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(-) Description

Title :  CRYSTAL STRUCTURE OF BOVINE LACTOPEROXIDASE AT 2.3A RESOLUTION
 
Authors :  A. K. Singh, N. Singh, S. Sharma, A. Bhushan, T. P. Singh
Date :  30 Mar 06  (Deposition) - 18 Apr 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Peroxidase, Oxidoreductase, Metal-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. K. Singh, N. Singh, S. Sharma, A. Bhushan, T. P. Singh
Crystal Structure Of Bovine Lactoperoxidase At 2. 3A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - LACTOPEROXIDASE
    Chains: A
    EC Number: 1.11.1.7
    Organism Common: CATTLE
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
    Synonym: LPO

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 15)

Asymmetric/Biological Unit (7, 15)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2CO31Ligand/IonCARBONATE ION
3HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4MAN1Ligand/IonALPHA-D-MANNOSE
5NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
6NO32Ligand/IonNITRATE ION
7OSM1Ligand/Ion1-(OXIDOSULFANYL)METHANAMINE

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:81 , ILE A:299 , ARG A:488 , GLN A:553 , NAG A:582 , CO3 A:688 , HOH A:969BINDING SITE FOR RESIDUE NAG A 581
02AC2SOFTWAREHIS A:550 , GLN A:553 , NAG A:581BINDING SITE FOR RESIDUE NAG A 582
03AC3SOFTWAREASN A:189 , SER A:192 , ALA A:198 , VAL A:199 , GLN A:201 , NAG A:584 , HOH A:812 , HOH A:877BINDING SITE FOR RESIDUE NAG A 583
04AC4SOFTWAREGLN A:201 , NAG A:583BINDING SITE FOR RESIDUE NAG A 584
05AC5SOFTWAREASN A:225 , ALA A:228 , TRP A:369 , NAG A:586BINDING SITE FOR RESIDUE NAG A 585
06AC6SOFTWARENAG A:585 , MAN A:587BINDING SITE FOR RESIDUE NAG A 586
07AC7SOFTWARENAG A:586 , HOH A:785BINDING SITE FOR RESIDUE MAN A 587
08AC8SOFTWAREASN A:317 , VAL A:320 , NAG A:589BINDING SITE FOR RESIDUE NAG A 588
09AC9SOFTWARENAG A:588 , HOH A:964BINDING SITE FOR RESIDUE NAG A 589
10BC1SOFTWAREGLU A:348 , TYR A:350 , ARG A:382 , ILE A:543 , THR A:544 , LYS A:545BINDING SITE FOR RESIDUE NO3 A 590
11BC2SOFTWAREALA A:30 , ARG A:31 , TRP A:32 , LEU A:33 , SER A:325 , ASN A:326 , VAL A:327 , MET A:430 , TRP A:436 , HOH A:708BINDING SITE FOR RESIDUE NO3 A 591
12BC3SOFTWAREASN A:81 , ARG A:82 , ARG A:490 , NAG A:581 , HOH A:969BINDING SITE FOR RESIDUE CO3 A 688
13BC4SOFTWAREASP A:96 , THR A:168 , PHE A:170 , ASP A:172 , SER A:174BINDING SITE FOR RESIDUE CA A 701
14BC5SOFTWAREMET A:87 , GLY A:90 , GLN A:91 , ASP A:94 , ASP A:98 , PHE A:99 , ALA A:100 , ARG A:239 , GLU A:242 , THR A:329 , PHE A:332 , ARG A:333 , GLY A:335 , HIS A:336 , VAL A:339 , PHE A:365 , ILE A:420 , ARG A:424 , OSM A:702 , HOH A:722 , HOH A:743 , HOH A:921BINDING SITE FOR RESIDUE HEM A 605
15BC6SOFTWAREGLN A:91 , HIS A:95 , ARG A:239 , GLU A:242 , HEM A:605BINDING SITE FOR RESIDUE OSM A 702

