2PVS - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   STRUCTURE OF HUMAN PANCREATIC LIPASE RELATED PROTEIN 2 MUTANT N336Q

Authors :   S. Spinelli, C. Eydoux, F. Carriere, C. Cambillau

Date :   10 May 07 (Deposition) - 18 Dec 07 (Release) - 20 Jan 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A,B  (4x)

Keywords :   Lipase, Galacto Lipids Hydrolysis, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Eydoux, S. Spinelli, T. L. Davis, J. R. Walker, A. Seitova, S. Dhe-Paganon, A. De Caro, C. Cambillau, F. Carriere
Structure Of Human Pancreatic Lipase-Related Protein 2 With The Lid In An Open Conformation.
Biochemistry V. 47 9553 2008
PubMed-ID: 18702514 | Reference-DOI: 10.1021/BI8005576
(for further references see the PDB file header)

Molecule 1 - PANCREATIC LIPASE-RELATED PROTEIN 2
	Chains	:	A, B
	EC Number	:	3.1.1.3
	Engineered	:	YES
	Expression System	:	PICHIA PASTORIS
	Expression System Strain	:	SMD 1168
	Expression System Taxid	:	4922
	Expression System Vector Type	:	PGAPZB
	Gene	:	PNLIPRP2, PLRP2
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (4x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 10)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	SO4	8	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 5)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 3)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 3 (1, 32)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	SO4	32	Ligand/Ion	SULFATE ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:107 , HIS A:108 , ARG A:111 , LYS B:80	BINDING SITE FOR RESIDUE SO4 A 451
02	AC2	SOFTWARE	HIS A:108 , ARG A:111	BINDING SITE FOR RESIDUE SO4 A 452
03	AC3	SOFTWARE	LYS A:80 , ASP A:83 , ARG B:107 , HIS B:108 , ARG B:111	BINDING SITE FOR RESIDUE SO4 A 453
04	AC4	SOFTWARE	GLU A:43 , ASN A:44 , PRO A:45 , ASN A:46 , ASN A:47	BINDING SITE FOR RESIDUE SO4 A 454
05	AC5	SOFTWARE	PHE A:314 , GLY A:316 , LYS A:317 , THR A:318	BINDING SITE FOR RESIDUE SO4 A 455
06	AC6	SOFTWARE	GLU A:187 , ARG A:190 , ASP A:192 , ASP A:195	BINDING SITE FOR RESIDUE CA A 502
07	AC7	SOFTWARE	HIS B:108 , ARG B:111	BINDING SITE FOR RESIDUE SO4 B 451
08	AC8	SOFTWARE	ASN B:44 , PRO B:45 , ASN B:46 , ASN B:47	BINDING SITE FOR RESIDUE SO4 B 452
09	AC9	SOFTWARE	LYS B:315 , GLY B:316 , LYS B:317 , THR B:318 , SER B:319	BINDING SITE FOR RESIDUE SO4 B 453
10	BC1	SOFTWARE	GLU B:187 , ARG B:190 , ASP B:192 , ASP B:195 , HOH B:511	BINDING SITE FOR RESIDUE CA B 501

Asymmetric Unit

No.	Residues
1	A:2	-	A:8
2	A:90	-	A:101
3	A:237	-	A:261
4	A:285	-	A:296
5	A:299	-	A:304
6	A:434	-	A:450
7	B:2	-	B:8
8	B:90	-	B:101
9	B:237	-	B:261
10	B:285	-	B:296
11	B:299	-	B:304
12	B:434	-	B:450

Asymmetric Unit

No.	Residues
1	Lys A:13	-	Pro A:14
2	Val A:210	-	Pro A:211
3	Phe A:297	-	Pro A:298
4	Lys B:13	-	Pro B:14
5	Val B:210	-	Pro B:211
6	Cys B:237	-	Lys B:238
7	Phe B:297	-	Pro B:298

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

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LIPASE_SER	PS00120	Lipases, serine active site.	LIPR2_HUMAN	165-174	2	A:146-155 B:146-155
2	PLAT	PS50095	PLAT domain profile.	LIPR2_HUMAN	357-469	2	A:338-450 B:338-450

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LIPASE_SER	PS00120	Lipases, serine active site.	LIPR2_HUMAN	165-174	1	A:146-155 -
2	PLAT	PS50095	PLAT domain profile.	LIPR2_HUMAN	357-469	1	A:338-450 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LIPASE_SER	PS00120	Lipases, serine active site.	LIPR2_HUMAN	165-174	1	- B:146-155
2	PLAT	PS50095	PLAT domain profile.	LIPR2_HUMAN	357-469	1	- B:338-450

Biological Unit 3 (2, 16)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LIPASE_SER	PS00120	Lipases, serine active site.	LIPR2_HUMAN	165-174	8	A:146-155 B:146-155
2	PLAT	PS50095	PLAT domain profile.	LIPR2_HUMAN	357-469	8	A:338-450 B:338-450

(no "Exon" information available for 2PVS)

Asymmetric 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:435
 aligned with LIPR2_HUMAN | P54317 from UniProtKB/Swiss-Prot  Length:469

