3K2C - JenaLib

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Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF PEPTIDYL-PROLYL CIS-TRANS ISOMERASE FROM ENCEPHALITOZOON CUNICULI AT 1.9 A RESOLUTION

Authors :   Ssgcid

Date :   29 Sep 09 (Deposition) - 13 Oct 09 (Release) - 13 Oct 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

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

Keywords :   Ssgcid, Nih, Niaid, Sbri, Uw, Decode, Peptidyl-Prolyl Cis- Trans Isomerase, Encephalitozoon Cuniculi, Cytoplasm, Isomerase, Rotamase, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Ssgcid, J. Abendroth, T. E. Edwards, B. Staker
Crystal Structure Of Peptidyl-Prolyl Cis-Trans Isomerase From Encephalitozoon Cuniculi At 1. 9 A Resolution
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
	Chains	:	A, B, C, D
	EC Number	:	5.2.1.8
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	AVA0421
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	CPR1, ECU08_0470
	Organism Common	:	MICROSPORIDIAN PARASITE
	Organism Scientific	:	ENCEPHALITOZOON CUNICULI
	Organism Taxid	:	6035
	Synonym	:	PPIASE, ROTAMASE, CYCLOPHILIN, CPH

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
2	PG5	2	Ligand/Ion	1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
2	PG5	2	Ligand/Ion	1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE
3	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 4)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
2	PG5	1	Ligand/Ion	1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 3 (3, 3)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
2	PG5	1	Ligand/Ion	1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 4 (3, 3)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
2	PG5	1	Ligand/Ion	1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE
3	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS B:73 , HOH B:220 , LYS C:47 , LYS C:52 , HOH C:193 , HOH C:216 , HOH C:428	BINDING SITE FOR RESIDUE SO4 C 200
2	AC2	SOFTWARE	HIS A:73 , HOH A:376 , HOH A:436 , LYS D:47 , LYS D:52 , HOH D:195 , HOH D:196	BINDING SITE FOR RESIDUE SO4 D 200
3	AC3	SOFTWARE	ASN A:105 , CYS A:106 , GLY A:107 , LYS A:128 , THR C:-5	BINDING SITE FOR RESIDUE PG5 A 201
4	AC4	SOFTWARE	LEU A:20 , GLU A:89 , LYS A:147 , TYR A:148 , HOH A:189	BINDING SITE FOR RESIDUE EDO A 202
5	AC5	SOFTWARE	ASN B:105 , CYS B:106 , GLY B:107 , LYS B:128 , THR D:-5	BINDING SITE FOR RESIDUE PG5 B 201
6	AC6	SOFTWARE	LEU B:20 , GLU B:89 , LYS B:147 , TYR B:148 , HOH B:199	BINDING SITE FOR RESIDUE EDO B 202

(no "SS Bond" information available for 3K2C)

(no "Cis Peptide Bond" information available for 3K2C)

(no "SAP(SNP)/Variant" information available for 3K2C)

Asymmetric Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CSA_PPIASE_2	PS50072	Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile.	CYPH_ENCCU	10-168	4	A:10-168 B:10-168 C:10-168 D:10-168
2	CSA_PPIASE_1	PS00170	Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature.	CYPH_ENCCU	51-68	4	A:51-68 B:51-68 C:51-68 D:51-68

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CSA_PPIASE_2	PS50072	Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile.	CYPH_ENCCU	10-168	2	A:10-168 B:10-168 - -
2	CSA_PPIASE_1	PS00170	Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature.	CYPH_ENCCU	51-68	2	A:51-68 B:51-68 - -

Biological Unit 2 (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CSA_PPIASE_2	PS50072	Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile.	CYPH_ENCCU	10-168	3	- B:10-168 C:10-168 D:10-168
2	CSA_PPIASE_1	PS00170	Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature.	CYPH_ENCCU	51-68	3	- B:51-68 C:51-68 D:51-68

Biological Unit 3 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CSA_PPIASE_2	PS50072	Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile.	CYPH_ENCCU	10-168	2	A:10-168 - C:10-168 -
2	CSA_PPIASE_1	PS00170	Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature.	CYPH_ENCCU	51-68	2	A:51-68 - C:51-68 -

Biological Unit 4 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CSA_PPIASE_2	PS50072	Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile.	CYPH_ENCCU	10-168	2	A:10-168 - - D:10-168
2	CSA_PPIASE_1	PS00170	Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature.	CYPH_ENCCU	51-68	2	A:51-68 - - D:51-68

