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Title :   CRYSTAL STRUCTURE OF THE COMPLEX OF BOVINE LACTOPEROXIDASE WITH P-HYDROXYCINNAMIC ACID AT 2.6 A RESOLUTION

Authors :   N. Pandey, A. K. Singh, R. P. Singh, M. Sinha, P. Kaur, S. Sharma, T. P. Sin

Date :   24 Oct 11 (Deposition) - 28 Dec 11 (Release) - 28 Dec 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.65

Chains :   Asym./Biol. Unit : A

Keywords :   Bovine Lactoperoxidase, Oxidoreductase, Phenyl Isothiocyanate, Iodide, Peg, P-Hydroxycinnamic Acid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Pandey, A. K. Singh, R. P. Singh, M. Sinha, P. Kaur, S. Sharma, T. P. Singh
Crystal Structure Of The Complex Of Bovine Lactoperoxidase With P-Hydroxycinnamic Acid At 2. 6 A Resolution
To Be Published
PubMed: search

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

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (10, 24)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
3	GOL	1	Ligand/Ion	GLYCEROL
4	HC4	1	Ligand/Ion	4'-HYDROXYCINNAMIC ACID
5	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
6	IOD	9	Ligand/Ion	IODIDE ION
7	NAG	5	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
8	PEG	2	Ligand/Ion	DI(HYDROXYETHYL)ETHER
9	SCN	1	Ligand/Ion	THIOCYANATE ION
10	SEP	1	Mod. Amino Acid	PHOSPHOSERINE

Asymmetric Unit (21, 21)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	MET A:101 , GLY A:104 , GLN A:105 , ASP A:108 , ASP A:112 , PHE A:113 , ALA A:114 , GLU A:258 , GLN A:259 , THR A:344 , PHE A:347 , ARG A:348 , GLY A:350 , HIS A:351 , LEU A:417 , LEU A:433 , ILE A:436 , ARG A:440 , HC4 A:700	BINDING SITE FOR RESIDUE HEM A 605
02	AC2	SOFTWARE	ASN A:95 , PRO A:209 , ILE A:315 , GOL A:621 , HOH A:629	BINDING SITE FOR RESIDUE NAG A 596
03	AC3	SOFTWARE	ASN A:205 , SER A:208 , LEU A:212 , ALA A:214 , VAL A:215 , GLN A:217 , HOH A:665 , HOH A:694 , HOH A:697	BINDING SITE FOR RESIDUE NAG A 599
04	AC4	SOFTWARE	ASN A:241 , ALA A:244 , TRP A:384 , NAG A:602	BINDING SITE FOR RESIDUE NAG A 601
05	AC5	SOFTWARE	NAG A:601	BINDING SITE FOR RESIDUE NAG A 602
06	AC6	SOFTWARE	ASN A:332 , SER A:334 , HOH A:657	BINDING SITE FOR RESIDUE NAG A 604
07	AC7	SOFTWARE	THR A:560	BINDING SITE FOR RESIDUE IOD A 607
08	AC8	SOFTWARE	ASN A:80	BINDING SITE FOR RESIDUE IOD A 608
09	AC9	SOFTWARE	THR A:425	BINDING SITE FOR RESIDUE IOD A 609
10	BC1	SOFTWARE	LYS A:462 , THR A:463	BINDING SITE FOR RESIDUE IOD A 611
11	BC2	SOFTWARE	HIS A:565 , ALA A:566 , PHE A:567	BINDING SITE FOR RESIDUE IOD A 612
12	BC3	SOFTWARE	TRP A:46 , VAL A:342	BINDING SITE FOR RESIDUE IOD A 615
13	BC4	SOFTWARE	ARG A:202	BINDING SITE FOR RESIDUE IOD A 617
14	BC5	SOFTWARE	ASP A:110 , THR A:184 , PHE A:186 , ASP A:188 , SER A:190	BINDING SITE FOR RESIDUE CA A 606
15	BC6	SOFTWARE	ASN A:230 , PHE A:254 , HC4 A:700 , HOH A:711	BINDING SITE FOR RESIDUE SCN A 620
16	BC7	SOFTWARE	HIS A:109 , PHE A:254 , ARG A:255 , GLU A:258 , PHE A:381 , PRO A:424 , HEM A:605 , SCN A:620	BINDING SITE FOR RESIDUE HC4 A 700
17	BC8	SOFTWARE	ARG A:76 , ASN A:80 , PRO A:149 , ARG A:418 , ASN A:419	BINDING SITE FOR RESIDUE PEG A 603
18	BC9	SOFTWARE	ASN A:30 , ARG A:32 , SER A:33 , LEU A:36 , HOH A:718	BINDING SITE FOR RESIDUE PEG A 619
19	CC1	SOFTWARE	ASN A:95 , ARG A:96 , ARG A:504 , ARG A:506 , NAG A:596	BINDING SITE FOR RESIDUE GOL A 621
20	CC2	SOFTWARE	ARG A:245 , VAL A:246	BINDING SITE FOR RESIDUE EDO A 623
21	CC3	SOFTWARE	PRO A:197 , HOH A:716	BINDING SITE FOR RESIDUE EDO A 624

