2PZD - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE HTRA2/OMI PDZ DOMAIN BOUND TO A PHAGE-DERIVED LIGAND (WTMFWV)

Authors :   B. A. Appleton, C. Wiesmann

Date :   17 May 07 (Deposition) - 07 Aug 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.75

Chains :   Asym./Biol. Unit : A,B

Keywords :   Pdz Domain, Serine Protease, Apoptosis, Mitochondria, Peptide-Binding Module, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Zhang, B. A. Appleton, P. Wu, C. Wiesmann, S. S. Sidhu
Structural And Functional Analysis Of The Ligand Specificit Of The Htra2/Omi Pdz Domain.
Protein Sci. V. 16 1738 2007
PubMed-ID: 17656586 | Reference-DOI: 10.1110/PS.072833207

Molecule 1 - SERINE PROTEASE HTRA2
	Chains	:	A, B
	EC Number	:	3.4.21.108
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	HTRA2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	HIGH TEMPERATURE REQUIREMENT PROTEIN A2, HTRA2, OMI STRESS- REGULATED ENDOPROTEASE, SERINE PROTEINASE OMI, SERINE PROTEASE 25

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	EDO	2	Ligand/Ion	1,2-ETHANEDIOL

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:368 , GLU A:425 , GLU B:425 , TYR B:428 , PHE B:465	BINDING SITE FOR RESIDUE EDO B 10
2	AC2	SOFTWARE	ARG A:359 , ARG A:360 , TYR A:428 , ARG A:432 , THR A:463	BINDING SITE FOR RESIDUE EDO A 11

(no "SS Bond" information available for 2PZD)

(no "Cis Peptide Bond" information available for 2PZD)

Asymmetric/Biological Unit (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_027350	G	399	S	HTRA2_HUMAN	Polymorphism	72470545	A/B	G	399	S
2	UniProt	VAR_077961	R	404	Q	HTRA2_HUMAN	Disease (MGCA8)	767006508	A/B	R	404	Q
3	UniProt	VAR_046135	R	404	W	HTRA2_HUMAN	Disease (PARK13)	---	A/B	R	404	W

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PDZ	PS50106	PDZ domain profile.	HTRA2_HUMAN	390-445	2	A:390-445 B:390-445

Asymmetric/Biological Unit (3, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000258080	1a	ENSE00001276828	chr2:74756504-74757639	1136	HTRA2_HUMAN	1-169	169	0	-	-
1.2c	ENST00000258080	2c	ENSE00000763573	chr2:74757744-74757948	205	HTRA2_HUMAN	169-237	69	0	-	-
1.3a	ENST00000258080	3a	ENSE00000763626	chr2:74758038-74758232	195	HTRA2_HUMAN	238-302	65	0	-	-
1.3d	ENST00000258080	3d	ENSE00001276808	chr2:74758466-74758498	33	HTRA2_HUMAN	303-313	11	0	-	-
1.3i	ENST00000258080	3i	ENSE00000920847	chr2:74758724-74758829	106	HTRA2_HUMAN	314-349	36	0	-	-
1.3j	ENST00000258080	3j	ENSE00001276754	chr2:74758983-74759052	70	HTRA2_HUMAN	349-372	24	2	A:359-372 B:359-372	14 14
1.4	ENST00000258080	4	ENSE00001276734	chr2:74759746-74759841	96	HTRA2_HUMAN	372-404	33	2	A:372-404 B:372-404	33 33
1.5f	ENST00000258080	5f	ENSE00000920849	chr2:74759947-74760472	526	HTRA2_HUMAN	404-458	55	2	A:404-463 (gaps) B:404-463 (gaps)	60 60

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:106
 aligned with HTRA2_HUMAN | O43464 from UniProtKB/Swiss-Prot  Length:458

