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(-) Description

Title :  CRYSTAL STRUCTURE OF THE COMPLEX OF BOVINE LACTOPEROXIDASE WITH ACETYL SALICYLIC ACID AT 2.5 A RESOLUTION
 
Authors :  A. K. Singh, N. Singh, S. Sharma, P. Kaur, T. P. Singh
Date :  27 Jul 07  (Deposition) - 07 Aug 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Drug, Complex, Antibiotic, Antimicrobial, Cleavage On Pair Of Basic Residues, Glycoprotein, Heme, Hydrogen Peroxide, Iron, Metal- Binding, Oxidoreductase, Peroxidase, Secreted (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. K. Singh, N. Singh, S. Sharma, P. Kaur, T. P. Singh
Crystal Structure Of The Complex Of Bovine Lactoperoxidase With Acetyl Salicylic Acid At 2. 5 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - LACTOPEROXIDASE
    Chains: A
    EC Number: 1.11.1.7
    Fragment: RESIDUES IN DATABASE 118-712
    Organism Common: BOVINE
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
    Synonym: PEROXIDASE, LPO

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 22)

Asymmetric/Biological Unit (8, 22)
No.NameCountTypeFull Name
1AIN1Ligand/Ion2-(ACETYLOXY)BENZOIC ACID
2CA1Ligand/IonCALCIUM ION
3HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4IOD7Ligand/IonIODIDE ION
5MAN2Ligand/IonALPHA-D-MANNOSE
6NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
7SCN1Ligand/IonTHIOCYANATE ION
8SEP1Mod. Amino AcidPHOSPHOSERINE

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:95 , ILE A:315 , ARG A:504 , NAG A:1002BINDING SITE FOR RESIDUE NAG A 1001
02AC2SOFTWARENAG A:1001 , MAN A:1010 , HOH A:1248BINDING SITE FOR RESIDUE NAG A 1002
03AC3SOFTWARENAG A:1002 , HOH A:1318BINDING SITE FOR RESIDUE MAN A 1010
04AC4SOFTWAREASN A:205 , SER A:208 , LEU A:210 , ALA A:214 , VAL A:215 , GLN A:217 , NAG A:1004 , HOH A:1281 , HOH A:1321BINDING SITE FOR RESIDUE NAG A 1003
05AC5SOFTWARENAG A:1003 , HOH A:1319 , HOH A:1320BINDING SITE FOR RESIDUE NAG A 1004
06AC6SOFTWAREASN A:241 , ALA A:244 , TRP A:384 , LYS A:388 , NAG A:1006 , HOH A:1323BINDING SITE FOR RESIDUE NAG A 1005
07AC7SOFTWARENAG A:1005 , MAN A:1009BINDING SITE FOR RESIDUE NAG A 1006
08AC8SOFTWARENAG A:1006 , HOH A:1324BINDING SITE FOR RESIDUE MAN A 1009
09AC9SOFTWAREASN A:332 , NAG A:1008 , HOH A:1326 , HOH A:1327 , HOH A:1330BINDING SITE FOR RESIDUE NAG A 1007
10BC1SOFTWARENAG A:1007 , HOH A:1325 , HOH A:1327 , HOH A:1329BINDING SITE FOR RESIDUE NAG A 1008
11BC2SOFTWAREHIS A:109 , ARG A:255 , PHE A:381 , PHE A:422 , GLN A:423 , PRO A:424 , HEM A:605 , HOH A:1025 , HOH A:1183BINDING SITE FOR RESIDUE AIN A 596
12BC3SOFTWAREASP A:110 , THR A:184 , PHE A:186 , ASP A:188 , SER A:190BINDING SITE FOR RESIDUE CA A 606
13BC4SOFTWAREARG A:202 , LYS A:474BINDING SITE FOR RESIDUE SCN A 607
14BC5SOFTWARETRP A:46 , VAL A:342BINDING SITE FOR RESIDUE IOD A 608
15BC6SOFTWAREASN A:80BINDING SITE FOR RESIDUE IOD A 609
16BC7SOFTWAREARG A:504BINDING SITE FOR RESIDUE IOD A 610
17BC8SOFTWAREPHE A:229BINDING SITE FOR RESIDUE IOD A 611
18BC9SOFTWARETRP A:530BINDING SITE FOR RESIDUE IOD A 612
19CC1SOFTWAREGLU A:363 , ARG A:397BINDING SITE FOR RESIDUE IOD A 613
20CC2SOFTWARELYS A:462 , THR A:463BINDING SITE FOR RESIDUE IOD A 614
21CC3SOFTWAREMET 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 , AIN A:596 , HOH A:1011 , HOH A:1025 , HOH A:1269BINDING SITE FOR RESIDUE HEM A 605

(-) 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 2QQT)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEROXIDASE_3PS50292 Animal heme peroxidase superfamily profile.PERL_BOVIN129-711  1A:12-594

