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Description

Title :   ATOMIC RESOLUTION CRYSTAL STRUCTURE OF THE PPIASE DOMAIN OF HUMAN CYCLOPHILIN G

Authors :   C. M. Stegmann, G. M. Sheldrick, M. C. Wahl

Date :   06 Apr 09 (Deposition) - 16 Jun 09 (Release) - 27 Apr 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   0.75

Chains :   Asym./Biol. Unit : A

Keywords :   Phosphoprotein, Pre-Mrna Splicing, Alternative Splicing, Nucleus, Rotamase, Isomerase, Cyclosporin, Peptidyl-Prolyl Cis-Trans Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. M. Stegmann, D. Seeliger, G. M. Sheldrick, B. L. De Groot, M. C. Wahl
The Thermodynamic Influence Of Trapped Water Molecules On A Protein-Ligand Interaction
Angew. Chem. Int. Ed. Engl. V. 48 5207 2009
PubMed-ID: 19499554 | Reference-DOI: 10.1002/ANIE.200900481

Compounds

Molecule 1 - PEPTIDYL-PROLYL CIS-TRANS ISOMERASE G
	Chains	:	A
	EC Number	:	5.2.1.8
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PETM-11
	Expression System Strain	:	ROSETTA (DE3) (NOVAGEN)
	Expression System Taxid	:	562
	Fragment	:	PPIASE DOMAIN, RESIDUES 1-177
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CYS63 OXIDIZED TO CYSTEINE SULFONIC ACID
	Synonym	:	CYCLOPHILIN G, CLK-ASSOCIATING RS-CYCLOPHILIN, CASP10, PEPTIDYL-PROLYL ISOMERASE G, PPIASE G, ROTAMASE G, CARS-CYCLOPHILIN, CARS-CYP, SR-CYCLOPHILIN, SR-CYP, SRCYP

Structural Features

Chains, Units

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (2, 3)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	MG	2	Ligand/Ion	MAGNESIUM ION
2	OCS	1	Mod. Amino Acid	CYSTEINESULFONIC ACID

Sites (2, 2)

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:2113 , HOH A:2114 , HOH A:2124 , HOH A:2268 , HOH A:2322 , HOH A:2323	BINDING SITE FOR RESIDUE MG A1001
2	AC2	SOFTWARE	HOH A:2125 , HOH A:2308 , HOH A:2309 , HOH A:2316 , HOH A:2348 , HOH A:2349	BINDING SITE FOR RESIDUE MG A1002

SS Bonds (0, 0)

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

Cis Peptide Bonds (0, 0)

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

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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

PROSITE Motifs (2, 2)

Asymmetric/Biological Unit (2, 2)

	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.	PPIG_HUMAN	11-176	1	A:11-176
2	CSA_PPIASE_1	PS00170	Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature.	PPIG_HUMAN	60-77	1	A:60-77

Exons (7, 7)

Asymmetric/Biological Unit (7, 7)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000260970	1a	ENSE00001387482	chr2:170440850-170441000	151	PPIG_HUMAN	-	0	0	-	-
1.3	ENST00000260970	3	ENSE00001368659	chr2:170460152-170460204	53	PPIG_HUMAN	-	0	0	-	-
1.4a	ENST00000260970	4a	ENSE00002155403	chr2:170460536-170460612	77	PPIG_HUMAN	1-21	21	1	A:6-21	16
1.5	ENST00000260970	5	ENSE00001740210	chr2:170460697-170460771	75	PPIG_HUMAN	21-46	26	1	A:21-46	26
1.6b	ENST00000260970	6b	ENSE00000934245	chr2:170462549-170462656	108	PPIG_HUMAN	46-82	37	1	A:46-82	37
1.7	ENST00000260970	7	ENSE00000934246	chr2:170463614-170463658	45	PPIG_HUMAN	82-97	16	1	A:82-97	16
1.8	ENST00000260970	8	ENSE00000782027	chr2:170465181-170465268	88	PPIG_HUMAN	97-126	30	1	A:97-126	30
1.9	ENST00000260970	9	ENSE00000934247	chr2:170470974-170471003	30	PPIG_HUMAN	126-136	11	1	A:126-136	11
1.10	ENST00000260970	10	ENSE00001016133	chr2:170471095-170471234	140	PPIG_HUMAN	136-183	48	1	A:136-177	42
1.11d	ENST00000260970	11d	ENSE00001016132	chr2:170487284-170487497	214	PPIG_HUMAN	183-254	72	0	-	-
1.12c	ENST00000260970	12c	ENSE00000934248	chr2:170488276-170488443	168	PPIG_HUMAN	254-310	57	0	-	-
1.13a	ENST00000260970	13a	ENSE00000782033	chr2:170489670-170489757	88	PPIG_HUMAN	310-339	30	0	-	-
1.14a	ENST00000260970	14a	ENSE00000782034	chr2:170492602-170492738	137	PPIG_HUMAN	340-385	46	0	-	-
1.15e	ENST00000260970	15e	ENSE00001824624	chr2:170492923-170497916	4994	PPIG_HUMAN	385-754	370	0	-	-

