2QVH - JenaLib

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Title :   CRYSTAL STRUCTURE OF O-SUCCINYLBENZOATE SYNTHASE COMPLEXED WITH O-SUCCINYL BENZOATE (OSB)

Authors :   R. Sugadev, S. K. Burley, S. Swaminathan, New York Sgx Research Cen Structural Genomics (Nysgxrc)

Date :   08 Aug 07 (Deposition) - 28 Aug 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.76

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

Keywords :   Tim Barrel, O-Succinylbenzoate, 9312B, Psi-Ii, Structural Genomics, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Sugadev, S. K. Burley, S. Swaminathan
Crystal Structure Of O-Succinylbenzoate Synthase Complexed With O-Succinyl Benzoate.
To Be Published
PubMed: search

Molecule 1 - O-SUCCINYLBENZOATE-COA SYNTHASE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PSGX3
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	TFU_1410
	Organism Scientific	:	THERMOBIFIDA FUSCA
	Organism Taxid	:	269800
	Strain	:	YX

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 8)

No.	Name	Count	Type	Full Name
1	MG	2	Ligand/Ion	MAGNESIUM ION
2	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
3	OSB	2	Ligand/Ion	2-SUCCINYLBENZOATE

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
3	OSB	2	Ligand/Ion	2-SUCCINYLBENZOATE

Biological Unit 2 (2, 6)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
3	OSB	2	Ligand/Ion	2-SUCCINYLBENZOATE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:130 , GLU A:156 , ASP A:179 , OSB A:5550 , HOH A:5658	BINDING SITE FOR RESIDUE MG A 401
2	AC2	SOFTWARE	ASP B:130 , GLU B:156 , ASP B:179 , OSB B:5551 , HOH B:5552	BINDING SITE FOR RESIDUE MG B 400
3	AC3	SOFTWARE	PHE A:16 , ASN A:73 , THR A:75 , LYS A:97 , ASP A:130 , ASN A:132 , GLU A:156 , ASP A:179 , LYS A:203 , SER A:227 , SER A:228 , VAL A:230 , GLY A:254 , THR A:257 , MG A:401 , HOH A:5582 , HOH A:5583 , HOH A:5658	BINDING SITE FOR RESIDUE OSB A 5550
4	AC4	SOFTWARE	PHE B:16 , ASN B:73 , THR B:75 , LYS B:97 , ASP B:130 , ASN B:132 , GLU B:156 , ASP B:179 , ARG B:183 , LYS B:203 , SER B:227 , SER B:228 , VAL B:230 , GLY B:254 , THR B:257 , MG B:400 , HOH B:5578 , HOH B:5587	BINDING SITE FOR RESIDUE OSB B 5551

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

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

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

(no "PROSITE Motif" information available for 2QVH)

(no "Exon" information available for 2QVH)

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:311
 aligned with Q47Q21_THEFY | Q47Q21 from UniProtKB/TrEMBL  Length:317

    Alignment length:311
                             1                                                                                                                                                                                                                                                                                                                     
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309 
         Q47Q21_THEFY     - -MTGRAFAIPLRTRFRGITVREGMLVRGAAGWGEFSPFAEYGPRECARWWAACYEAAELGWPAPVRDTVPVNATVPAVGPEEAARIVASSGCTTAKVKVAERGQSEANDVARVEAVRDALGPRGRVRIDVNGAWDVDTAVRMIRLLDRFELEYVEQPCATVDELAEVRRRVSVPIAADESIRRAEDPLRVRDAEAADVVVLKVQPLGGVRAALRLAEECGLPVVVSSAVETSVGLAAGVALAAALPELPYACGLATLRLLHADVCDDPLLPVHGVLPVRRVDVSEQRLAEVEIDPAAWQARLAAARAAWEQ 310
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2qvhA01 A:2-60,A:286-312 Enolase-like, N-terminal domain   2qvhA02 A:61-285 Enolase superfamily                                                                                                                                                                                             2qvhA01 A:2-60,A:286-312    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeeee..eeeeeeeeee....eeee......hhhhhhhhhhhhhhhhhh........eee..eee...hhhhhhhhhhh....eeeee......hhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhh...eeeee....hhhhhhhhhh.....eeehhhhhh....hhhhhh....eeeehhhhhhhhhhhhhhhhhhh..eee.....hhhhhhhhhhhhhhh..........hhhhh..............eee......hhhhhhh.ee.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qvh A   2 SLTGRAFAIPLRTRFRGITVREGmLVRGAAGWGEFSPFAEYGPRECARWWAACYEAAELGWPAPVRDTVPVNATVPAVGPEEAARIVASSGCTTAKVKVAERGQSEANDVARVEAVRDALGPRGRVRIDVNGAWDVDTAVRmIRLLDRFELEYVEQPCATVDELAEVRRRVSVPIAADESIRRAEDPLRVRDAEAADVVVLKVQPLGGVRAALRLAEECGLPVVVSSAVETSVGLAAGVALAAALPELPYACGLATLRLLHADVCDDPLLPVHGVLPVRRVDVSEQRLAEVEIDPAAWQARLAAARAAWEQ 312
                                    11        21   |    31        41        51        61        71        81        91       101       111       121       131       141 |     151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311 
                                                  25-MSE                                                                                                               143-MSE

