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Title :   CRYSTAL STRUCTURE OF YOPM-LEUCINE RICH EFFECTOR PROTEIN FROM YERSINIA PESTIS

Authors :   A. G. Evdokimov, D. E. Anderson, K. M. Routzahn, D. S. Waugh

Date :   28 Nov 00 (Deposition) - 10 Oct 01 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.35

Chains :   Asym. Unit : A
Biol. Unit 1: A  (4x)

Keywords :   Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. G. Evdokimov, D. E. Anderson, K. M. Routzahn, D. S. Waugh
Unusual Molecular Architecture Of The Yersinia Pestis Cytotoxin Yopm: A Leucine-Rich Repeat Protein With The Shortest Repeating Unit.
J. Mol. Biol. V. 312 807 2001
PubMed-ID: 11575934 | Reference-DOI: 10.1006/JMBI.2001.4973

Molecule 1 - OUTER PROTEIN YOPM
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Strain	:	BL21DE3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	MODIFIED PMAL
	Gene	:	YOPM
	Organism Scientific	:	YERSINIA PESTIS
	Organism Taxid	:	632

		1
Asymmetric Unit	:	A
Biological Unit 1 (4x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 19)

No.	Name	Count	Type	Full Name
1	ACT	9	Ligand/Ion	ACETATE ION
2	CA	2	Ligand/Ion	CALCIUM ION
3	HG	8	Ligand/Ion	MERCURY (II) ION

Biological Unit 1 (1, 36)

No.	Name	Count	Type	Full Name
1	ACT	36	Ligand/Ion	ACETATE ION
2	CA	-1	Ligand/Ion	CALCIUM ION
3	HG	-1	Ligand/Ion	MERCURY (II) ION

Asymmetric Unit (19, 19)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:381 , LEU A:382 , ARG A:383 , MET A:384 , ASN A:385	BINDING SITE FOR RESIDUE ACT A 1001
02	AC2	SOFTWARE	VAL A:221 , GLY A:223 , TYR A:243 , ASP A:245 , ACT A:1006	BINDING SITE FOR RESIDUE ACT A 1002
03	AC3	SOFTWARE	THR A:251 , LEU A:252 , ASP A:271 , LEU A:272 , PRO A:273 , HOH A:3091	BINDING SITE FOR RESIDUE ACT A 1003
04	AC4	SOFTWARE	TRP A:46 , ASN A:49 , ARG A:58 , SER A:85 , HOH A:3127	BINDING SITE FOR RESIDUE ACT A 1004
05	AC5	SOFTWARE	ASP A:128 , LEU A:129 , PRO A:147 , GLU A:148 , LEU A:149 , ASN A:151 , HOH A:3218	BINDING SITE FOR RESIDUE ACT A 1005
06	AC6	SOFTWARE	ASP A:245 , ASN A:246 , ASN A:263 , ACT A:1002 , ACT A:1009 , HOH A:3047	BINDING SITE FOR RESIDUE ACT A 1006
07	AC7	SOFTWARE	TYR A:40 , ARG A:66 , PRO A:257 , PRO A:276 , GLN A:277 , SER A:278 , HOH A:3044 , HOH A:3069	BINDING SITE FOR RESIDUE ACT A 1007
08	AC8	SOFTWARE	LEU A:292 , SER A:293 , GLU A:294 , LEU A:295 , LEU A:312 , CYS A:313 , ASP A:314 , LEU A:315	BINDING SITE FOR RESIDUE ACT A 1008
09	AC9	SOFTWARE	ACT A:1006 , HOH A:3132	BINDING SITE FOR RESIDUE ACT A 1009
10	BC1	SOFTWARE	ASN A:246 , ASP A:266 , ASN A:326 , HOH A:3110 , HOH A:3112 , HOH A:3164	BINDING SITE FOR RESIDUE CA A 2001
11	BC2	SOFTWARE	ASP A:266 , ASN A:307 , GLU A:308 , HOH A:3111 , HOH A:3113 , HOH A:3114 , HOH A:3115	BINDING SITE FOR RESIDUE CA A 2002
12	BC3	SOFTWARE	CYS A:68 , GLN A:72 , ALA A:73 , PRO A:90	BINDING SITE FOR RESIDUE HG A 2003
13	BC4	SOFTWARE	GLN A:72 , PRO A:91 , HIS A:92	BINDING SITE FOR RESIDUE HG A 2004
14	BC5	SOFTWARE	SER A:206 , ILE A:330 , HIS A:348	BINDING SITE FOR RESIDUE HG A 2005
15	BC6	SOFTWARE	HOH A:3064	BINDING SITE FOR RESIDUE HG A 2006
16	BC7	SOFTWARE	HIS A:363 , GLU A:365	BINDING SITE FOR RESIDUE HG A 2007
17	BC8	SOFTWARE	ASN A:224 , HIS A:348 , PRO A:368	BINDING SITE FOR RESIDUE HG A 2008
18	BC9	SOFTWARE	CYS A:100	BINDING SITE FOR RESIDUE HG A 2009
19	CC1	SOFTWARE	CYS A:100	BINDING SITE FOR RESIDUE HG A 2010

