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(-) Description

Title :  FIRST STRUCTURAL EVIDENCE OF SUBSTRATE SPECIFICITY IN MAMMALIAN PEROXIDASES: CRYSTAL STRUCTURES OF SUBSTRATE COMPLEXES WITH LACTOPEROXIDASES FROM TWO DIFFERENT SPECIES
 
Authors :  I. A. Sheikh, N. Singh, A. K. Singh, M. Sinha, S. B. Singh, A. Bhushan, P. K A. Srinivasan, S. Sharma, T. P. Singh
Date :  02 Oct 08  (Deposition) - 31 Mar 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Peroxidase, Complex, Heme, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. A. Sheikh, A. K. Singh, N. Singh, M. Sinha, S. B. Singh, A. Bhushan, P. Kaur, A. Srinivasan, S. Sharma, T. P. Singh
Structural Evidence Of Substrate Specificity In Mammalian Peroxidases: Structure Of The Thiocyanate Complex With Lactoperoxidase And Its Interactions At 2. 4 A Resolution
J. Biol. Chem. V. 284 14849 2009
PubMed-ID: 19339248  |  Reference-DOI: 10.1074/JBC.M807644200

(-) Compounds

Molecule 1 - LACTOPEROXIDASE
    Chains: A
    EC Number: 1.11.1.7
    Fragment: UNP RESIDUES 118-712
    Organism Common: DOMESTIC WATER BUFFALO
    Organism Scientific: BUBALUS BUBALIS
    Organism Taxid: 89462

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 23)

Asymmetric/Biological Unit (8, 23)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2CA1Ligand/IonCALCIUM ION
3HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4IOD7Ligand/IonIODIDE ION
5MAN2Ligand/IonALPHA-D-MANNOSE
6NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
7SCN2Ligand/IonTHIOCYANATE ION
8SEP1Mod. Amino AcidPHOSPHOSERINE

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREMET A:101 , GLY A:104 , GLN A:105 , ASP A:108 , ASP A:112 , PHE A:113 , ALA A:114 , ARG A:255 , GLU A:258 , GLN A:259 , THR A:344 , PHE A:347 , ARG A:348 , GLY A:350 , HIS A:351 , ILE A:436 , ARG A:440 , SCN A:608 , HOH A:628 , HOH A:635 , HOH A:781 , HOH A:867BINDING SITE FOR RESIDUE HEM A 605
02AC2SOFTWAREARG A:202 , LYS A:474BINDING SITE FOR RESIDUE SCN A 607
03AC3SOFTWAREGLU A:258 , HEM A:605 , HOH A:636BINDING SITE FOR RESIDUE SCN A 608
04AC4SOFTWAREASP A:110 , THR A:184 , PHE A:186 , ASP A:188 , SER A:190BINDING SITE FOR RESIDUE CA A 609
05AC5SOFTWAREASN A:80BINDING SITE FOR RESIDUE IOD A 610
06AC6SOFTWAREARG A:96 , ARG A:504BINDING SITE FOR RESIDUE IOD A 611
07AC7SOFTWAREPHE A:229BINDING SITE FOR RESIDUE IOD A 612
08AC8SOFTWARETRP A:530BINDING SITE FOR RESIDUE IOD A 613
09AC9SOFTWAREGLU A:363 , ARG A:397BINDING SITE FOR RESIDUE IOD A 614
10BC1SOFTWARETRP A:46 , VAL A:342BINDING SITE FOR RESIDUE IOD A 615
11BC2SOFTWARELYS A:462 , THR A:463BINDING SITE FOR RESIDUE IOD A 616
12BC3SOFTWAREASN A:95 , ILE A:315 , ARG A:504 , GLN A:568 , NAG A:618BINDING SITE FOR RESIDUE NAG A 617
13BC4SOFTWAREHIS A:565 , GLN A:568 , NAG A:617 , HOH A:803BINDING SITE FOR RESIDUE NAG A 618
14BC5SOFTWAREASN A:205 , SER A:208 , LEU A:210 , ALA A:214 , VAL A:215 , GLN A:217 , NAG A:620 , HOH A:766 , HOH A:920BINDING SITE FOR RESIDUE NAG A 619
15BC6SOFTWARENAG A:619 , HOH A:808 , HOH A:811 , HOH A:829BINDING SITE FOR RESIDUE NAG A 620
16BC7SOFTWAREASN A:241 , ALA A:244 , TRP A:384 , NAG A:622BINDING SITE FOR RESIDUE NAG A 621
17BC8SOFTWARENAG A:621 , MAN A:623 , HOH A:840 , HOH A:890 , HOH A:902 , HOH A:949BINDING SITE FOR RESIDUE NAG A 622
18BC9SOFTWARENAG A:622 , HOH A:868 , HOH A:902 , HOH A:910BINDING SITE FOR RESIDUE MAN A 623
19CC1SOFTWAREASN A:332 , NAG A:625 , HOH A:986BINDING SITE FOR RESIDUE NAG A 624
20CC2SOFTWARENAG A:624 , BMA A:626 , HOH A:703 , HOH A:806 , HOH A:943BINDING SITE FOR RESIDUE NAG A 625
21CC3SOFTWARENAG A:625 , MAN A:627 , HOH A:699BINDING SITE FOR RESIDUE BMA A 626
22CC4SOFTWAREBMA A:626 , HOH A:942 , HOH A:1001BINDING SITE FOR RESIDUE MAN A 627

(-) SS Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1A:6 -A:167
2A:15 -A:28
3A:129 -A:139
4A:133 -A:157
5A:237 -A:248
6A:456 -A:513
7A:554 -A:579

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys A:233 -Pro A:234
2Tyr A:572 -Pro A:573

