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(-) Description

Title :  CRYSTAL STRUCTURE OF SHEEP LACTOPEROXIDASE IN COMPLEX WITH TETRAHYDROFURAN AT 2.7 A RESOLUTION
 
Authors :  S. Yamini, R. P. Singh, A. K. Singh, M. Sinha, P. Kaur, S. Sharma, T. P. Sin
Date :  19 Mar 11  (Deposition) - 06 Apr 11  (Release) - 29 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Lactoperoxidase, Sheep, Tetrahydrofuran, Heme Moiety, Distal Binding Site, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Yamini, R. P. Singh, A. K. Singh, M. Sinha, P. Kaur, S. Sharma, T. P. Singh
Crystal Structure Of Sheep Lactoperoxidase In Complex With Tetrahydrofuran At 2. 7 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - AIRWAY LACTOPEROXIDASE
    Chains: A
    EC Number: 1.11.1.7
    Fragment: UNP RESIDUES 118-712
    Organism Common: DOMESTIC SHEEP,LAMBS,WILD SHEEP
    Organism Scientific: OVIS ARIES
    Organism Taxid: 9940

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 19)

Asymmetric/Biological Unit (8, 19)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3FU12Ligand/IonTETRAHYDROFURAN
4HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
5IOD10Ligand/IonIODIDE ION
6NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
7SCN1Ligand/IonTHIOCYANATE ION
8SEP1Mod. Amino AcidPHOSPHOSERINE

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:205 , SER A:208 , ALA A:214 , VAL A:215 , GLN A:217BINDING SITE FOR RESIDUE NAG A 598
02AC2SOFTWAREASN A:241 , ALA A:244 , TRP A:384 , LYS A:388BINDING SITE FOR RESIDUE NAG A 602
03AC3SOFTWAREASP A:110 , THR A:184 , PHE A:186 , ASP A:188 , SER A:190BINDING SITE FOR RESIDUE CA A 1001
04AC4SOFTWAREMET A:101 , GLY A:104 , GLN A:105 , ASP A:108 , ASP A:112 , PHE A:113 , ALA A:114 , GLU A:258 , THR A:344 , PHE A:347 , ARG A:348 , GLY A:350 , HIS A:351 , VAL A:354 , PHE A:380 , LEU A:417 , LEU A:433 , ILE A:436 , ARG A:440 , FU1 A:596BINDING SITE FOR RESIDUE HEM A 605
05AC5SOFTWARETRP A:46 , VAL A:342 , TRP A:452BINDING SITE FOR RESIDUE IOD A 707
06AC6SOFTWAREASN A:80 , PRO A:145BINDING SITE FOR RESIDUE IOD A 708
07AC7SOFTWAREGLU A:363 , ARG A:397 , THR A:560 , LYS A:561BINDING SITE FOR RESIDUE IOD A 711
08AC8SOFTWAREHIS A:565 , ALA A:566 , PHE A:567BINDING SITE FOR RESIDUE IOD A 712
09AC9SOFTWARESER A:359BINDING SITE FOR RESIDUE IOD A 713
10BC1SOFTWARELYS A:462 , THR A:463BINDING SITE FOR RESIDUE IOD A 715
11BC2SOFTWAREGLN A:217BINDING SITE FOR RESIDUE IOD A 718
12BC3SOFTWAREPRO A:424BINDING SITE FOR RESIDUE IOD A 719
13BC4SOFTWAREHIS A:377 , HIS A:429BINDING SITE FOR RESIDUE IOD A 720
14BC5SOFTWAREARG A:96 , ARG A:504 , ARG A:506BINDING SITE FOR RESIDUE EDO A 722
15BC6SOFTWAREASN A:230 , SER A:235 , CYS A:248BINDING SITE FOR RESIDUE SCN A 615
16BC7SOFTWAREGLN A:105 , HIS A:109 , ARG A:255 , GLU A:258 , FU1 A:597 , HEM A:605BINDING SITE FOR RESIDUE FU1 A 596
17BC8SOFTWARESER A:254 , ARG A:255 , GLU A:258 , PHE A:381 , PRO A:424 , FU1 A:596BINDING SITE FOR RESIDUE FU1 A 597