(no "Exon" information available for 3K2C)

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:174
 aligned with CYPH_ENCCU | Q8SRE1 from UniProtKB/Swiss-Prot  Length:172

    Alignment length:176
                                  1                                                                                                                                                                         
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164      
           CYPH_ENCCU     - ------MAKEASGNVYFDVYANEESLGRIVMKLEDDIVPKTAKNFRTLCERPKGEGYKGSTFHRIIPGFMVQGGDYTAHNGTGGRSIYGEKFPDENFELKHTKEGILSMANCGAHTNGSQFFITLGKTQWLDEKHVVFGEVVEGMDVVHKIAKYGSESGQVKKGYRIEIRDCGVLG 170
               SCOP domains d3k2ca_   A: automated matches                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........--....eeeeeee..eeeeeeeeee....hhhhhhhhhhhhhh..........eeeee...eeee................................eeee...........eeee...hhhhh....eeeeeeehhhhhhhhhh.............eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------CSA_PPIASE_2  PDB: A:10-168 UniProt: 10-168                                                                                                                    -- PROSITE (1)
                PROSITE (2) --------------------------------------------------------CSA_PPIASE_1      ------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k2c A  -5 TQGPGSMA--ASGNVYFDVYANEESLGRIVMKLEDDIVPKTAKNFRTLCERPKGEGYKGSTFHRIIPGFMVQGGDYTAHNGTGGRSIYGEKFPDENFELKHTKEGILSMANCGAHTNGSQFFITLGKTQWLDEKHVVFGEVVEGMDVVHKIAKYGSESGQVKKGYRIEIRDCGVLG 170
                                   | -|       14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164      
                                   2  5

Chain B from PDB  Type:PROTEIN  Length:173
 aligned with CYPH_ENCCU | Q8SRE1 from UniProtKB/Swiss-Prot  Length:172

    Alignment length:175
                                  1                                                                                                                                                                        
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164     
           CYPH_ENCCU     - ------MAKEASGNVYFDVYANEESLGRIVMKLEDDIVPKTAKNFRTLCERPKGEGYKGSTFHRIIPGFMVQGGDYTAHNGTGGRSIYGEKFPDENFELKHTKEGILSMANCGAHTNGSQFFITLGKTQWLDEKHVVFGEVVEGMDVVHKIAKYGSESGQVKKGYRIEIRDCGVL 169
               SCOP domains d3k2cb_   B: automated matches                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........--....eeeeeee..eeeeeeeeee....hhhhhhhhhhhhhh..........eeeee...eeee................................eeee...........eeee...hhhhh....eeeeeeehhhhhhhhhh.............eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------CSA_PPIASE_2  PDB: B:10-168 UniProt: 10-168                                                                                                                    - PROSITE (1)
                PROSITE (2) --------------------------------------------------------CSA_PPIASE_1      ----------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k2c B  -5 TQGPGSMA--ASGNVYFDVYANEESLGRIVMKLEDDIVPKTAKNFRTLCERPKGEGYKGSTFHRIIPGFMVQGGDYTAHNGTGGRSIYGEKFPDENFELKHTKEGILSMANCGAHTNGSQFFITLGKTQWLDEKHVVFGEVVEGMDVVHKIAKYGSESGQVKKGYRIEIRDCGVL 169
                                   | -|       14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164     
                                   2  5

Chain C from PDB  Type:PROTEIN  Length:178
 aligned with CYPH_ENCCU | Q8SRE1 from UniProtKB/Swiss-Prot  Length:172

    Alignment length:178
                             1     7      8                                                                                                                                                                   
                             |     | -    |   13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163        
           CYPH_ENCCU     - -MAKEASG------NVYFDVYANEESLGRIVMKLEDDIVPKTAKNFRTLCERPKGEGYKGSTFHRIIPGFMVQGGDYTAHNGTGGRSIYGEKFPDENFELKHTKEGILSMANCGAHTNGSQFFITLGKTQWLDEKHVVFGEVVEGMDVVHKIAKYGSESGQVKKGYRIEIRDCGVLGS 171
               SCOP domains d3k2cc_ C: automated matches                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh.........eeeeeee..eeeeeeeeee....hhhhhhhhhhhhhh..........eeeee...eeee................................eeee...........eeee...hhhhh....eeeeeeehhhhhhhhhh.............eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------CSA_PPIASE_2  PDB: C:10-168 UniProt: 10-168                                                                                                                    --- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------CSA_PPIASE_1      ------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k2c C -10 TLEAQTQGPGSMAGNVYFDVYANEESLGRIVMKLEDDIVPKTAKNFRTLCERPKGEGYKGSTFHRIIPGFMVQGGDYTAHNGTGGRSIYGEKFPDENFELKHTKEGILSMANCGAHTNGSQFFITLGKTQWLDEKHVVFGEVVEGMDVVHKIAKYGSESGQVKKGYRIEIRDCGVLGS 171
                                    -1  ||    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163        
                                        2|                                                                                                                                                                    
                                         7

