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(-) Description

Title :  CRYSTAL STRUCTURE OF BUFFALO LACTOPEROXIDASE AT 2.75A RESOLUTION
 
Authors :  I. A. Sheikh, A. S. Ethayathulla, A. K. Singh, N. Singh, S. Sharma, T. P. S
Date :  31 Mar 06  (Deposition) - 02 May 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
Chains :  Asym./Biol. Unit :  A
Keywords :  Lactoperoxidase, Buffalo, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. A. Sheikh, A. S. Ethayathulla, A. K. Singh, N. Singh, S. Sharma, T. P. Singh
Crystal Structure Of Buffalo Lactoperoxidase At 2. 75A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - LACTOPEROXIDASE
    Chains: A
    EC Number: 1.11.1.7
    Organism Common: WATER BUFFALO
    Organism Scientific: BUBALUS BUBALIS
    Organism Taxid: 89462
    Secretion: MILK

 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
3CO31Ligand/IonCARBONATE ION
4HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
5IOD8Ligand/IonIODIDE ION
6MAN2Ligand/IonALPHA-D-MANNOSE
7NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
8SCN1Ligand/IonTHIOCYANATE ION

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:81 , PRO A:193 , ILE A:299 , ARG A:488 , NAG A:582 , CO3 A:1001BINDING SITE FOR RESIDUE NAG A 581
02AC2SOFTWAREHIS A:550 , NAG A:581BINDING SITE FOR RESIDUE NAG A 582
03AC3SOFTWAREASN A:189 , SER A:192 , LEU A:194 , ALA A:198 , VAL A:199 , GLN A:201 , NAG A:584BINDING 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 , LYS A:373 , NAG A:586BINDING SITE FOR RESIDUE NAG A 585
06AC7SOFTWARENAG A:585 , MAN A:587BINDING SITE FOR RESIDUE NAG A 586
07AD1SOFTWARENAG A:586BINDING SITE FOR RESIDUE MAN A 587
08AD2SOFTWAREASN A:317 , NAG A:589BINDING SITE FOR RESIDUE NAG A 588
09AD3SOFTWARENAG A:588 , BMA A:590BINDING SITE FOR RESIDUE NAG A 589
10BC1SOFTWARENAG A:589 , MAN A:591BINDING SITE FOR RESIDUE BMA A 590
11BC2SOFTWAREBMA A:590BINDING SITE FOR RESIDUE MAN A 591
12BC3SOFTWAREGLU A:242 , HEM A:605 , HOH A:2184BINDING SITE FOR RESIDUE SCN A 1502
13BC4SOFTWAREASN A:81 , ARG A:82 , ARG A:488 , ARG A:490 , NAG A:581BINDING SITE FOR RESIDUE CO3 A 1001
14BC5SOFTWAREASP A:96 , THR A:168 , PHE A:170 , ASP A:172 , SER A:174BINDING SITE FOR RESIDUE CA A 1503
15BC6SOFTWAREASN A:66BINDING SITE FOR RESIDUE IOD A 2001
16BC7SOFTWARESER A:182 , GLN A:452BINDING SITE FOR RESIDUE IOD A 2002
17BC8SOFTWAREARG A:186 , HOH A:2138BINDING SITE FOR RESIDUE IOD A 2003
18BC9SOFTWAREASN A:200 , PHE A:213BINDING SITE FOR RESIDUE IOD A 2004
19CC1SOFTWARETRP A:514 , HOH A:2191BINDING SITE FOR RESIDUE IOD A 2005
20CC2SOFTWAREARG A:382 , ILE A:543 , THR A:544BINDING SITE FOR RESIDUE IOD A 2006
21CC3SOFTWARETRP A:32 , VAL A:327 , TRP A:436BINDING SITE FOR RESIDUE IOD A 2007
22CC4SOFTWARELYS A:446 , THR A:447BINDING SITE FOR RESIDUE IOD A 2008
23CC5SOFTWAREMET 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 , GLN A:243 , THR A:329 , PHE A:332 , ARG A:333 , GLY A:335 , HIS A:336 , ILE A:420 , ARG A:424 , SCN A:1502 , HOH A:2042 , HOH A:2080 , HOH A:2088BINDING SITE FOR RESIDUE HEM A 605

