3CKD - JenaLib

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF THE SHIGELLA TYPE III EFFECTOR IPAH

Authors :   R. Lam, A. U. Singer, M. E. Cuff, T. Skarina, O. Kagan, R. Dileo, A. M. Edwa A. Joachimiak, A. Savchenko, Midwest Center For Structural Geno (Mcsg)

Date :   14 Mar 08 (Deposition) - 25 Mar 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.65

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

Keywords :   E3 Ubiquitin Ligase, Helical, Type Iii Effector, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. U. Singer, J. R. Rohde, R. Lam, T. Skarina, O. Kagan, R. Dileo, N. Y. Chirgadze, M. E. Cuff, A. Joachimiak, M. Tyers, P. J. Sansonetti, C. Parsot, A. Savchenko
Structure Of The Shigella T3Ss Effector Ipah Defines A New Class Of E3 Ubiquitin Ligases.
Nat. Struct. Mol. Biol. V. 15 1293 2008
PubMed-ID: 18997778 | Reference-DOI: 10.1038/NSMB.1511

Molecule 1 - INVASION PLASMID ANTIGEN, SECRETED BY THE MXI-SPA SECRETION MACHINERY
	Chains	:	A, B, C
	EC Number	:	6.3.2.19
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	P15-TV-LIC
	Expression System Strain	:	BL21-GOLD(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	IPAH1.4, CP0265
	Organism Scientific	:	SHIGELLA FLEXNERI 2A STR. 301
	Organism Taxid	:	198214
	Strain	:	301 / SEROTYPE 2A

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 21)

No.	Name	Count	Type	Full Name
1	GOL	3	Ligand/Ion	GLYCEROL
2	MSE	15	Mod. Amino Acid	SELENOMETHIONINE
3	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
4	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 5)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL
2	MSE	5	Mod. Amino Acid	SELENOMETHIONINE
3	PEG	-1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
4	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 6)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL
2	MSE	5	Mod. Amino Acid	SELENOMETHIONINE
3	PEG	-1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
4	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 3 (4, 10)

No.	Name	Count	Type	Full Name
1	GOL	3	Ligand/Ion	GLYCEROL
2	MSE	5	Mod. Amino Acid	SELENOMETHIONINE
3	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
4	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG C:521 , GLN C:552	BINDING SITE FOR RESIDUE SO4 C 600
2	AC2	SOFTWARE	ARG B:521 , GLU B:548 , GLN B:552	BINDING SITE FOR RESIDUE SO4 B 601
3	AC3	SOFTWARE	SER C:402 , ARG C:405 , ARG C:409	BINDING SITE FOR RESIDUE GOL C 602
4	AC4	SOFTWARE	SER C:350 , ALA C:351	BINDING SITE FOR RESIDUE GOL C 603
5	AC5	SOFTWARE	THR C:482 , ARG C:555	BINDING SITE FOR RESIDUE GOL C 604
6	AC6	SOFTWARE	GLY C:398 , LEU C:401 , ARG C:565	BINDING SITE FOR RESIDUE PEG C 605

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

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

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

(no "PROSITE Motif" information available for 3CKD)

(no "Exon" information available for 3CKD)

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:262
 aligned with IPA7_SHIFL | P18014 from UniProtKB/Swiss-Prot  Length:565

    Alignment length:282
                                   282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552  
           IPA7_SHIFL   273 PLADAVTAWFPENKQSDVSQIWHAFEHEEHANTFSAFLDRLSDTVSARNTSGFREQVAAWLEKLSASAELRQQSFAVAADATESCEDRVALTWNNLRKTLLVHQASEGLFDNDTGALLSLGREMFRLEILEDIARDKVRTLHFVDEIEVYLAFQTMLAEKLQLSTAVKEMRFYGVSGVTANDLRTAEAMVRSREENEFTDWFSLWGPWHAVLKRTEADRWAQAEEQKYEMLENEYSQRVADRLKASGLSGDADAEREAGAQVMRETEQQIYRQLTDEVLALR 554
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3ckdA01 A:284-3   64 Shigella T3SS effector        IpaH domain                   3ckdA02 A:365-498 Shigella T3SS effector IpaH defines                                                                                 3ckdA03 A:499-565  [code=1.20.58.90, no name defined]               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhh.......---...hhhhh...hhhhhhhhhhhhhh.-------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh......----------.....hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ckd A 284 SLADAVTAWFPENKQ---SQIWHAFEHEEHANTFSAFLDRLSDT-------GFREQVAAWLEKLSASAELRQQSFAVAADATESCEDRVALTWNNLRKTLLVHQASEGLFDNDTGALLSLGREmFRLEILEDIARDKVRTLHFVDEIEVYLAFQTmLAEKLQL----------GVSGVTANDLRTAEAmVRSREENEFTDWFSLWGPWHAVLKRTEADRWAQAEEQKYEmLENEYSQRVADRLKASGLSGDADAEREAGAQVmRETEQQIYRQLTDEVLALR 565
                                   293    |  303       313       323   |     - |     343       353       363       373       383       393       403   |   413       423       433     | 443  |      -   |   463       473       483       493       503       513       523       533       543  |    553       563  
                                        298 302                      327     335                                                                     407-MSE                         439-MSE446        457            472-MSE                                  513-MSE                          546-MSE

Chain B from PDB  Type:PROTEIN  Length:244
 aligned with IPA7_SHIFL | P18014 from UniProtKB/Swiss-Prot  Length:565

