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Title :   X-RAY STRUCTURE OF YDII_ECOLI NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ER29.

Authors :   A. P. Kuzin, W. Edstrom, S. M. Vorobiev, I. Lee, F. Forouhar, L. Ma, Y. Chiang, X. Rong, T. B. Acton, G. T. Montelione, J. F. Hunt, L. Tong, Northeast Structural Genomics Consortium (Nesg)

Date :   10 Feb 04 (Deposition) - 24 Feb 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Er29, Ydii, Structural Genomics, Psi, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. P. Kuzin, W. Edstrom, S. M. Vorobiev, I. Lee, F. Forouhar, L. Ma, Y. Chiang, X. Rong, T. B. Acton, G. T. Montelione, J. F. Hunt, L. Tong
X-Ray Structure Of Ydii_ecoli Northeast Structural Genomics Consortium Target Er29
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - HYPOTHETICAL PROTEIN YDII
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET21D
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	YDII, B1686
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 20)

No.	Name	Count	Type	Full Name
1	MSE	16	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS D:106 , GLY D:108 , SER D:109 , ARG D:110 , HIS D:111	BINDING SITE FOR RESIDUE SO4 D 801
2	AC2	SOFTWARE	HIS B:106 , GLY B:108 , SER B:109 , ARG B:110 , HIS B:111 , HOH B:574	BINDING SITE FOR RESIDUE SO4 B 802
3	AC3	SOFTWARE	HIS C:106 , GLY C:108 , SER C:109 , ARG C:110 , HIS C:111	BINDING SITE FOR RESIDUE SO4 C 803
4	AC4	SOFTWARE	HIS A:106 , GLY A:108 , SER A:109 , ARG A:110 , HIS A:111	BINDING SITE FOR RESIDUE SO4 A 804

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

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

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

(no "PROSITE Motif" information available for 1SBK)

(no "Exon" information available for 1SBK)

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:138
 aligned with MENI_ECOLI | P77781 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:138
                                                                                                                                                                 136  
                                    10        20        30        40        50        60        70        80        90       100       110       120       130     |  
           MENI_ECOLI     1 MIWKRKITLEALNAMGEGNMVGFLDIRFEHIGDDTLEATMPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLCTEGEQKVVGLEINANHVRSAREGRVRGVCKPLHLGSRHQVWQIEIFDEKGRLCCSSRLTTAIL--   -
               SCOP domains d1sbka_ A: Hypothetical protein YdiI                                                                                                       SCOP domains
               CATH domains -1sbkA00 A:2-138  [code=3.10.129.10, no name defined]                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhhhhhhh.hhhhhh..eeeee....eeeeee............hhhhhhhhhhhhhhhhhhhh.....eeeeeeeeeee.......eeeeeeeeeee...eeeeeeeee.....eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1sbk A   1 mIWKRKITLEALNAmGEGNmVGFLDIRFEHIGDDTLEATmPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLCTEGEQKVVGLEINANHVRSAREGRVRGVCKPLHLGSRHQVWQIEIFDEKGRLCCSSRLTTAILLE 138
                            |       10    |   20        30        40        50        60        70        80        90       100       110       120       130        
                            |            15-MSE|                  40-MSE                                                                                              
                            1-MSE             20-MSE

Chain B from PDB  Type:PROTEIN  Length:138
 aligned with MENI_ECOLI | P77781 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:138
                                                                                                                                                                 136  
                                    10        20        30        40        50        60        70        80        90       100       110       120       130     |  
           MENI_ECOLI     1 MIWKRKITLEALNAMGEGNMVGFLDIRFEHIGDDTLEATMPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLCTEGEQKVVGLEINANHVRSAREGRVRGVCKPLHLGSRHQVWQIEIFDEKGRLCCSSRLTTAIL--   -
               SCOP domains d1sbkb_ B: Hypothetical protein YdiI                                                                                                       SCOP domains
               CATH domains -1sbkB00 B:2-138  [code=3.10.129.10, no name defined]                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhhhhhh..hhhhhh..eeeee....eeeeee............hhhhhhhhhhhhhhhhhhhh.....eeeeeeeeeee.......eeeeeeeeeee...eeeeeeeee.....eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1sbk B   1 mIWKRKITLEALNAmGEGNmVGFLDIRFEHIGDDTLEATmPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLCTEGEQKVVGLEINANHVRSAREGRVRGVCKPLHLGSRHQVWQIEIFDEKGRLCCSSRLTTAILLE 138
                            |       10    |   20        30        40        50        60        70        80        90       100       110       120       130        
                            1-MSE        15-MSE|                  40-MSE                                                                                              
                                              20-MSE