(no "SS Bond" information available for 1G9U)

(no "Cis Peptide Bond" information available for 1G9U)

(no "SAP(SNP)/Variant" information available for 1G9U)

Asymmetric Unit (1, 11)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LRR	PS51450	Leucine-rich repeat profile.	YOPM_YERPE	132-153 92-113 174-195 154-173 216-237 196-215 258-279 238-257 318-339 298-317 358-379	11	A:132-153 A:92-113 A:174-195 A:154-173 A:216-237 A:196-215 A:258-279 A:238-257 A:318-339 A:298-317 A:358-379

Biological Unit 1 (1, 44)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	LRR	PS51450	Leucine-rich repeat profile.	YOPM_YERPE	132-153 92-113 174-195 154-173 216-237 196-215 258-279 238-257 318-339 298-317 358-379	44	A:132-153 A:92-113 A:174-195 A:154-173 A:216-237 A:196-215 A:258-279 A:238-257 A:318-339 A:298-317 A:358-379

(no "Exon" information available for 1G9U)

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
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Chain A from PDB  Type:PROTEIN  Length:353
 aligned with YOPM_YERPE | P17778 from UniProtKB/Swiss-Prot  Length:409

    Alignment length:353
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383   
           YOPM_YERPE    34 KSKTEYYNAWSEWERNAPPGNGEQREMAVSRLRDCLDRQAHELELNNLGLSSLPELPPHLESLVASCNSLTELPELPQSLKSLLVDNNNLKALSDLPPLLEYLGVSNNQLEKLPELQNSSFLKIIDVDNNSLKKLPDLPPSLEFIAAGNNQLEELPELQNLPFLTAIYADNNSLKKLPDLPLSLESIVAGNNILEELPELQNLPFLTTIYADNNLLKTLPDLPPSLEALNVRDNYLTDLPELPQSLTFLDVSENIFSGLSELPPNLYYLNASSNEIRSLCDLPPSLEELNVSNNKLIELPALPPRLERLIASFNHLAEVPELPQNLKQLHVEYNPLREFPDIPESVEDLRMNS 386
               SCOP domains d1g9ua_ A: Leucine rich effector protein YopM                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1g9uA00 A:34-386 Ribonuclease Inhibitor                                                                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh..eee.................eee.................eee.................eee..........hhhhh....eee.................eee...................eee.................eee...................eee.................eee.................eee.................eee.................eee.................eee.................eee.................eee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------LRR  PDB: A:92-113    ------------------LRR  PDB: A:132-153   LRR  PDB: A:154-173 LRR  PDB: A:174-195   LRR  PDB: A:196-215 LRR  PDB: A:216-237   LRR  PDB: A:238-257 LRR  PDB: A:258-279   ------------------LRR  PDB: A:298-317 LRR  PDB: A:318-339   ------------------LRR  PDB: A:358-379   ------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1g9u A  34 KSKTEYYNAWSEWERNAPPGNGEQREMAVSRLRDCLDRQAHELELNNLGLSSLPELPPHLESLVASCNSLTELPELPQSLKSLLVDNNNLKALSDLPPLLEYLGVSNNQLEKLPELQNSSFLKIIDVDNNSLKKLPDLPPSLEFIAAGNNQLEELPELQNLPFLTAIYADNNSLKKLPDLPLSLESIVAGNNILEELPELQNLPFLTTIYADNNLLKTLPDLPPSLEALNVRDNYLTDLPELPQSLTFLDVSENIFSGLSELPPNLYYLNASSNEIRSLCDLPPSLEELNVSNNKLIELPALPPRLERLIASFNHLAEVPELPQNLKQLHVEYNPLREFPDIPESVEDLRMNS 386
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383

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(

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Folds(

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Superfamilies( (-)

)

Families(

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Protein Domains( (-)

)

Organisms( (-)

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Class: Alpha and beta proteins (a/b) (23833)

Fold: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) (112)

Superfamily: L domain-like (93)

Family: Leucine rich effector protein YopM (2)

Protein domain: Leucine rich effector protein YopM (2)

Yersinia pestis [TaxId: 632] (2)

d1g9ua_

Asymmetric Unit

Classes(

)

Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Horseshoe (92)

Topology: Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) (73)

Homologous Superfamily: Ribonuclease Inhibitor (73)

Yersinia pestis. Organism_taxid: 632. (2)

1g9uA00

A:34-386

(no "Pfam Domain" information available for 1G9U)

Asymmetric Unit(hide GO term definitions)

Chain A (YOPM_YERPE | P17778)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
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:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	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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	YOPM_YERPE \| P17778	:	1jl5

1d0b	SHORT BACTERIAL LRR
1dfj	MAMMALIAN LRR

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 19)

Sites (19, 19)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 11)

Exons (0, 0)

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