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ERH)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEROXIDASE_3PS50292 Animal heme peroxidase superfamily profile.PERL_BUBBU129-711  1A:12-594

(-) Exons   (0, 0)

(no "Exon" information available for 3ERH)

(-) Sequences/Alignments

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:595
 aligned with PERL_BUBBU | A5JUY8 from UniProtKB/Swiss-Prot  Length:712

    Alignment length:595
                                   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       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707     
           PERL_BUBBU   118 SWEVGCGAPVPLVKCDENSPYRTITGDCNNRRSPALGAANRALARWLPAEYEDGLALPFGWTQRKTRNGFRVPLAREVSNKIVGYLDEEGVLDQNRSLLFMQWGQIVDHDLDFAPETELGSNEHSKTQCEEYCIQGDNCFPIMFPKNDPKLKTQGKCMPFFRAGFVCPTPPYQSLAREQINAVTSFLDASLVYGSEPSLASRLRNLSSPLGLMAVNQEAWDHGLAYLPFNNKKPSPCEFINTTARVPCFLAGDFRASEQILLATAHTLLLREHNRLARELKKLNPHWNGEKLYQEARKILGAFIQIITFRDYLPIVLGSEMQKWIPPYQGYNNSVDPRISNVFTFAFRFGHMEVPSTVSRLDENYQPWGPEAELPLHTLFFNTWRIIKDGGIDPLTRGLLAKKSKLMNQDKMVTSELRNKLFQPTHKIHGFDLAAINLQRCRDHGMPGYNSWRGFCGLSQPKTLKGLQTVLKNKILAKKLMDLYKTPDNIDIWIGGNAEPMVERGRVGPLLACLLGRQFQQIRDGDRFWWENPGVFTEKQRDSLQKFSFSRLICDNTHITKVPLHAFQANNYPHDFVDCSTVDKLDLSPWASREN 712
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................................ee...............................hhhhhhhhh.........eeeeeehhhhhhhhhhhhhhh...........hhhhhh............ee....hhhhhhh..ee.....................ee.......hhhhhh.hhhhhhhhh..............................hhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.hhhhhh................hhhhhhhhhhhhh..eee.............eee.hhhh..hhhhhh...hhhhhhhhhhheee........hhhhhh.ee......eeehhhhhhhhhhhhh...hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh...........hhhhhhhhh..hhhhhhhhhh...ee..............ee.hhh....hhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------PEROXIDASE_3  PDB: A:12-594 UniProt: 129-711                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           - PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3erh A   1 SWEVGCGAPVPLVKCDENSPYRTITGDCNNRRSPALGAANRALARWLPAEYEDGLALPFGWTQRKTRNGFRVPLAREVSNKIVGYLDEEGVLDQNRSLLFMQWGQIVDHDLDFAPETELGSNEHSKTQCEEYCIQGDNCFPIMFPKNDPKLKTQGKCMPFFRAGFVCPTPPYQSLAREQINAVTSFLDASLVYGSEPsLASRLRNLSSPLGLMAVNQEAWDHGLAYLPFNNKKPSPCEFINTTARVPCFLAGDFRASEQILLATAHTLLLREHNRLARELKKLNPHWNGEKLYQEARKILGAFIQIITFRDYLPIVLGSEMQKWIPPYQGYNNSVDPRISNVFTFAFRFGHMEVPSTVSRLDENYQPWGPEAELPLHTLFFNTWRIIKDGGIDPLTRGLLAKKSKLMNQDKMVTSELRNKLFQPTHKIHGFDLAAINLQRCRDHGMPGYNSWRGFCGLSQPKTLKGLQTVLKNKILAKKLMDLYKTPDNIDIWIGGNAEPMVERGRVGPLLACLLGRQFQQIRDGDRFWWENPGVFTEKQRDSLQKFSFSRLICDNTHITKVPLHAFQANNYPHDFVDCSTVDKLDLSPWASREN 595
                                    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       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590     
                                                                                                                                                                                                                               198-SEP
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 3ERH)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ERH)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ERH)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PERL_BUBBU | A5JUY8)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    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:0004601    peroxidase activity    Catalysis of the reaction: donor + hydrogen peroxide = oxidized donor + 2 H2O.
    GO:0036393    thiocyanate peroxidase activity    Catalysis of the reaction: thiocyanate (SCN-) + hydrogen peroxide (H2O2) = hypothiocyanite (OSCN-) + 2 H2O. Catalyzes the hydrogen peroxide oxidation of thiocyanate.
biological process
    GO:0019731    antibacterial humoral response    An immune response against bacteria mediated through a body fluid. Examples of this process are the antibacterial humoral responses in Mus musculus and Drosophila melanogaster.
    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:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    GO:0042744    hydrogen peroxide catabolic process    The chemical reactions and pathways resulting in the breakdown of hydrogen peroxide (H2O2).
    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.
    GO:0006979    response to oxidative stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
    GO:0018969    thiocyanate metabolic process    The chemical reactions and pathways involving thiocyanate, the anion of thiocyanic acid, a toxic cyanide derivative commonly formed as a by-product in the production of gas for fuel, coke, and substances for chemical industries.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PERL_BUBBU | A5JUY8: 2gjm 2o86 2z5z 3faq 3fnl 4y55

(-) Related Entries Specified in the PDB File

2r5l CRYSTAL STRUCTURE OF LACTOPEROXIDASE AT 2.4A RESOLUTION
3bxi STRUCTURE OF THE COMPLEX OF BOVINE LACTOPEROXIDASE WITH ITS CATALYZED PRODUCT HYPOTHIOCYANATE ION AT 2.3A RESOLUTION
3eri CRYSTAL STRUCTURES OF SUBSTRATE COMPLEXES WITH LACTOPEROXIDASES FROM TWO DIFFERENT SPECIES