1FD9 - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE MACROPHAGE INFECTIVITY POTENTIATOR PROTEIN (MIP) A MAJOR VIRULENCE FACTOR FROM LEGIONELLA PNEUMOPHILA

Authors :   A. Riboldi-Tunnicliffe, S. Jessen, B. Konig, J. Rahfeld, J Hacker, G. R. Hilgenfeld

Date :   20 Jul 00 (Deposition) - 25 Jul 01 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.41

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Fkbp Domain, Long Alpha Helix, Dimerisation Via Helical Interactions, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Riboldi-Tunnicliffe, B. Konig, S. Jessen, M. S. Weiss, J. Rahfeld, J. Hacker, G. Fischer, R. Hilgenfeld
Crystal Structure Of Mip, A Prolylisomerase From Legionella Pneumophila
Nat. Struct. Biol. V. 8 779 2001
PubMed-ID: 11524681 | Reference-DOI: 10.1038/NSB0901-779
(for further references see the PDB file header)

Molecule 1 - PROTEIN (MACROPHAGE INFECTIVITY POTENTIATOR PROTEIN)
	Chains	:	A
	EC Number	:	5.2.1.8
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PBLL106
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	LEGIONELLA PNEUMOPHILA
	Organism Taxid	:	446
	Synonym	:	MIP, PEPTIDYL-PROLYL CIS-TRANS ISOMERASE, PPIASE, ROTAMASE

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:130 , HOH A:404 , HOH A:405 , HOH A:406	BINDING SITE FOR RESIDUE ZN A 401
2	AC2	SOFTWARE	GLU A:164 , HIS A:205 , HOH A:403 , HOH A:406	BINDING SITE FOR RESIDUE ZN A 402

(no "SS Bond" information available for 1FD9)

(no "Cis Peptide Bond" information available for 1FD9)

(no "SAP(SNP)/Variant" information available for 1FD9)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FKBP_PPIASE	PS50059	FKBP-type peptidyl-prolyl cis-trans isomerase domain profile.	MIP_LEGPC	144-230	1	A:124-210
				MIP_LEGPH	144-230	1	A:124-210
				MIP_LEGPN	144-230	1	A:124-210

Biological Unit 1 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FKBP_PPIASE	PS50059	FKBP-type peptidyl-prolyl cis-trans isomerase domain profile.	MIP_LEGPC	144-230	2	A:124-210
				MIP_LEGPH	144-230	2	A:124-210
				MIP_LEGPN	144-230	2	A:124-210

(no "Exon" information available for 1FD9)

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:204
 aligned with MIP_LEGPC | A5IGB8 from UniProtKB/Swiss-Prot  Length:233

    Alignment length:204
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228    
            MIP_LEGPC    29 TDKDKLSYSIGADLGKNFKNQGIDVNPEAMAKGMQDAMSGAQLALTEQQMKDVLNKFQKDLMAKRTAEFNKKADENKVKGEAFLTENKNKPGVVVLPSGLQYKVINAGNGVKPGKSDTVTVEYTGRLIDGTVFDSTEKTGKPATFQVSQVIPGWTEALQLMPAGSTWEIYVPSGLAYGPRSVGGPIGPNETLIFKIHLISVKKS 232
               SCOP domains d1fd9a_ A: Macrophage infectivity potentiator protein (MIP)                                                                                                                                                  SCOP domains
               CATH domains 1fd9A02 A:9-106 Helix hairpin bin                                                                 1fd9A01 A:107-212  [code=3.10.50.40, no name defined]                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee.....eeeeee...........eeeeeeeeee....eeeehhhhh..eeee.hhhhhhhhhhhh......eeeeeehhhhh...............eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                PROSITE (3) -------------------------------------------------------------------------------------------------------------------FKBP_PPIASE  PDB: A:124-210 UniProt: 144-230                                           -- PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1fd9 A   9 TDKDKLSYSIGADLGKNFKNQGIDVNPEAMAKGMQDAMSGAQLALTEQQMKDVLNKFQKDLMAKRTAEFNKKADENKVKGEAFLTENKNKPGVVVLPSGLQYKVINSGNGVKPGKSDTVTVEYTGRLIDGTVFDSTEKTGKPATFQVSQVIPGWTEALQLMPAGSTWEIYVPSGLAYGPRSVGGPIGPNETLIFKIHLISVKKS 212
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208

Chain A from PDB  Type:PROTEIN  Length:204
 aligned with MIP_LEGPH | Q5ZXE0 from UniProtKB/Swiss-Prot  Length:233