(-) 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:1-3131
1.6ENSBTAT000000169866ENSBTAE00000137903chr19:8444165-8444294130PERL_BOVIN148-191441A:31-7444
1.7ENSBTAT000000169867ENSBTAE00000137906chr19:8445032-8445238207PERL_BOVIN192-260691A:75-14369
1.8ENSBTAT000000169868ENSBTAE00000137912chr19:8446677-8447001325PERL_BOVIN261-3691091A:144-252109
1.9ENSBTAT000000169869ENSBTAE00000137915chr19:8448604-8448764161PERL_BOVIN369-422541A:252-30554
1.10ENSBTAT0000001698610ENSBTAE00000137918chr19:8457180-8457432253PERL_BOVIN423-507851A:306-39085
1.11ENSBTAT0000001698611ENSBTAE00000137921chr19:8458505-8458678174PERL_BOVIN507-565591A:390-44859
1.12ENSBTAT0000001698612ENSBTAE00000137923chr19:8459302-8459539238PERL_BOVIN565-644801A:448-52780
1.13ENSBTAT0000001698613ENSBTAE00000279432chr19:8459727-8460382656PERL_BOVIN644-712691A:527-59569

(-) 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_BOVIN | P80025 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_BOVIN   118 SWEVGCGAPVPLVKCDENSPYRTITGDCNNRRSPALGAANRALARWLPAEYEDGLALPFGWTQRKTRNGFRVPLAREVSNKIVGYLDEEGVLDQNRSLLFMQWGQIVDHDLDFAPETELGSNEHSKTQCEEYCIQGDNCFPIMFPKNDPKLKTQGKCMPFFRAGFVCPTPPYQSLAREQINAVTSFLDASLVYGSEPSLASRLRNLSSPLGLMAVNQEAWDHGLAYLPFNNKKPSPCEFINTTARVPCFLAGDFRASEQILLATAHTLLLREHNRLARELKKLNPHWNGEKLYQEARKILGAFIQIITFRDYLPIVLGSEMQKWIPPYQGYNNSVDPRISNVFTFAFRFGHMEVPSTVSRLDENYQPWGPEAELPLHTLFFNTWRIIKDGGIDPLVRGLLAKKSKLMNQDKMVTSELRNKLFQPTHKIHGFDLAAINLQRCRDHGMPGYNSWRGFCGLSQPKTLKGLQTVLKNKILAKKLMDLYKTPDNIDIWIGGNAEPMVERGRVGPLLACLLGRQFQQIRDGDRFWWENPGVFTEKQRDSLQKVSFSRLICDNTHITKVPLHAFQANNYPHDFVDCSTVDKLDLSPWASREN 712
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------An_peroxidase-2qqtA01 A:21-567                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     ---------------------------- Pfam domains
         Sec.struct. author ........................................ee...............................hhhhhhhhh.........eeeeeehhhhhhhhhhhhhhh...........hhhhhh............ee....hhhhhhhh.ee.....................ee.......hhhhhh.hhhhhhhhh..............................hhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhh..eee.............eee.hhhh..hhhhhh...hhhhhhhhhhheee........hhhhhh.ee......eeehhhhhhhhhhhhh...hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhh.........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 1 (1) Exon 1.5  PDB: A:1-31          -------------------------------------------Exon 1.7  PDB: A:75-143 UniProt: 192-260                             Exon 1.8  PDB: A:144-252 UniProt: 261-369                                                                    -----------------------------------------------------Exon 1.10  PDB: A:306-390 UniProt: 423-507                                           ---------------------------------------------------------Exon 1.12  PDB: A:448-527 UniProt: 565-644                                      -------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------Exon 1.6  PDB: A:31-74 UniProt: 148-191     ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9  PDB: A:252-305 UniProt: 369-422             ------------------------------------------------------------------------------------Exon 1.11  PDB: A:390-448 UniProt: 507-565                 ------------------------------------------------------------------------------Exon 1.13  PDB: A:527-595 UniProt: 644-712                            Transcript 1 (2)
                 2qqt A   1 SWEVGCGAPVPLVKCDENSPYRTITGDCNNRRSPALGAANRALARWLPAEYEDGLALPFGWTQRKTRNGFRVPLAREVSNKIVGYLDEEGVLDQNRSLLFMQWGQIVDHDLDFAPETELGSNEHSKTQCEEYCIQGDNCFPIMFPKNDPKLKTQGKCMPFFRAGFVCPTPPYQSLAREQINAVTSFLDASLVYGSEPsLASRLRNLSSPLGLMAVNQEAWDHGLAYLPFNNKKPSPCEFINTTARVPCFLAGDFRASEQILLATAHTLLLREHNRLARELKKLNPHWNGEKLYQEARKILGAFIQIITFRDYLPIVLGSEMQKWIPPYQGYNNSVDPRISNVFTFAFRFGHMEVPSTVSRLDENYQPWGPEAELPLHTLFFNTWRIIKDGGIDPLVRGLLAKKSKLMNQDKMVTSELRNKLFQPTHKIHGFDLAAINLQRCRDHGMPGYNSWRGFCGLSQPKTLKGLQTVLKNKILAKKLMDLYKTPDNIDIWIGGNAEPMVERGRVGPLLACLLGRQFQQIRDGDRFWWENPGVFTEKQRDSLQKVSFSRLICDNTHITKVPLHAFQANNYPHDFVDCSTVDKLDLSPWASREN 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 2QQT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

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

(-) 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: 2gj1 2ips 2nqx 2pt3 2pum 2qpk 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

2pt3 CRYSTAL STRUCTURE OF BOVINE LACTOPEROXIDASE AT 2.34 A RESOLUTION REVEALS MULTIPLE ANION BINDING SITES
2pum CRYSTAL STRUCTURE OF BOVINE LACTOPEROXIDASE COMPLEX WITH CATECHOL AND IODIDE AT 2.7 A RESOLUTION