Asymmetric/Biological Unit

No.	Residues
1	A:6	-	A:167
2	A:15	-	A:28
3	A:129	-	A:139
4	A:133	-	A:157
5	A:237	-	A:248
6	A:456	-	A:513
7	A:554	-	A:579

Asymmetric/Biological Unit

No.	Residues
1	Lys A:233	-	Pro A:234
2	Tyr A:572	-	Pro A:573

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

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEROXIDASE_3	PS50292	Animal heme peroxidase superfamily profile.	PERL_BOVIN	129-711	1	A:12-594

Asymmetric/Biological Unit (9, 9)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSBTAT00000016986	1	ENSBTAE00000279445	chr19:8430632-8430751	120	PERL_BOVIN	-	0	0	-	-
1.2	ENSBTAT00000016986	2	ENSBTAE00000137885	chr19:8435757-8435834	78	PERL_BOVIN	1-26	26	0	-	-
1.3	ENSBTAT00000016986	3	ENSBTAE00000137889	chr19:8437178-8437265	88	PERL_BOVIN	26-55	30	0	-	-
1.4	ENSBTAT00000016986	4	ENSBTAE00000137892	chr19:8441906-8442066	161	PERL_BOVIN	55-109	55	0	-	-
1.5	ENSBTAT00000016986	5	ENSBTAE00000137896	chr19:8443636-8443753	118	PERL_BOVIN	109-148	40	1	A:1-31	31
1.6	ENSBTAT00000016986	6	ENSBTAE00000137903	chr19:8444165-8444294	130	PERL_BOVIN	148-191	44	1	A:31-74	44
1.7	ENSBTAT00000016986	7	ENSBTAE00000137906	chr19:8445032-8445238	207	PERL_BOVIN	192-260	69	1	A:75-143	69
1.8	ENSBTAT00000016986	8	ENSBTAE00000137912	chr19:8446677-8447001	325	PERL_BOVIN	261-369	109	1	A:144-252	109
1.9	ENSBTAT00000016986	9	ENSBTAE00000137915	chr19:8448604-8448764	161	PERL_BOVIN	369-422	54	1	A:252-305	54
1.10	ENSBTAT00000016986	10	ENSBTAE00000137918	chr19:8457180-8457432	253	PERL_BOVIN	423-507	85	1	A:306-390	85
1.11	ENSBTAT00000016986	11	ENSBTAE00000137921	chr19:8458505-8458678	174	PERL_BOVIN	507-565	59	1	A:390-448	59
1.12	ENSBTAT00000016986	12	ENSBTAE00000137923	chr19:8459302-8459539	238	PERL_BOVIN	565-644	80	1	A:448-527	80
1.13	ENSBTAT00000016986	13	ENSBTAE00000279432	chr19:8459727-8460382	656	PERL_BOVIN	644-712	69	1	A:527-595	69

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 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................................ee...............................hhhhhhhhh.........eeeeeehhhhhhhhhhhhhhh...........hhhhhhhhhh........ee....hhhhhhhh.ee.....................ee.......hhhhhh.hhhhhhhh...............................hhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh................hhhhhhhhhhhh...ee...............ee.hhhh..hhhhhh...hhhhhhhhhhheee........hhhhhh.ee......eeehhhhhhhhhhhhh...hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh..........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)
                 3uba 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 '\|'

(no "SCOP Domain" information available for 3UBA)

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

(no "Pfam Domain" information available for 3UBA)

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.

Asymmetric/Biological Unit
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3gc1	CRYSTAL STRUCTURES OF LACTOPEROXIDASE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (10, 24)

Sites (21, 21)

SS Bonds (7, 7)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (9, 9)

Sequences/Alignments

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Gene Ontology (19, 19)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File