    Alignment length:452
                                    27        37        47        57        67        77        87        97       107       117       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  
          LIPR2_HUMAN    18 KEVCYGQLGCFSDEKPWAGTLQRPVKLLPWSPEDIDTRFLLYTNENPNNFQLITGTEPDTIEASNFQLDRKTRFIIHGFLDKAEDSWPSDMCKKMFEVEKVNCICVDWRHGSRAMYTQAVQNIRVVGAETAFLIQALSTQLGYSLEDVHVIGHSLGAHTAAEAGRRLGGRVGRITGLDPAGPCFQDEPEEVRLDPSDAVFVDVIHTDSSPIVPSLGFGMSQKVGHLDFFPNGGKEMPGCKKNVLSTITDIDGIWEGIGGFVSCNHLRSFEYYSSSVLNPDGFLGYPCASYDEFQESKCFPCPAEGCPKMGHYADQFKGKTSAVEQTFFLNTGESGNFTSWRYKVSVTLSGKEKVNGYIRIALYGSNENSKQYEIFKGSLKPDASHTCAIDVDFNVGKIQKVKFLWNKRGINLSEPKLGASQITVQSGEDGTEYNFCSSDTVEENVLQSLYPC 469
               SCOP domains d2pvsa1 A:-2-336 automated matches                                                                                                                                                                                                                                                                                                                d2pvsa2 A:337-450 automated matches                                                                                SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh.....................hhhhhh.eeeee........eee....hhhhhh.......eeeeee.........hhhhhhhhhhhhhh.eeeeeeehhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhh.....eeeee..........hhhhh.hhhhh.eeeee...ee........ee......eeeee..........--------------...hhhhhhhhhhhhhhhhhhh........ee..hhhhhhh..............hhhhhhh........eeeee..........eeeeeeeeeee...eeeeeeeeee........eeeeeeee....eeeeeeee........eeeeeee.---......eeeeeeeeee.....eeeee..........eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------LIPASE_SER--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PLAT  PDB: A:338-450 UniProt: 357-469                                                                             PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pvs A  -2 KEVCYGQLGCFSDEKPWAGTLQRPVKLLPWSPEDIDTRFLLYTNENPNNFQLITGTEPDTIEASNFQLDRKTRFIIHGFLDKAEDSWPSDMCKKMFEVEKVNCICVDWRHGSRAMYTQAVQNIRVVGAETAFLIQALSTQLGYSLEDVHVIGHSLGAHTAAEAGRRLGGRVGRITGLDPAGPCFQDEPEEVRLDPSDAVFVDVIHTDSSPIVPSLGFGMSQKVGHLDFFPNGGKEMPGCK--------------EGIGGFVSCNHLRSFEYYSSSVLNPDGFLGYPCASYDEFQESKCFPCPAEGCPKMGHYADQFKGKTSAVEQTFFLNTGESGQFTSWRYKVSVTLSGKEKVNGYIRIALYGSNENSKQYEIFKGSLKPDASHTCAIDVDFNVGKIQKVKFLWNK---NLSEPKLGASQITVQSGEDGTEYNFCSSDTVEENVLQSLYPC 450
                             ||      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238         -    |  258       268       278       288       298       308       318       328       338       348       358       368       378       388       398      |  -|      418       428       438       448  
                             ||                                                                                                                                                                                                                                          238            253                                                                                                                                                     405 409                                         
                            -1|                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
                              1

Chain B from PDB  Type:PROTEIN  Length:445
 aligned with LIPR2_HUMAN | P54317 from UniProtKB/Swiss-Prot  Length:469