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:1 -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 2GJM)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2GJM)

(-) 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_BUBBU | A5JUY8 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_BUBBU    130 VKCDENSPYRTITGDCNNRRSPALGAANRALARWLPAEYEDGLALPFGWTQRKTRNGFRVPLAREVSNKIVGYLDEEGVLDQNRSLLFMQWGQIVDHDLDFAPETELGSNEHSKTQCEEYCIQGDNCFPIMFPKNDPKLKTQGKCMPFFRAGFVCPTPPYQSLAREQINAVTSFLDASLVYGSEPSLASRLRNLSSPLGLMAVNQEAWDHGLAYLPFNNKKPSPCEFINTTARVPCFLAGDFRASEQILLATAHTLLLREHNRLARELKKLNPHWNGEKLYQEARKILGAFIQIITFRDYLPIVLGSEMQKWIPPYQGYNNSVDPRISNVFTFAFRFGHMEVPSTVSRLDENYQPWGPEAELPLHTLFFNTWRIIKDGGIDPLTRGLLAKKSKLMNQDKMVTSELRNKLFQPTHKIHGFDLAAINLQRCRDHGMPGYNSWRGFCGLSQPKTLKGLQTVLKNKILAKKLMDLYKTPDNIDIWIGGNAEPMVERGRVGPLLACLLGRQFQQIRDGDRFWWENPGVFTEKQRDSLQKFSFSRLICDNTHITKVPLHAFQANNYPHDFVDCSTVDKLDLSPWASREN  712
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............................ee...............................hhhhhhhhh.........eeeeeehhhhhhhhhhhhhhh...........hhhhhhhhhh........ee....hhhhhhh..ee.....................ee.......hhhhhh.hhhhhhhhh..............................hhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.hhhhhh................hhhhhhhhhhhhh..eee.............eee.hhh...hhhhhh...hhhhhhhhhhheee........hhhhhh.ee......eeehhhhhhhhhhhhh...hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh...........hhhhhhhhh..hhhhhhhhhh...eee............eee........hhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2gjm A   1B VKCDENSPYRTITGDCNNRRSPALGAANRALARWLPAEYEDGLALPFGWTQRKTRNGFRVPLAREVSNKIVGYLDEEGVLDQNRSLLFMQWGQIVDHDLDFAPETELGSNEHSKTQCEEYCIQGDNCFPIMFPKNDPKLKTQGKCMPFFRAGFVCPTPPYQSLAREQINAVTSFLDASLVYGSEPSLASRLRNLSSPLGLMAVNQEAWDHGLAYLPFNNKKPSPCEFINTTARVPCFLAGDFRASEQILLATAHTLLLREHNRLARELKKLNPHWNGEKLYQEARKILGAFIQIITFRDYLPIVLGSEMQKWIPPYQGYNNSVDPRISNVFTFAFRFGHMEVPSTVSRLDENYQPWGPEAELPLHTLFFNTWRIIKDGGIDPLTRGLLAKKSKLMNQDKMVTSELRNKLFQPTHKIHGFDLAAINLQRCRDHGMPGYNSWRGFCGLSQPKTLKGLQTVLKNKILAKKLMDLYKTPDNIDIWIGGNAEPMVERGRVGPLLACLLGRQFQQIRDGDRFWWENPGVFTEKQRDSLQKFSFSRLICDNTHITKVPLHAFQANNYPHDFVDCSTVDKLDLSPWASREN  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|                               
                           1B|                                                                                                                                                          156B                                                                                                                                                304                                                                                                                                                                                                                                                  549                               
                            1A
   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 2GJM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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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  2gjm
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  1.11.1.7
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2GJM)