    Alignment length:106
                                                                                                                               458    
                                                                                                                            457  |    
                                   368       378       388       398       408       418       428       438       448        |- |    
          HTRA2_HUMAN   359 RRYIGVMMLTLSPSILAELQLREPSFPDVQHGVLIHKVILGSPAHRAGLRPGDVILAIGEQMVQNAEDVYEAVRTQSQLAVQIRRGRETLTLYVTPEVT--E----   -
               SCOP domains d2pzda_ A: automated matches                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..eeeee.hhhhhhhhhhhh.........eeeeee...hhhhhhh.....eeeee..ee..hhhhhhhhhhhh..eeeeeee..eeeeeee..ee.....ee. Sec.struct. author
             SAPs(SNPs) (1) ----------------------------------------S----Q------------------------------------------------------------ SAPs(SNPs) (1)
             SAPs(SNPs) (2) ---------------------------------------------W------------------------------------------------------------ SAPs(SNPs) (2)
                    PROSITE -------------------------------PDZ  PDB: A:390-445 UniProt: 390-445                    ------------------- PROSITE
           Transcript 1 (1) Exon 1.3j     -------------------------------Exon 1.5f  PDB: A:404-463 (gaps) UniProt: 404-458        ---- Transcript 1 (1)
           Transcript 1 (2) -------------Exon 1.4  PDB: A:372-404         ------------------------------------------------------------ Transcript 1 (2)
                 2pzd A 359 RRYIGVMMLTLSPSILAELQLREPSFPDVQHGVLIHKVILGSPAHRAGLRPGDVILAIGEQMVQNAEDVYEAVRTQSQLAVQIRRGRETLTLYVTPEVTGWTMFWV 467
                                   368       378       388       398       408       418       428       438       448       461      
                                                                                                                            457|      
                                                                                                                             461

Chain B from PDB  Type:PROTEIN  Length:106
 aligned with HTRA2_HUMAN | O43464 from UniProtKB/Swiss-Prot  Length:458

    Alignment length:106
                                                                                                                               458    
                                                                                                                            457  |    
                                   368       378       388       398       408       418       428       438       448        |- |    
          HTRA2_HUMAN   359 RRYIGVMMLTLSPSILAELQLREPSFPDVQHGVLIHKVILGSPAHRAGLRPGDVILAIGEQMVQNAEDVYEAVRTQSQLAVQIRRGRETLTLYVTPEVT--E----   -
               SCOP domains d2pzdb_ B: automated matches                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -PDZ_2-2pzdB01 B:360-453                                                                       ----------- Pfam domains (1)
           Pfam domains (2) -PDZ_2-2pzdB02 B:360-453                                                                       ----------- Pfam domains (2)
         Sec.struct. author .ee..eeeee.hhhhhhhhhhhh.........eeeeee...hhhhhhh.....eeeee..ee..hhhhhhhhhhhh..eeeeeee..eeeeeee..ee.....ee. Sec.struct. author
             SAPs(SNPs) (1) ----------------------------------------S----Q------------------------------------------------------------ SAPs(SNPs) (1)
             SAPs(SNPs) (2) ---------------------------------------------W------------------------------------------------------------ SAPs(SNPs) (2)
                    PROSITE -------------------------------PDZ  PDB: B:390-445 UniProt: 390-445                    ------------------- PROSITE
           Transcript 1 (1) Exon 1.3j     -------------------------------Exon 1.5f  PDB: B:404-463 (gaps) UniProt: 404-458        ---- Transcript 1 (1)
           Transcript 1 (2) -------------Exon 1.4  PDB: B:372-404         ------------------------------------------------------------ Transcript 1 (2)
                 2pzd B 359 RRYIGVMMLTLSPSILAELQLREPSFPDVQHGVLIHKVILGSPAHRAGLRPGDVILAIGEQMVQNAEDVYEAVRTQSQLAVQIRRGRETLTLYVTPEVTGWTMFWV 467
                                   368       378       388       398       408       418       428       438       448       461      
                                                                                                                            457|      
                                                                                                                             461

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: PDZ domain-like (299)

Superfamily: PDZ domain-like (299)

Family: automated matches (94)

Protein domain: automated matches (94)

Human (Homo sapiens) [TaxId: 9606] (71)

1a	d2pzda_	A:
1b	d2pzdb_	B:

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

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PDZ-like (184)

Family: PDZ_2 (11)

Homo sapiens (Human) (3)

1a	PDZ_2-2pzdB01	B:360-453
1b	PDZ_2-2pzdB02	B:360-453

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (HTRA2_HUMAN | O43464)