Chain D from PDB  Type:PROTEIN  Length:178
 aligned with CYPH_ENCCU | Q8SRE1 from UniProtKB/Swiss-Prot  Length:172

    Alignment length:178
                             1     7      8                                                                                                                                                                   
                             |     | -    |   13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163        
           CYPH_ENCCU     - -MAKEASG------NVYFDVYANEESLGRIVMKLEDDIVPKTAKNFRTLCERPKGEGYKGSTFHRIIPGFMVQGGDYTAHNGTGGRSIYGEKFPDENFELKHTKEGILSMANCGAHTNGSQFFITLGKTQWLDEKHVVFGEVVEGMDVVHKIAKYGSESGQVKKGYRIEIRDCGVLGS 171
               SCOP domains d3k2cd_ D: automated matches                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------Pro_isomerase-3k2cD01 D:10-168                                                                                                                                 --- Pfam domains (1)
           Pfam domains (2) ----------------Pro_isomerase-3k2cD02 D:10-168                                                                                                                                 --- Pfam domains (2)
           Pfam domains (3) ----------------Pro_isomerase-3k2cD03 D:10-168                                                                                                                                 --- Pfam domains (3)
           Pfam domains (4) ----------------Pro_isomerase-3k2cD04 D:10-168                                                                                                                                 --- Pfam domains (4)
         Sec.struct. author hhhhhh.........eeeeeee..eeeeeeeeee....hhhhhhhhhhhhhh..........eeeee...eeee................................eeee...........eeee...hhhhh....eeeeeeehhhhhhhhhh.............eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------CSA_PPIASE_2  PDB: D:10-168 UniProt: 10-168                                                                                                                    --- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------CSA_PPIASE_1      ------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k2c D -10 TLEAQTQGPGSMAGNVYFDVYANEESLGRIVMKLEDDIVPKTAKNFRTLCERPKGEGYKGSTFHRIIPGFMVQGGDYTAHNGTGGRSIYGEKFPDENFELKHTKEGILSMANCGAHTNGSQFFITLGKTQWLDEKHVVFGEVVEGMDVVHKIAKYGSESGQVKKGYRIEIRDCGVLGS 171
                                    -1  ||    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163        
                                        2|                                                                                                                                                                    
                                         7

Legend:		→ Mismatch	(orange background)
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	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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Cyclophilin-like (169)

Superfamily: Cyclophilin-like (169)

Family: Cyclophilin (peptidylprolyl isomerase) (160)

Protein domain: automated matches (38)

Fungus (Encephalitozoon cuniculi) [TaxId: 6035] (1)

1a	d3k2ca_	A:
1b	d3k2cb_	B:
1c	d3k2cc_	C:
1d	d3k2cd_	D:

(no "CATH Domain" information available for 3K2C)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Cyclophil-like (65)

Family: Pro_isomerase (53)

Encephalitozoon cuniculi (Microsporidian parasite) (1)

1a	Pro_isomerase-3k2cD01	D:10-168
1b	Pro_isomerase-3k2cD02	D:10-168
1c	Pro_isomerase-3k2cD03	D:10-168
1d	Pro_isomerase-3k2cD04	D:10-168

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (CYPH_ENCCU | Q8SRE1)

molecular function
	GO:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
	GO:0003755	peptidyl-prolyl cis-trans isomerase activity	Catalysis of the reaction: peptidyl-proline (omega=180) = peptidyl-proline (omega=0).
biological process
	GO:0006457	protein folding	The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
	GO:0000413	protein peptidyl-prolyl isomerization	The modification of a protein by cis-trans isomerization of a proline residue.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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Ligands, Modified Residues, Ions (3, 6)

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