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:1B-A:14
2A:115 -A:125
3A:119 -A:143
4A:221 -A:232
5A:440 -A:497
6A:538 -A:564

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys A:217 -Pro A:218
2Tyr A:557 -Pro A:558

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2GJ1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2GJ1)

(-) Exons   (9, 9)

Asymmetric/Biological Unit (9, 9)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSBTAT000000169861ENSBTAE00000279445chr19:8430632-8430751120PERL_BOVIN-00--
1.2ENSBTAT000000169862ENSBTAE00000137885chr19:8435757-843583478PERL_BOVIN1-26260--
1.3ENSBTAT000000169863ENSBTAE00000137889chr19:8437178-843726588PERL_BOVIN26-55300--
1.4ENSBTAT000000169864ENSBTAE00000137892chr19:8441906-8442066161PERL_BOVIN55-109550--
1.5ENSBTAT000000169865ENSBTAE00000137896chr19:8443636-8443753118PERL_BOVIN109-148401A:1-1719
1.6ENSBTAT000000169866ENSBTAE00000137903chr19:8444165-8444294130PERL_BOVIN148-191441A:17-6044
1.7ENSBTAT000000169867ENSBTAE00000137906chr19:8445032-8445238207PERL_BOVIN192-260691A:61-12969
1.8ENSBTAT000000169868ENSBTAE00000137912chr19:8446677-8447001325PERL_BOVIN261-3691091A:130-236109
1.9ENSBTAT000000169869ENSBTAE00000137915chr19:8448604-8448764161PERL_BOVIN369-422541A:236-28954
1.10ENSBTAT0000001698610ENSBTAE00000137918chr19:8457180-8457432253PERL_BOVIN423-507851A:290-375 (gaps)86
1.11ENSBTAT0000001698611ENSBTAE00000137921chr19:8458505-8458678174PERL_BOVIN507-565591A:375-43259
1.12ENSBTAT0000001698612ENSBTAE00000137923chr19:8459302-8459539238PERL_BOVIN565-644801A:432-51180
1.13ENSBTAT0000001698613ENSBTAE00000279432chr19:8459727-8460382656PERL_BOVIN644-712691A:511-580 (gaps)70

(-) 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:583
 aligned with PERL_BOVIN | P80025 from UniProtKB/Swiss-Prot  Length:712