Chain B from PDB  Type:PROTEIN  Length:311
 aligned with Q47Q21_THEFY | Q47Q21 from UniProtKB/TrEMBL  Length:317

    Alignment length:311
                             1                                                                                                                                                                                                                                                                                                                     
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309 
         Q47Q21_THEFY     - -MTGRAFAIPLRTRFRGITVREGMLVRGAAGWGEFSPFAEYGPRECARWWAACYEAAELGWPAPVRDTVPVNATVPAVGPEEAARIVASSGCTTAKVKVAERGQSEANDVARVEAVRDALGPRGRVRIDVNGAWDVDTAVRMIRLLDRFELEYVEQPCATVDELAEVRRRVSVPIAADESIRRAEDPLRVRDAEAADVVVLKVQPLGGVRAALRLAEECGLPVVVSSAVETSVGLAAGVALAAALPELPYACGLATLRLLHADVCDDPLLPVHGVLPVRRVDVSEQRLAEVEIDPAAWQARLAAARAAWEQ 310
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2qvhB01 B:2-60,B:286-312 Enolase-like, N-terminal domain   2qvhB02 B:61-285 Enolase superfamily                                                                                                                                                                                             2qvhB01 B:2-60,B:286-312    CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------------------MR_MLE-2qvhB01 B:113-179                                           ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------------MR_MLE-2qvhB02 B:113-179                                           ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ....eeeeeeeeeee..eeeeeeeeee....eeee......hhhhhhhhhhhhhhhhhh........eee..eee...hhhhhhhhhhh....eeeee......hhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhh...eeeee....hhhhhhhhhhhh...eeehhhhhh....hhhhhh....eeeehhhhhhhhhhhhhhhhhhh..eee.....hhhhhhhhhhhhhhh..........hhhhh..............eee......hhhhhhhhee.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qvh B   2 SLTGRAFAIPLRTRFRGITVREGmLVRGAAGWGEFSPFAEYGPRECARWWAACYEAAELGWPAPVRDTVPVNATVPAVGPEEAARIVASSGCTTAKVKVAERGQSEANDVARVEAVRDALGPRGRVRIDVNGAWDVDTAVRmIRLLDRFELEYVEQPCATVDELAEVRRRVSVPIAADESIRRAEDPLRVRDAEAADVVVLKVQPLGGVRAALRLAEECGLPVVVSSAVETSVGLAAGVALAAALPELPYACGLATLRLLHADVCDDPLLPVHGVLPVRRVDVSEQRLAEVEIDPAAWQARLAAARAAWEQ 312
                                    11        21   |    31        41        51        61        71        81        91       101       111       121       131       141 |     151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311 
                                                  25-MSE                                                                                                               143-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 2QVH)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Enolase-like; domain 1 (252)

Homologous Superfamily: Enolase-like, N-terminal domain (130)

Thermobifida fusca yx. Organism_taxid: 269800. Strain: yx. (2)

1a	2qvhA01	A:2-60,A:286-312
1b	2qvhB01	B:2-60,B:286-312

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Enolase superfamily (142)

Thermobifida fusca yx. Organism_taxid: 269800. Strain: yx. (2)

2a	2qvhA02	A:61-285
2b	2qvhB02	B:61-285

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Enolase_TIM (82)

Family: MR_MLE (48)

Thermobifida fusca (strain YX) (2)

1a	MR_MLE-2qvhB01	B:113-179
1b	MR_MLE-2qvhB02	B:113-179

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q47Q21_THEFY | Q47Q21)

molecular function
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0016836	hydro-lyase activity	Catalysis of the cleavage of a carbon-oxygen bond by elimination of water.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0009063	cellular amino acid catabolic process	The chemical reactions and pathways resulting in the breakdown of amino acids, organic acids containing one or more amino substituents.
	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.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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2opj	CRYSTAL STRUCTURE OF O-SUCCINYLBENZOATE SYNTHASE

Description

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Ligands, Modified Residues, Ions (3, 8)

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