    Alignment length:281
                                   283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553 
           IPA7_SHIFL   274 LADAVTAWFPENKQSDVSQIWHAFEHEEHANTFSAFLDRLSDTVSARNTSGFREQVAAWLEKLSASAELRQQSFAVAADATESCEDRVALTWNNLRKTLLVHQASEGLFDNDTGALLSLGREMFRLEILEDIARDKVRTLHFVDEIEVYLAFQTMLAEKLQLSTAVKEMRFYGVSGVTANDLRTAEAMVRSREENEFTDWFSLWGPWHAVLKRTEADRWAQAEEQKYEMLENEYSQRVADRLKASGLSGDADAEREAGAQVMRETEQQIYRQLTDEVLALR 554
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3ckdB01 B:285-363  Shigella T3SS effector Ip         aH domain                         3ckdB02 B:372-498 Shigella T3SS effector IpaH defi       nes                                                                   3ckdB03 B:499-565  [code=1.20.58.90, no name defined]               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh.........hh-hhh......hhhhhhhhhhhhh...---------hhhhhhhhhhhhhhhhhhhhhhhhh.--------.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh-------hhhhhhhhhhhhhhhhh...------------.hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ckd B 285 LADAVTAWFPENKQSDVS-IWHAFEHEEHANTFSAFLDRLSDTV---------EQVAAWLEKLSASAELRQQSFAVAAD--------VALTWNNLRKTLLVHQASEGLFDNDTGALLSLGREmFRLEILEDIARDKV-------EIEVYLAFQTmLAEKLQLST------------VTANDLRTAEAmVRSREENEFTDWFSLWGPWHAVLKRTEADRWAQAEEQKYEmLENEYSQRVADRLKASGLSGDADAEREAGAQVmRETEQQIYRQLTDEVLALR 565
                                   294       304       314       324   |     -   |   344       354        |-       374       384       394       404  |    414      |  -    |  434    |  444   |     -      |464       474       484       494       504       514       524       534       544 |     554       564 
                                           302 |                     328       338                      363      372                                407-MSE       421     429       439-MSE  448          461        472-MSE                                  513-MSE                          546-MSE               
                                             304

Chain C from PDB  Type:PROTEIN  Length:272
 aligned with IPA7_SHIFL | P18014 from UniProtKB/Swiss-Prot  Length:565

    Alignment length:283
                                   281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551   
           IPA7_SHIFL   272 RPLADAVTAWFPENKQSDVSQIWHAFEHEEHANTFSAFLDRLSDTVSARNTSGFREQVAAWLEKLSASAELRQQSFAVAADATESCEDRVALTWNNLRKTLLVHQASEGLFDNDTGALLSLGREMFRLEILEDIARDKVRTLHFVDEIEVYLAFQTMLAEKLQLSTAVKEMRFYGVSGVTANDLRTAEAMVRSREENEFTDWFSLWGPWHAVLKRTEADRWAQAEEQKYEMLENEYSQRVADRLKASGLSGDADAEREAGAQVMRETEQQIYRQLTDEVLALR 554
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3ckdC01 C:283-364 Shigella T3SS effector IpaH d   omain                           3ckdC02 C:365-498 Shigella T3SS effector IpaH defines                                                                                 3ckdC03 C:499-565  [code=1.20.58.90, no name defined]               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh...---hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...--------.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ckd C 283 HSLADAVTAWFPENKQSDVSQIWHAFEHEEHANTFSAFLDRLSDTVS---TSGFREQVAAWLEKLSASAELRQQSFAVAADATESCEDRVALTWNNLRKTLLVHQASEGLFDNDTGALLSLGREmFRLEILEDIARDKVRTLHFVDEIEVYLAFQTmLAEKLQLST--------GVSGVTANDLRTAEAmVRSREENEFTDWFSLWGPWHAVLKRTEADRWAQAEEQKYEmLENEYSQRVADRLKASGLSGDADAEREAGAQVmRETEQQIYRQLTDEVLALR 565
                                   292       302       312       322      |  -|      342       352       362       372       382       392       402    |  412       422       432      |442     |   -    |  462       472       482       492       502       512|      522       532       542   |   552       562   
                                                                        329 333                                                                       407-MSE                         439-MSE  448      457            472-MSE                                  513-MSE                          546-MSE

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 '\|'

(no "SCOP Domain" information available for 3CKD)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Methane Monooxygenase Hydroxylase; Chain G, domain 1 (192)

Homologous Superfamily: [code=1.20.58.90, no name defined] (8)

301 (Shigella flexneri 2a str) (1)

1a	3ckdA03	A:499-565
1b	3ckdB03	B:499-565
1c	3ckdC03	C:499-565

Homologous Superfamily: Shigella T3SS effector IpaH defines (1)

301 (Shigella flexneri 2a str) (1)

2a	3ckdA02	A:365-498
2b	3ckdC02	C:365-498
2c	3ckdB02	B:372-498

Topology: Substrate Binding Domain Of Dnak; Chain:A; Domain 2 (103)

Homologous Superfamily: Shigella T3SS effector IpaH domain (1)

301 (Shigella flexneri 2a str) (1)

3a	3ckdA01	A:284-364
3b	3ckdB01	B:285-363
3c	3ckdC01	C:283-364

(no "Pfam Domain" information available for 3CKD)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (IPA7_SHIFL | P18014)

molecular function
	GO:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	GO:0004842	ubiquitin-protein transferase activity	Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
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:0016567	protein ubiquitination	The process in which one or more ubiquitin groups are added to a protein.
cellular component
	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:0030430	host cell cytoplasm	The cytoplasm of a host cell.

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Description

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Ligands, Modified Residues, Ions (4, 21)

Sites (6, 6)

SS Bonds (0, 0)

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