    Alignment length:452
                                    27        37        47        57        67        77        87        97       107       117       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  
          LIPR2_HUMAN    18 KEVCYGQLGCFSDEKPWAGTLQRPVKLLPWSPEDIDTRFLLYTNENPNNFQLITGTEPDTIEASNFQLDRKTRFIIHGFLDKAEDSWPSDMCKKMFEVEKVNCICVDWRHGSRAMYTQAVQNIRVVGAETAFLIQALSTQLGYSLEDVHVIGHSLGAHTAAEAGRRLGGRVGRITGLDPAGPCFQDEPEEVRLDPSDAVFVDVIHTDSSPIVPSLGFGMSQKVGHLDFFPNGGKEMPGCKKNVLSTITDIDGIWEGIGGFVSCNHLRSFEYYSSSVLNPDGFLGYPCASYDEFQESKCFPCPAEGCPKMGHYADQFKGKTSAVEQTFFLNTGESGNFTSWRYKVSVTLSGKEKVNGYIRIALYGSNENSKQYEIFKGSLKPDASHTCAIDVDFNVGKIQKVKFLWNKRGINLSEPKLGASQITVQSGEDGTEYNFCSSDTVEENVLQSLYPC 469
               SCOP domains d2pvsb1 B:-2-336 automated matches                                                                                                                                                                                                                                                                                                                d2pvsb2 B:337-450 automated matches                                                                                SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Lipase-2pvsB01 B:-2-335                                                                                                                                                                                                                                                                                                                          ----PLAT-2pvsB03 B:340-448                                                                                       -- Pfam domains (1)
           Pfam domains (2) Lipase-2pvsB02 B:-2-335                                                                                                                                                                                                                                                                                                                          ----PLAT-2pvsB04 B:340-448                                                                                       -- Pfam domains (2)
         Sec.struct. author ....hhhhh.....................hhhhhh.eeeeee..eeeeeeee...hhhhhhhh......eeeeee.........hhhhhhhhhhh....eeeeeeehhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeehhhhhhhhhhhhhh.....eeeee..........hhhhh.hhhhh.eeeee...ee........ee......eeeee............-------........hhhhhhhhhhhhhhhhhhhhh......ee...hhhhhh..............hhhhhhh........eeeee..........eeeeee..ee....eeeeeeeeee....eeeeeeee..ee......eeeeee........eeeeeeee..........ee.eeeeee.....eeeee..........eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------LIPASE_SER--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PLAT  PDB: B:338-450 UniProt: 357-469                                                                             PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pvs B  -2 KEVCYGQLGCFSDEKPWAGTLQRPVKLLPWSPEDIDTRFLLYTNENPNNFQLITGTEPDTIEASNFQLDRKTRFIIHGFLDKAEDSWPSDMCKKMFEVEKVNCICVDWRHGSRAMYTQAVQNIRVVGAETAFLIQALSTQLGYSLEDVHVIGHSLGAHTAAEAGRRLGGRVGRITGLDPAGPCFQDEPEEVRLDPSDAVFVDVIHTDSSPIVPSLGFGMSQKVGHLDFFPNGGKEMPGCKKN-------IDGIWEGIGGFVSCNHLRSFEYYSSSVLNPDGFLGYPCASYDEFQESKCFPCPAEGCPKMGHYADQFKGKTSAVEQTFFLNTGESGQFTSWRYKVSVTLSGKEKVNGYIRIALYGSNENSKQYEIFKGSLKPDASHTCAIDVDFNVGKIQKVKFLWNKRGINLSEPKLGASQITVQSGEDGTEYNFCSSDTVEENVLQSLYPC 450
                             ||      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238 |     248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448  
                            -1|                                                                                                                                                                                                                                            240     248                                                                                                                                                                                                          
                              1

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 "CATH Domain" information available for 2PVS)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: AB_hydrolase (347)

Family: Lipase (7)

Homo sapiens (Human) (6)

1a	Lipase-2pvsB01	B:-2-335
1b	Lipase-2pvsB02	B:-2-335

Clan: PLAT (25)

Family: PLAT (25)

Homo sapiens (Human) (7)

2a	PLAT-2pvsB03	B:340-448
2b	PLAT-2pvsB04	B:340-448

Asymmetric Unit(hide GO term definitions)

Chain A,B (LIPR2_HUMAN | P54317)

molecular function
	GO:0047372	acylglycerol lipase activity	Catalysis of the reaction: H2O + acylglycerol = a fatty acid + glycerol.
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0052689	carboxylic ester hydrolase activity	Catalysis of the hydrolysis of a carboxylic ester bond.
	GO:0047714	galactolipase activity	Catalysis of the reaction: 1,2-diacyl-3-beta-D-galactosyl-sn-glycerol + 2 H2O = 3-beta-D-galactosyl-sn-glycerol + 2 carboxylates.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004620	phospholipase activity	Catalysis of the hydrolysis of a glycerophospholipid.
	GO:0004806	triglyceride lipase activity	Catalysis of the reaction: triacylglycerol + H2O = diacylglycerol + a carboxylate.
biological process
	GO:0019376	galactolipid catabolic process	The chemical reactions and pathways resulting in the breakdown of galactolipids, any glycolipid containing one of more residues of galactose and/or N-acetylgalactosamine.
	GO:0016042	lipid catabolic process	The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
	GO:0044241	lipid digestion	The whole of the physical, chemical, and biochemical processes carried out by living organisms to break down ingested lipids into components that may be easily absorbed and directed into metabolism.
	GO:0006629	lipid metabolic process	The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
	GO:0009395	phospholipid catabolic process	The chemical reactions and pathways resulting in the breakdown of phospholipids, any lipid containing phosphoric acid as a mono- or diester.
	GO:0006641	triglyceride metabolic process	The chemical reactions and pathways involving triglyceride, any triester of glycerol. The three fatty acid residues may all be the same or differ in any permutation. Triglycerides are important components of plant oils, animal fats and animal plasma lipoproteins.
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.

Asymmetric Unit
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	Cis Peptide Bonds
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		Lys A:13 - Pro A:14	[ RasMol ]
		Lys B:13 - Pro B:14	[ RasMol ]
		Phe A:297 - Pro A:298	[ RasMol ]
		Phe B:297 - Pro B:298	[ RasMol ]
		Val A:210 - Pro A:211	[ RasMol ]
		Val B:210 - Pro B:211	[ RasMol ]

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	2pvs
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	LIPR2_HUMAN \| P54317	:	2oxe

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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 10)

Sites (10, 10)

SS Bonds (12, 12)

Cis Peptide Bonds (7, 7)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

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