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:172
 aligned with PPIG_HUMAN | Q13427 from UniProtKB/Swiss-Prot  Length:754

    Alignment length:172
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175  
           PPIG_HUMAN     6 QRPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTGKSTQKPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNKEFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGEL 177
               SCOP domains d2wfia_ A: automated matches                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----Pro_isomerase-2wfiA01 A:11-176                                                                                                                                        - Pfam domains
         Sec.struct. author ...eeeeeeee..eeeeeeeeee....hhhhhhhhhhhhhh..................eeeee...eeee................................eeee...........eeee...hhhhh....eeeeeeehhhhhhhhhh............eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----CSA_PPIASE_2  PDB: A:11-176 UniProt: 11-176                                                                                                                           - PROSITE (1)
                PROSITE (2) ------------------------------------------------------CSA_PPIASE_1      ---------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.4a       ------------------------Exon 1.6b  PDB: A:46-82              --------------Exon 1.8  PDB: A:97-126       ---------Exon 1.10  PDB: A:136-177 UniProt: 136-183 Transcript 1 (1)
           Transcript 1 (2) ---------------Exon 1.5  PDB: A:21-46    -----------------------------------Exon 1.7        ----------------------------Exon 1.9   ----------------------------------------- Transcript 1 (2)
                 2wfi A   6 QRPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTGKSTQKPLHYKScLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNKEFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGEL 177
                                    15        25        35        45        55       |65        75        85        95       105       115       125       135       145       155       165       175  
                                                                                    63-OCS

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 (1, 1)

Asymmetric/Biological 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)

Human (Homo sapiens) [TaxId: 9606] (14)

d2wfia_

CATH Domains (0, 0)

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

Pfam Domains (1, 1)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Cyclophil-like (65)

Family: Pro_isomerase (53)

Homo sapiens (Human) (42)

Pro_isomerase-2wfiA01

A:11-176

Gene Ontology (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PPIG_HUMAN | Q13427)

molecular function
	GO:0016018	cyclosporin A binding	Interacting selectively and non-covalently with cyclosporin A, a cyclic undecapeptide that contains several N-methylated and unusual amino acids.
	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:0042277	peptide binding	Interacting selectively and non-covalently with peptides, any of a group of organic compounds comprising two or more amino acids linked by peptide bonds.
	GO:0003755	peptidyl-prolyl cis-trans isomerase activity	Catalysis of the reaction: peptidyl-proline (omega=180) = peptidyl-proline (omega=0).
	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).
biological process
	GO:0008380	RNA splicing	The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
	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.
	GO:0016363	nuclear matrix	The dense fibrillar network lying on the inner side of the nuclear membrane.
	GO:0016607	nuclear speck	A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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.

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Related Entries

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UniProtKB/Swiss-Prot
	PPIG_HUMAN \| Q13427	:	2gw2 2wfj

Related Entries Specified in the PDB File

2gw2	CRYSTAL STRUCTURE OF THE PEPTIDYL-PROLYL ISOMERASE DOMAINOF HUMAN CYCLOPHILIN G
2wfj	ATOMIC RESOLUTION CRYSTAL STRUCTURE OF THE PPIASE DOMAIN OF HUMAN CYCLOPHILIN G IN COMPLEX WITH CYCLOSPORIN A.