    Alignment length:583
                                   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       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709   
          PERL_BOVIN    130 VKCDENSPYRTITGDCNNRRSPALGAANRALARWLPAEYEDGLALPFGWTQRKTRNGFRVPLAREVSNKIVGYLDEEGVLDQNRSLLFMQWGQIVDHDLDFAPETELGSNEHSKTQCEEYCIQGDNCFPIMFPKNDPKLKTQGKCMPFFRAGFVCPTPPYQSLAREQINAVTSFLDASLVYGSEPSLASRLRNLSSPLGLMAVNQEAWDHGLAYLPFNNKKPSPCEFINTTARVPCFLAGDFRASEQILLATAHTLLLREHNRLARELKKLNPHWNGEKLYQEARKILGAFIQIITFRDYLPIVLGSEMQKWIPPYQGYNNSVDPRISNVFTFAFRFGHMEVPSTVSRLDENYQPWGPEAELPLHTLFFNTWRIIKDGGIDPLVRGLLAKKSKLMNQDKMVTSELRNKLFQPTHKIHGFDLAAINLQRCRDHGMPGYNSWRGFCGLSQPKTLKGLQTVLKNKILAKKLMDLYKTPDNIDIWIGGNAEPMVERGRVGPLLACLLGRQFQQIRDGDRFWWENPGVFTEKQRDSLQKVSFSRLICDNTHITKVPLHAFQANNYPHDFVDCSTVDKLDLSPWASREN  712
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............................ee...............................hhhhhhhhhh........eeeeeehhhhhhhhhhhhhhh...........hhhhhh............ee....hhhhhhh..ee.....................ee.......hhhhhh.hhhhhhhhh..............................hhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.hhhhhh................hhhhhhhhhhhhh..eee.............eee.hhhh..hhhhhh...hhhhhhhhhhheee........hhhhhh.ee......eeehhhhhhhhhhhhh...hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh...........hhhhhhhhh..hhhhhhhhhh...ee..............ee.hhh....hhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.5           -------------------------------------------Exon 1.7  PDB: A:61-129 UniProt: 192-260                             Exon 1.8  PDB: A:130-236 UniProt: 261-369                                                                    -----------------------------------------------------Exon 1.10  PDB: A:290-375 (gaps) UniProt: 423-507                                    ---------------------------------------------------------Exon 1.12  PDB: A:432-511 UniProt: 565-644                                      -------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------Exon 1.6  PDB: A:17-60 UniProt: 148-191     ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9  PDB: A:236-289 UniProt: 369-422             ------------------------------------------------------------------------------------Exon 1.11  PDB: A:375-432 UniProt: 507-565                 ------------------------------------------------------------------------------Exon 1.13  PDB: A:511-580 (gaps) UniProt: 644-712                     Transcript 1 (2)
                2gj1 A    1 VKCDENSPYRTITGDCNNRRSPALGAANRALARWLPAEYEDGLALPFGWTQRKTRNGFRVPLAREVSNKIVGYLDEEGVLDQNRSLLFMQWGQIVDHDLDFAPETELGSNEHSKTQCEEYCIQGDNCFPIMFPKNDPKLKTQGKCMPFFRAGFVCPTPPYQSLAREQINAVTSFLDASLVYGSEPSLASRLRNLSSPLGLMAVNQEAWDHGLAYLPFNNKKPSPCEFINTTARVPCFLAGDFRASEQILLATAHTLLLREHNRLARELKKLNPHWNGEKLYQEARKILGAFIQIITFRDYLPIVLGSEMQKWIPPYQGYNNSVDPRISNVFTFAFRFGHMEVPSTVSRLDENYQPWGPEAELPLHTLFFNTWRIIKDGGIDPLVRGLLAKKSKLMNQDKMVTSELRNKLFQPTHKIHGFDLAAINLQRCRDHGMPGYNSWRGFCGLSQPKTLKGLQTVLKNKILAKKLMDLYKTPDNIDIWIGGNAEPMVERGRVGPLLACLLGRQFQQIRDGDRFWWENPGVFTEKQRDSLQKVSFSRLICDNTHITKVPLHAFQANNYPHDFVDCSTVDKLDLSPWASREN  580
                             ||      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148      156B       166       176       186       196       206       216       226       236       246       256       266       276       286       296     ||307       317       327       337       347       357       367       377       387       397       407      |416       426       436       446       456       466       476       486       496       506       516       526       536       546||     557       567       577   
                             ||                                                                                                                                                        156A|                                                                                                                                               302|                                                                                                          413A                                                                                                                                   547|                               
                            1A|                                                                                                                                                         156B                                                                                                                                                304                                                                                                                                                                                                                                                  549                               
                             1B
   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 2GJ1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2GJ1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2GJ1)

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PERL_BOVIN | P80025)
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:0001580    detection of chemical stimulus involved in sensory perception of bitter taste    The series of events required for a bitter taste stimulus to be received and converted to a molecular signal.
    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:0016323    basolateral plasma membrane    The region of the plasma membrane that includes the basal end and sides of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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_BOVIN | P80025: 2ips 2nqx 2pt3 2pum 2qpk 2qqt 2qrb 3bxi 3eri 3gc1 3gcj 3gck 3gcl 3i6n 3krq 3nyh 3ogw 3py4 3q9k 3ql6 3r4x 3r5o 3s4f 3tgy 3tuw 3uba 3v6q 4gm7 4gn6 4ksz 4njb 4nt3 4pnx 5b72 5gh0 5gls 5wv3

(-) Related Entries Specified in the PDB File

1cxp CRYOGENIC CRYSTAL STRUCTURE OF HUMAN MYELOPEROXIDASE ISOFORM C