(-) 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  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Cys A:6 -Gly A:7
2Ser A:121 -Ser A:122
3Lys A:233 -Pro A:234
4Tyr A:572 -Pro A:573
5Ile A:582 -Asp A:583

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3R5Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3R5Q)

(-) Exons   (0, 0)

(no "Exon" information available for 3R5Q)

(-) 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 Q9MZY2_SHEEP | Q9MZY2 from UniProtKB/TrEMBL  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     
         Q9MZY2_SHEEP   118 SWEVGCGAPVPLVKCDENSPYRTITGDCNNRRSPALGAANRALARWLPAEYEDGLAVPFGWTQRKTRNGFRVPLAREVSNKIVGYLDEEGVLDQNRSLLFMQWGQIVDHDLDFAPETELGSSEHSKVQCEEYCIQGDNCFPIMFPKNDPKLKTQGKCMPFFRAGFVCPTPPYQSLARDQINSVTSFLDASLVYGSEPSLASRLRNLSSPLGLMAVNQEAWDHGLAYPPFNNMKPSPCEFINTTARVPCFQAGDSRASEQILLATVHTLLLREHNRLARELKRLNPHWDGEKLYQEARKILGAFIQIITFRDYLPIVLGSEMQKWIPRYQGYNNSVDPRISNVFTFAFRFGHMEVPSTVSRLDENYQPRGPEAELPLHTLFFNTWRIIKDGGIDPLVRGLLAKKSKLMNQNKMVTSELRNKLFQPTHKIHGFDLAAINLQRCRDHGMPGYNSWRGFCGLSQPKTLKGLQAVLKNKILAKKLLDLYKTPDNIDIWIGGNAEPMVERGRVGPLLACLLGRQFQQIRDGDRFWWENPGVFTEKQRDSLQKVSFSRLICDNTHITKVPLHAFQANNYPHDFVDCSAIDKLDLSPWASREN 712
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------An_peroxidase-3r5qA01 A:21-567                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     ---------------------------- Pfam domains
         Sec.struct. author ........................................ee...............................hhhhhhhhhh........eeeeeehhhhhhhhhhhhhhh...........hhhhhhhhhh........ee....hhhhhhhh.ee.....................ee.......hhhhhh.hhhhhhhhee......ee.....................hhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhh...eee.............eee.hhhh..hhhhhh...hhhhhhhhhhheee........hhhhhh............hhhhhhhhhhhhh...hhhhhhhhh......hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.............hhhhhhh..hhhhhhhhhh...ee..............ee.hhh....hhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r5q A   1 SWEVGCGAPVPLVKCDENSPYRTITGDCNNRRSPALGAANRALARWLPAEYEDGLAVPFGWTQRKTRNGFRVPLAREVSNKIVGYLDEEGVLDQNRSLLFMQWGQIVDHDLDFAPETELGSSEHSKVQCEEYCIQGDNCFPIMFPKNDPKLKTQGKCMPFFRAGFVCPTPPYQSLARDQINSVTSFLDASLVYGSEPsLASRLRNLSSPLGLMAVNQEAWDHGLAYPPFNNMKPSPCEFINTTARVPCFQAGDSRASEQILLATVHTLLLREHNRLARELKRLNPHWDGEKLYQEARKILGAFIQIITFRDYLPIVLGSEMQKWIPRYQGYNNSVDPRISNVFTFAFRFGHMEVPSTVSRLDENYQPRGPEAELPLHTLFFNTWRIIKDGGIDPLVRGLLAKKSKLMNQNKMVTSELRNKLFQPTHKIHGFDLAAINLQRCRDHGMPGYNSWRGFCGLSQPKTLKGLQAVLKNKILAKKLLDLYKTPDNIDIWIGGNAEPMVERGRVGPLLACLLGRQFQQIRDGDRFWWENPGVFTEKQRDSLQKVSFSRLICDNTHITKVPLHAFQANNYPHDFVDCSAIDKLDLSPWASREN 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)
    → 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 3R5Q)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3R5Q)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: An_peroxidase] (45)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9MZY2_SHEEP | Q9MZY2)
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: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: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: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.

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        Q9MZY2_SHEEP | Q9MZY2: 2ikc

(-) Related Entries Specified in the PDB File

2ikc 3r4x 3r55 3r5o