Chain C from PDB  Type:PROTEIN  Length:138
 aligned with MENI_ECOLI | P77781 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:138
                                                                                                                                                                 136  
                                    10        20        30        40        50        60        70        80        90       100       110       120       130     |  
           MENI_ECOLI     1 MIWKRKITLEALNAMGEGNMVGFLDIRFEHIGDDTLEATMPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLCTEGEQKVVGLEINANHVRSAREGRVRGVCKPLHLGSRHQVWQIEIFDEKGRLCCSSRLTTAIL--   -
               SCOP domains d1sbkc_ C: Hypothetical protein YdiI                                                                                                       SCOP domains
               CATH domains -1sbkC00 C:2-138  [code=3.10.129.10, no name defined]                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhhhhhh..hhhhhh..eeeee....eeeeee............hhhhhhhhhhhhhhhhhhh......eeeeeeeeeee.......eeeeeeeeeee...eeeeeeeee.....eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1sbk C   1 mIWKRKITLEALNAmGEGNmVGFLDIRFEHIGDDTLEATmPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLCTEGEQKVVGLEINANHVRSAREGRVRGVCKPLHLGSRHQVWQIEIFDEKGRLCCSSRLTTAILLE 138
                            |       10    |   20        30        40        50        60        70        80        90       100       110       120       130        
                            1-MSE        15-MSE|                  40-MSE                                                                                              
                                              20-MSE

Chain D from PDB  Type:PROTEIN  Length:138
 aligned with MENI_ECOLI | P77781 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:138
                                                                                                                                                                 136  
                                    10        20        30        40        50        60        70        80        90       100       110       120       130     |  
           MENI_ECOLI     1 MIWKRKITLEALNAMGEGNMVGFLDIRFEHIGDDTLEATMPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLCTEGEQKVVGLEINANHVRSAREGRVRGVCKPLHLGSRHQVWQIEIFDEKGRLCCSSRLTTAIL--   -
               SCOP domains d1sbkd_ D: Hypothetical protein YdiI                                                                                                       SCOP domains
               CATH domains -1sbkD00 D:2-138  [code=3.10.129.10, no name defined]                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhhhhhh..hhhhhh..eeeee....eeeeee............hhhhhhhhhhhhhhhhhhh......eeeeeeeeeee.......eeeeeeeeeee...eeeeeeeee.....eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1sbk D   1 mIWKRKITLEALNAmGEGNmVGFLDIRFEHIGDDTLEATmPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLCTEGEQKVVGLEINANHVRSAREGRVRGVCKPLHLGSRHQVWQIEIFDEKGRLCCSSRLTTAILLE 138
                            |       10    |   20        30        40        50        60        70        80        90       100       110       120       130        
                            1-MSE        15-MSE|                  40-MSE                                                                                              
                                              20-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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Thioesterase/thiol ester dehydrase-isomerase (151)

Superfamily: Thioesterase/thiol ester dehydrase-isomerase (151)

Family: PaaI/YdiI-like (44)

Protein domain: Hypothetical protein YdiI (3)

Escherichia coli [TaxId: 562] (3)

1a	d1sbka_	A:
1b	d1sbkb_	B:
1c	d1sbkc_	C:
1d	d1sbkd_	D:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: Thiol Ester Dehydrase; Chain A (90)

Homologous Superfamily: [code=3.10.129.10, no name defined] (90)

Escherichia coli. Organism_taxid: 562. (8)

1a	1sbkA00	A:2-138
1b	1sbkB00	B:2-138
1c	1sbkC00	C:2-138
1d	1sbkD00	D:2-138

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (MENI_ECOLI | P77781)

molecular function
	GO:0061522	1,4-dihydroxy-2-naphthoyl-CoA thioesterase activity	Catalysis of the reaction 1,4-dihydroxy-2-naphthoyl-CoA + H2O = 1,4-dihydroxy-2-naphthoate + CoA.
	GO:0016289	CoA hydrolase activity	Catalysis of the reaction: X-CoA + H2O = X + CoA; X may be any group.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0016790	thiolester hydrolase activity	Catalysis of the reaction: RCO-SR' + H2O = RCOOH + HSR'. This reaction is the hydrolysis of a thiolester bond, an ester formed from a carboxylic acid and a thiol (i.e., RCO-SR'), such as that found in acetyl-coenzyme A.
biological process
	GO:0009234	menaquinone biosynthetic process	The chemical reactions and pathways resulting in the formation of any of the menaquinones. Structurally, menaquinones consist of a methylated naphthoquinone ring structure and side chains composed of a variable number of unsaturated isoprenoid residues. Menaquinones that have vitamin K activity and are known as vitamin K2.

Asymmetric/Biological Unit
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	MENI_ECOLI \| P77781	:	1vh5 1vi8 4k49 4k4a 4k4b

Description

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Ligands, Modified Residues, Ions (2, 20)

Sites (4, 4)

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