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(-) Description

Title :  CRYSTAL STRUCTURE OF SHEEP LACTOPEROXIDASE AT 3.25 A RESOLUTION REVEALS THE BINDING SITES FOR FORMATE
 
Authors :  I. A. Sheikh, N. Singh, A. K. Singh, S. Sharma, T. P. Singh
Date :  02 Oct 06  (Deposition) - 17 Oct 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.25
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Peroxidase, Formate, Heme, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. A. Sheikh, N. Singh, A. K. Singh, S. Sharma, T. P. Singh
Crystal Structure Of Sheep Lactoperoxidase At 3. 25 A Resolution Reveals The Binding Sites For Formate
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - MILK LACTOPEROXIDASE
    Chains: A, B
    EC Number: 1.11.1.7
    Fragment: RESIDUES 1-595
    Organism Common: SHEEP
    Organism Scientific: OVIS ARIES
    Organism Taxid: 9940
    Synonym: PEROXIDASE, AIRWAY LACTOPEROXIDASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 28)

Asymmetric/Biological Unit (6, 28)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2CO32Ligand/IonCARBONATE ION
3FMT6Ligand/IonFORMIC ACID
4HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
5MAN2Ligand/IonALPHA-D-MANNOSE
6NAG14Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (28, 28)

Asymmetric Unit (28, 28)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:95 , ARG A:96 , ARG A:504 , NAG A:597 , CO3 A:2001BINDING SITE FOR RESIDUE NAG A 596
02AC2SOFTWAREARG A:504 , NAG A:596BINDING SITE FOR RESIDUE NAG A 597
03AC3SOFTWAREASN A:205 , SER A:208 , LEU A:210 , VAL A:215 , GLN A:217 , NAG A:599 , HOH A:3023BINDING SITE FOR RESIDUE NAG A 598
04AC4SOFTWARENAG A:598BINDING SITE FOR RESIDUE NAG A 599
05AC5SOFTWAREASN A:241 , ALA A:244 , TRP A:384 , NAG A:601 , PHE B:70 , LYS B:485BINDING SITE FOR RESIDUE NAG A 600
06AC6SOFTWARENAG A:600 , MAN A:602 , LYS B:485BINDING SITE FOR RESIDUE NAG A 601
07AC7SOFTWARENAG A:601BINDING SITE FOR RESIDUE MAN A 602
08AC8SOFTWAREASN A:332 , VAL A:335 , HOH A:3054BINDING SITE FOR RESIDUE NAG A 603
09AC9SOFTWAREASN B:95 , ARG B:504 , GLN B:568 , NAG B:597 , CO3 B:2002BINDING SITE FOR RESIDUE NAG B 596
10BC1SOFTWAREARG B:504 , HIS B:565 , GLN B:568 , NAG B:596BINDING SITE FOR RESIDUE NAG B 597
11BC2SOFTWARELEU A:206 , ASN B:205 , VAL B:215 , GLN B:217 , NAG B:599 , HOH B:3014BINDING SITE FOR RESIDUE NAG B 598
12BC3SOFTWARENAG B:598BINDING SITE FOR RESIDUE NAG B 599
13BC4SOFTWAREPHE A:70 , LYS A:485 , ASN B:241 , ALA B:244 , TRP B:384 , LYS B:388 , NAG B:601BINDING SITE FOR RESIDUE NAG B 600
14BC5SOFTWARENAG B:600 , MAN B:602BINDING SITE FOR RESIDUE NAG B 601
15BC6SOFTWAREPRO B:370 , NAG B:601BINDING SITE FOR RESIDUE MAN B 602
16BC7SOFTWAREASN B:332 , ASP B:524BINDING SITE FOR RESIDUE NAG B 603
17BC8SOFTWAREASP A:110 , THR A:184 , PHE A:186 , ASP A:188 , SER A:190BINDING SITE FOR RESIDUE CA A 1001
18BC9SOFTWAREASP B:110 , THR B:184 , PHE B:186 , ASP B:188 , SER B:190BINDING SITE FOR RESIDUE CA B 1002
19CC1SOFTWAREASN A:95 , ARG A:504 , ARG A:506 , NAG A:596BINDING SITE FOR RESIDUE CO3 A 2001
20CC2SOFTWAREASN B:95 , ARG B:96 , ARG B:504 , ARG B:506 , NAG B:596BINDING SITE FOR RESIDUE CO3 B 2002
21CC3SOFTWAREMET A:101 , GLY A:104 , GLN A:105 , ASP A:108 , ASP A:112 , 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 , ILE A:436 , ARG A:440 , FMT A:3003BINDING SITE FOR RESIDUE HEM A 605
22CC4SOFTWAREMET B:101 , GLY B:104 , GLN B:105 , ASP B:108 , ASP B:112 , PHE B:113 , ALA B:114 , GLU B:116 , ARG B:255 , GLU B:258 , THR B:344 , PHE B:347 , ARG B:348 , HIS B:351 , VAL B:354 , PHE B:380 , LEU B:417 , GLN B:423 , ARG B:440 , FMT B:3006 , HOH B:3027BINDING SITE FOR RESIDUE HEM B 605
23CC5SOFTWAREARG A:397 , ILE A:559 , THR A:560BINDING SITE FOR RESIDUE FMT A 3001
24CC6SOFTWARETRP A:46 , LEU A:47 , ASN A:341 , VAL A:342 , TRP A:452BINDING SITE FOR RESIDUE FMT A 3002
25CC7SOFTWAREHIS A:109 , ARG A:255 , HEM A:605BINDING SITE FOR RESIDUE FMT A 3003
26CC8SOFTWAREGLU B:363 , TYR B:365 , THR B:560BINDING SITE FOR RESIDUE FMT B 3004
27CC9SOFTWAREALA B:44 , ARG B:45 , TRP B:46 , LEU B:47 , SER B:340 , ASN B:341 , VAL B:342 , TRP B:452BINDING SITE FOR RESIDUE FMT B 3005
28DC1SOFTWAREGLN B:105 , HIS B:109 , ARG B:255 , HEM B:605BINDING SITE FOR RESIDUE FMT B 3006

