HOH B:2262 , HOH B:2263BINDING SITE FOR RESIDUE SO4 B1394
20CC2SOFTWAREARG B:62 , PRO B:73 , LEU B:83 , HIS B:164 , HOH B:2264BINDING SITE FOR RESIDUE SO4 B1395
21CC3SOFTWAREILE B:240 , HIS B:294 , MET B:310 , ARG B:312 , PHE B:333 , LEU B:351 , HOH B:2235 , HOH B:2265 , HOH B:2266BINDING SITE FOR RESIDUE PG4 B1396
22CC4SOFTWAREPHE A:246 , GLU B:285BINDING SITE FOR RESIDUE GOL B1397
23CC5SOFTWAREGLU B:17 , GLN B:19 , PRO B:32 , ALA B:184 , LYS B:187 , HOH B:2267BINDING SITE FOR RESIDUE GOL B1398

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Y4D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Y4D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Y4D)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DYP_PEROXIDASEPS51404 DyP-type peroxidase family.EFEB_ECOLI58-415
 		  2A:23-380
B:23-380
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DYP_PEROXIDASEPS51404 DyP-type peroxidase family.EFEB_ECOLI58-415
 		  2A:23-380
B:23-380

(-) Exons   (0, 0)

(no "Exon" information available for 2Y4D)

(-) Sequences/Alignments

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:372
 aligned with EFEB_ECOLI | P31545 from UniProtKB/Swiss-Prot  Length:423

    Alignment length:376
                                    57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417      
           EFEB_ECOLI    48 DARNEKQPFYGEHQAGILTPQQAAMMLVAFDVLASDKADLERLFRLLTQRFAFLTQGGAAPETPNPRLPPLDSGILGGYIAPDNLTITLSVGHSLFDERFGLAPQMPKKLQKMTRFPNDSLDAALCHGDVLLQICANTQDTVIHALRDIIKHTPDLLSVRWKREGFISDHAARSKGKETPINLLGFKDGTANPDSQNDKLMQKVVWVTADQQEPAWTIGGSYQAVRLIQFRVEFWDRTPLKEQQTIFGRDKQTGAPLGMQHEHDVPDYASDPEGKVIALDSHIRLANPRTAESESSLMLRRGYSYSLGVTNSGQLDMGLLFVCYQHDLEKGFLTVQKRLNGEALEEYVKPIGGGYFFALPGVKDANDYFGSALLRV 423
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh..................eeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhee...................ee.....eeeeeee.hhhh....hhhhh...............hhhh....eeeeeee.hhhhhhhhhhhhhhhh...eeeeeeeeee.hhhhhhh......................hhhhhhhhh........hhhhh..eeeeeeeeeehhhhhhh.hhhhhhhhhh..................hhhhh.........hhhhhhh.----..........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
                 2y4d A  13 DARNEKQPFYGEHQAGILTPQQAAMMLVAFDVLASDKADLERLFRLLTQRFAFLTQGGAAPETPNPRLPPLDSGILGGYIAPDNLTITLSVGHSLFDERFGLAPQMPKKLQKMTRFPNDSLDAALCHGDVLLQICANTQDTVIHALRDIIKHTPDLLSVRWKREGFISDHAARSKGKETPINLLGFKDGTANPDSQNDKLMQKVVWVTADQQEPAWTIGGSYQAVRLIQFRVEFWDRTPLKEQQTIFGRDKQTGAPLGMQHEHDVPDYASDPEGKVIALDSHIRLANP----SESSLMLRRGYSYSLGVTNSGQLDMGLLFVCYQHDLEKGFLTVQKRLNGEALEEYVKPIGGGYFFALPGVKDANDYFGSALLRV 388
                                    22        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       | -  |    312       322       332       342       352       362       372       382      
                                                                                                                                                                                                                                                                                                                         300  305                                                                                   


Chain B from PDB  Type:PROTEIN  Length:372
 aligned with EFEB_ECOLI | P31545 from UniProtKB/Swiss-Prot  Length:423

    Alignment length:376
                                    57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417      
           EFEB_ECOLI    48 DARNEKQPFYGEHQAGILTPQQAAMMLVAFDVLASDKADLERLFRLLTQRFAFLTQGGAAPETPNPRLPPLDSGILGGYIAPDNLTITLSVGHSLFDERFGLAPQMPKKLQKMTRFPNDSLDAALCHGDVLLQICANTQDTVIHALRDIIKHTPDLLSVRWKREGFISDHAARSKGKETPINLLGFKDGTANPDSQNDKLMQKVVWVTADQQEPAWTIGGSYQAVRLIQFRVEFWDRTPLKEQQTIFGRDKQTGAPLGMQHEHDVPDYASDPEGKVIALDSHIRLANPRTAESESSLMLRRGYSYSLGVTNSGQLDMGLLFVCYQHDLEKGFLTVQKRLNGEALEEYVKPIGGGYFFALPGVKDANDYFGSALLRV 423
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh..................eeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhee...................ee.....eeeeeee.hhhhhhhhhhhhh...............hhhh....eeeeeee.hhhhhhhhhhhhhhh....eeeeeeeeee.hhhhhhh......................hhhhhhhhh........hhhhh..eeeeeeeeeehhhhhhh.hhhhhhhhhh..................hhhhh.........hhhhhhh.----..........eeeeeee.....eeeeeeeeeee.....hhhhhhhhhh.hhhhh.eeeeeeeeeee...........hhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------DYP_PEROXIDASE  PDB: B:23-380 UniProt: 58-415                                                                                                                                                                                                                                                                                                                         -------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y4d B  13 DARNEKQPFYGEHQAGILTPQQAAMMLVAFDVLASDKADLERLFRLLTQRFAFLTQGGAAPETPNPRLPPLDSGILGGYIAPDNLTITLSVGHSLFDERFGLAPQMPKKLQKMTRFPNDSLDAALCHGDVLLQICANTQDTVIHALRDIIKHTPDLLSVRWKREGFISDHAARSKGKETPINLLGFKDGTANPDSQNDKLMQKVVWVTADQQEPAWTIGGSYQAVRLIQFRVEFWDRTPLKEQQTIFGRDKQTGAPLGMQHEHDVPDYASDPEGKVIALDSHIRLANP----SESSLMLRRGYSYSLGVTNSGQLDMGLLFVCYQHDLEKGFLTVQKRLNGEALEEYVKPIGGGYFFALPGVKDANDYFGSALLRV 388
                                    22        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       | -  |    312       322       332       342       352       362       372       382      
                                                                                                                                                                                                                                                                                                                         300  305
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2Y4D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Y4D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Y4D)

(-) Gene Ontology  (11, 11)

Asymmetric 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).

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        EFEB_ECOLI | P31545: 2y4e 2y4f

(-) Related Entries Specified in the PDB File

2y4e X-RAY CRYSTALLOGRAPHIC STRUCTURE OF E. COLI PPIX-EFEB
2y4f X-RAY CRYSTALLOGRAPHIC STRUCTURE OF E. COLI HEME-EFEB