    Alignment length:204
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228    
            MIP_LEGPH    29 TDKDKLSYSIGADLGKNFKNQGIDVNPEAMAKGMQDAMSGAQLALTEQQMKDVLNKFQKDLMAKRTAEFNKKADENKVKGEAFLTENKNKPGVVVLPSGLQYKVINSGNGVKPGKSDTVTVEYTGRLIDGTVFDSTEKTGKPATFQVSQVIPGWTEALQLMPAGSTWEIYVPSGLAYGPRSVGGPIGPNETLIFKIHLISVKKS 232
               SCOP domains d1fd9a_ A: Macrophage infectivity potentiator protein (MIP)                                                                                                                                                  SCOP domains
               CATH domains 1fd9A02 A:9-106 Helix hairpin bin                                                                 1fd9A01 A:107-212  [code=3.10.50.40, no name defined]                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee.....eeeeee...........eeeeeeeeee....eeeehhhhh..eeee.hhhhhhhhhhhh......eeeeeehhhhh...............eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------FKBP_PPIASE  PDB: A:124-210 UniProt: 144-230                                           -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1fd9 A   9 TDKDKLSYSIGADLGKNFKNQGIDVNPEAMAKGMQDAMSGAQLALTEQQMKDVLNKFQKDLMAKRTAEFNKKADENKVKGEAFLTENKNKPGVVVLPSGLQYKVINSGNGVKPGKSDTVTVEYTGRLIDGTVFDSTEKTGKPATFQVSQVIPGWTEALQLMPAGSTWEIYVPSGLAYGPRSVGGPIGPNETLIFKIHLISVKKS 212
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208

Chain A from PDB  Type:PROTEIN  Length:204
 aligned with MIP_LEGPN | Q70YI1 from UniProtKB/Swiss-Prot  Length:233

    Alignment length:204
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228    
            MIP_LEGPN    29 TDKDKLSYSIGADLGKNFKNQGIDVNPEAMAKGMQDAMSGAQLALTEQQMKDVLNKFQKDLMAKRTAEFNKKADENKVKGEAFLTENKNKPGVVVLPSGLQYKVINAGNGVKPGKSDTVTVEYTGRLIDGTVFDSTEKTGKPATFQVSQVIPGWTEALQLMPAGSTWEIYVPSGLAYGPRSVGGPIGPNETLIFKIHLISVKKS 232
               SCOP domains d1fd9a_ A: Macrophage infectivity potentiator protein (MIP)                                                                                                                                                  SCOP domains
               CATH domains 1fd9A02 A:9-106 Helix hairpin bin                                                                 1fd9A01 A:107-212  [code=3.10.50.40, no name defined]                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee.....eeeeee...........eeeeeeeeee....eeeehhhhh..eeee.hhhhhhhhhhhh......eeeeeehhhhh...............eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------FKBP_PPIASE  PDB: A:124-210 UniProt: 144-230                                           -- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1fd9 A   9 TDKDKLSYSIGADLGKNFKNQGIDVNPEAMAKGMQDAMSGAQLALTEQQMKDVLNKFQKDLMAKRTAEFNKKADENKVKGEAFLTENKNKPGVVVLPSGLQYKVINSGNGVKPGKSDTVTVEYTGRLIDGTVFDSTEKTGKPATFQVSQVIPGWTEALQLMPAGSTWEIYVPSGLAYGPRSVGGPIGPNETLIFKIHLISVKKS 212
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: FKBP-like (309)

Superfamily: FKBP-like (198)

Family: FKBP immunophilin/proline isomerase (153)

Protein domain: Macrophage infectivity potentiator protein (MIP) (2)

Legionella pneumophila [TaxId: 446] (1)

d1fd9a_

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: Chitinase A; domain 3 (225)

Homologous Superfamily: [code=3.10.50.40, no name defined] (98)

Legionella pneumophila. Organism_taxid: 446. (1)

1fd9A01

A:107-212

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Helix Hairpins (718)

Homologous Superfamily: Helix hairpin bin (1)

Legionella pneumophila. Organism_taxid: 446. (1)

1fd9A02

A:9-106

(no "Pfam Domain" information available for 1FD9)

Asymmetric Unit(hide GO term definitions)

Chain A (MIP_LEGPC | A5IGB8)

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:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
	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:0009279	cell outer membrane	A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain A (MIP_LEGPH | Q5ZXE0)

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:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
	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:0009279	cell outer membrane	A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain A (MIP_LEGPN | Q70YI1)

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:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
	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:0009279	cell outer membrane	A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Asymmetric Unit
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Biological Unit
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	1fd9
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	MIP_LEGPH \| Q5ZXE0
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	MIP_LEGPN \| Q70YI1
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	MIP_LEGPH \| Q5ZXE0	:	2uz5 2vcd

(no "Related Entries Specified in the PDB File" available for 1FD9)

Description

Compounds

Structural Features

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Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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