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Description

Title :   CRYSTAL STRUCTURE OF THE PEPTIDYL-PROLYL ISOMERASE DOMAIN OF HUMAN CYCLOPHILIN G

Authors :   G. Bernstein, W. Tempel, T. Davis, E. M. Newman, P. J. Finerty Jr. , F. Mackenzie, J. Weigelt, M. Sundstrom, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, S. Dhe-Paganon, Structural Genomics Consortium (Sgc)

Date :   03 May 06 (Deposition) - 13 Jun 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym./Biol. Unit : A

Keywords :   Mutation, Surface Mutagenesis, Mutant, Ppiase, Domain, Cis- Trans Isomerization, Peptidyl-Prolyl Isomerase, Protein Folding, Structural Genomics, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Bernstein, W. Tempel, T. Davis, E. M. Newman, P. J. Finerty Jr. , F. Mackenzie, J. Weigelt, M. Sundstrom, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, S. Dhe-Paganon, Structural Genomics Consortium (Sgc)
Crystal Structure Of The Peptidyl-Prolyl Isomerase Domain Of Human Cyclophilin G
To Be Published
PubMed: search
(for further references see the PDB file header)

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	:	PET28A
	Expression System Strain	:	BL21(DE3)CODON PLUS RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 1-179
	Gene	:	PPIG
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PEPTIDYL-PROLYL ISOMERASE G, PPIASE G, ROTAMASE G, CYCLOPHILIN G, CLK-ASSOCIATING RS-CYCLOPHILIN, CARS- CYCLOPHILIN, CARS-CYP, SR-CYCLOPHILIN, SRCYP, SR-CYP, CASP10

Structural Features

Chains, Units

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (1, 4)

Asymmetric/Biological Unit (1, 4)

No.	Name	Count	Type	Full Name
1	UNX	4	Ligand/Ion	UNKNOWN ATOM OR ION

Sites (4, 4)

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:152	BINDING SITE FOR RESIDUE UNX A 1001
2	AC2	SOFTWARE	HIS A:59 , TYR A:60 , LYS A:61 , CYS A:63 , PHE A:79	BINDING SITE FOR RESIDUE UNX A 1002
3	AC3	SOFTWARE	ALA A:113 , ASN A:114 , HIS A:138	BINDING SITE FOR RESIDUE UNX A 1003
4	AC4	SOFTWARE	GLU A:38 , LYS A:48 , HOH A:210	BINDING SITE FOR RESIDUE UNX A 1004

SS Bonds (0, 0)

(no "SS Bond" information available for 2GW2)

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 2GW2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 2GW2)

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:7-21	15
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:136-179	44
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:173
 aligned with PPIG_HUMAN | Q13427 from UniProtKB/Swiss-Prot  Length:754

    Alignment length:173
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176   
           PPIG_HUMAN     7 RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTGKSTQKPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNKEFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGELIP 179
               SCOP domains d2gw2a_ A: automated matches                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee..eeeeeeeeee....hhhhhhhhhhhhhh....................eee...eeee................................eeee...........eeee...hhhhh....eeeeeeehhhhhhhhhh............eeeeeeeee.. 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:136-179 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)
                 2gw2 A   7 RPRCFFDIAINNQPAGRVVFELFSDVCPKTCENFRCLCTGEKGTGKSTQKPLHYKSCLFHRVVKDFMVQGGDFSEGNGRGGESIYGGFFEDESFAVKHNAAFLLSMANRGKDTNGSQFFITTKPTPHLDGHHVVFGQVISGQEVVREIENQKTDAASKPFAEVRILSCGELIP 179
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176

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)

d2gw2a_

CATH Domains (0, 0)

(no "CATH Domain" information available for 2GW2)

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 2GW2)

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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	PPIG_HUMAN \| Q13427	:	2wfi 2wfj

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