(-) SS Bonds  (14, 14)

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
8B:6 -B:167
9B:15 -B:28
10B:129 -B:139
11B:133 -B:157
12B:237 -B:248
13B:456 -B:513
14B:554 -B:579

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Tyr A:572 -Pro A:573

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2IKC)

(-) Exons   (0, 0)

(no "Exon" information available for 2IKC)

(-) 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 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........................................................................hhhhhhhhh.........eeeeeehhhhhhhhhhhhhhh.............................ee....hhhhhhh..ee..............................hhhhhh.hhhhhhhhee......ee.....................hhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.hhhhhh................hhhhhhhhhhhh...ee..ee...ee......ee.hhhh..hhhhhh...hhhhhhhhhhheee........hhhhhh............hhhhhhhhhhhhh....hhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh...........hhhhhhhhh..hhhhhhhhh....ee..............ee.hhh....hhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ikc 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     


Chain B 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 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................................ee...............................hhhhhhhhhh........eeeeeehhhhhhhhhhhhhhh...........hhhhhhhh..........ee.....hhhhhh..ee.....................ee.......hhhhhh.hhhhhhhhee......ee.....................hhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.hhhhhh................hhhhhhhhhhhhh..eee.ee...ee.....eee.hhhh..hhhhhh...hhhhhhhhhhheee........hhhhhh............hhhhhhhhhhhhhh..hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh...........hhhhhhhhh..hhhhhhhhhh...eee............eee.hhh....hhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ikc B   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
   Legend:   → Mismatch (orange background)
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  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 2IKC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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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 Related Entries

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

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        Q9MZY2_SHEEP | Q9MZY2: 3r5q

(-) Related Entries Specified in the PDB File

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