molecular function
	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:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0004252	serine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
	GO:0008236	serine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
	GO:0051082	unfolded protein binding	Interacting selectively and non-covalently with an unfolded protein.
biological process
	GO:0008344	adult locomotory behavior	Locomotory behavior in a fully developed and mature organism.
	GO:0007628	adult walking behavior	The behavior of an adult relating to the progression of that organism along the ground by the process of lifting and setting down each leg.
	GO:0006915	apoptotic process	A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
	GO:0044257	cellular protein catabolic process	The chemical reactions and pathways resulting in the breakdown of a protein by individual cells.
	GO:0071363	cellular response to growth factor stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a growth factor stimulus.
	GO:0034605	cellular response to heat	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism.
	GO:0035458	cellular response to interferon-beta	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interferon-beta stimulus. Interferon-beta is a type I interferon.
	GO:0034599	cellular response to oxidative stress	Any process that results in a change in state or activity of a cell (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:0071300	cellular response to retinoic acid	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a retinoic acid stimulus.
	GO:0006672	ceramide metabolic process	The chemical reactions and pathways involving ceramides, any N-acylated sphingoid.
	GO:0097194	execution phase of apoptosis	A stage of the apoptotic process that starts with the controlled breakdown of the cell through the action of effector caspases or other effector molecules (e.g. cathepsins, calpains etc.). Key steps of the execution phase are rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
	GO:0030900	forebrain development	The process whose specific outcome is the progression of the forebrain over time, from its formation to the mature structure. The forebrain is the anterior of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes especially the cerebral hemispheres, the thalamus, and the hypothalamus and especially in higher vertebrates is the main control center for sensory and associative information processing, visceral functions, and voluntary motor functions).
	GO:0097193	intrinsic apoptotic signaling pathway	A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway starts with reception of an intracellular signal (e.g. DNA damage, endoplasmic reticulum stress, oxidative stress etc.), and ends when the execution phase of apoptosis is triggered. The intrinsic apoptotic signaling pathway is crucially regulated by permeabilization of the mitochondrial outer membrane (MOMP).
	GO:0008630	intrinsic apoptotic signaling pathway in response to DNA damage	A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced by the detection of DNA damage, and ends when the execution phase of apoptosis is triggered.
	GO:0007005	mitochondrion organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrion; includes mitochondrial morphogenesis and distribution, and replication of the mitochondrial genome as well as synthesis of new mitochondrial components.
	GO:0045786	negative regulation of cell cycle	Any process that stops, prevents or reduces the rate or extent of progression through the cell cycle.
	GO:0060548	negative regulation of cell death	Any process that decreases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death.
	GO:1901215	negative regulation of neuron death	Any process that stops, prevents or reduces the frequency, rate or extent of neuron death.
	GO:1902176	negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway	Any process that stops, prevents or reduces the frequency, rate or extent of an oxidative stress-induced intrinsic apoptotic signaling pathway.
	GO:0048666	neuron development	The process whose specific outcome is the progression of a neuron over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell.
	GO:0019742	pentacyclic triterpenoid metabolic process	The chemical reactions and pathways involving pentacyclic triterpenoid compounds, terpenoids with six isoprene units and 5 carbon rings.
	GO:0043065	positive regulation of apoptotic process	Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
	GO:0010942	positive regulation of cell death	Any process that increases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death.
	GO:0043280	positive regulation of cysteine-type endopeptidase activity involved in apoptotic process	Any process that activates or increases the activity of a cysteine-type endopeptidase involved in the apoptotic process.
	GO:2001269	positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway	Any process that activates or increases the frequency, rate or extent of cysteine-type endopeptidase activity involved in apoptotic signaling pathway.
	GO:2001241	positive regulation of extrinsic apoptotic signaling pathway in absence of ligand	Any process that activates or increases the frequency, rate or extent of extrinsic apoptotic signaling pathway in absence of ligand.
	GO:1903955	positive regulation of protein targeting to mitochondrion	Any process that activates or increases the frequency, rate or extent of protein targeting to mitochondrion.
	GO:0016540	protein autoprocessing	Processing which a protein carries out itself. This involves actions such as the autolytic removal of residues to generate the mature form of the protein.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:1903146	regulation of mitophagy	Any process that modulates the frequency, rate or extent of mitochondrion degradation (mitophagy).
	GO:0040014	regulation of multicellular organism growth	Any process that modulates the frequency, rate or extent of growth of the body of an organism so that it reaches its usual body size.
	GO:0009635	response to herbicide	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 a herbicide stimulus. Herbicides are chemicals used to kill or control the growth of plants.
cellular component
	GO:0035631	CD40 receptor complex	A protein complex that contains at least CD40 (a cell surface receptor of the tumour necrosis factor receptor (TNFR) superfamily), and other signaling molecules.
	GO:0000785	chromatin	The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome.
	GO:0009898	cytoplasmic side of plasma membrane	The leaflet the plasma membrane that faces the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
	GO:0005856	cytoskeleton	Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005758	mitochondrial intermembrane space	The region between the inner and outer lipid bilayers of the mitochondrial envelope.
	GO:0031966	mitochondrial membrane	Either of the lipid bilayers that surround the mitochondrion and form the mitochondrial envelope.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Asymmetric/Biological Unit
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	2pzd
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	3.4.21.108
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	617248
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	HTRA2_HUMAN \| O43464	:	1lcy 5fht

Description

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Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 6)

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Exons (3, 6)

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