3GC2 - JenaLib

Title :   1.85 ANGSTROM CRYSTAL STRUCTURE OF O-SUCCINYLBENZOATE SYNTHASE FROM SALMONELLA TYPHIMURIUM IN COMPLEX WITH SUCCINIC ACID

Authors :   G. Minasov, Z. Wawrzak, T. Skarina, O. Onopriyenko, S. N. Peterson, A. S W. F. Anderson, Center For Structural Genomics Of Infectious (Csgid), Center For Structural Genomics Of Infectious Diseas (Csgid)

Date :   21 Feb 09 (Deposition) - 10 Mar 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

Chains :   Asym./Biol. Unit : A

Keywords :   O-Succinylbenzoate Synthase, Succinic Acid, Idp00994, Lyase, Magnesium, Menaquinone Biosynthesis, Metal-Binding, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Minasov, Z. Wawrzak, T. Skarina, O. Onopriyenko, S. N. Peterson, A. Savchenko, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
1. 85 Angstrom Crystal Structure Of O-Succinylbenzoate Synthase From Salmonella Typhimurium In Complex With Succinic Acid
To Be Published
PubMed: search

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 13)

Sites (7, 7)

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:131 , LYS A:133 , ASP A:161 , LYS A:235 , SER A:262 , SER A:263 , GLY A:288 , HOH A:410 , HOH A:587 , HOH A:596 , HOH A:597 , HOH A:634	BINDING SITE FOR RESIDUE SIN A 400
2	AC2	SOFTWARE	GLU A:40 , GLU A:93 , GLU A:100 , ARG A:276 , ARG A:301 , NA A:322 , HOH A:423 , HOH A:493 , HOH A:592	BINDING SITE FOR RESIDUE SIN A 401
3	AC3	SOFTWARE	GLU A:127 , ILE A:129 , HIS A:157 , ARG A:159 , ALA A:187 , HOH A:422 , HOH A:586 , HOH A:601	BINDING SITE FOR RESIDUE EPE A 402
4	AC4	SOFTWARE	ASP A:161 , ASN A:163 , GLU A:190 , ASP A:213 , HOH A:388 , HOH A:410	BINDING SITE FOR RESIDUE NA A 321
5	AC5	SOFTWARE	GLU A:40 , GLU A:93 , SIN A:401 , HOH A:590 , HOH A:614 , HOH A:642	BINDING SITE FOR RESIDUE NA A 322
6	AC6	SOFTWARE	ARG A:8 , GLN A:60 , GLU A:138	BINDING SITE FOR RESIDUE CL A 323
7	AC7	SOFTWARE	ILE A:300 , ARG A:313 , HOH A:438	BINDING SITE FOR RESIDUE CL A 324

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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:322
 aligned with MENC_SALTY | P58486 from UniProtKB/Swiss-Prot  Length:320

    Alignment length:322
                              1                                                                                                                                                                                                                                                                                                                               
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318  
           MENC_SALTY     - --MRSAQVYRWQIPMDAGVVLRDRRLKTRDGLYVCLRDGEREGWGEISPLPGFSQETWEEAQTALLTWVNDWLQGSEGLPEMPSVAFGASCALAELTGVLPEAADYRAAPLCTGDPDDLVLRLADMPGEKIAKVKVGLYEAVRDGMVVNLLLEAIPDLHLRLDANRAWTPLKAQQFAKYVNPDYRARIAFLEEPCKTRDDSRAFARETGIAIAWDESLREADFTFEAEEGVRAVVIKPTLTGSLDKVREQVAAAHALGLTAVISSSIESSLGLTQLARIAAWLTPGTLPGLDTLHLMQAQQIRPWPGSALPCLKREELERLL 320
               SCOP domains d3gc2a1 A:-1-99 automated matches                                                                    d3gc2a2 A:100-320 automated matches                                                                                                                                                                                           SCOP domains
               CATH domains 3gc2A01 A:-1-96,A:296-320 Enolase-like, N-terminal domain                                         3gc2A02 A:97-294 Enolase superfamily                                                                                                                                                                  -3gc2A01 A:-1-96,A:296-320 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeee.............eeeeeeeeeee..eeeeeee.........hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.................hhhhhhhhhhh....eeeeee....hhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhh.hhhhhh.eeeee....hhhhhhhhhhhhh..eeehhhhhh..........eeeeeehhhhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhh........hhhhh..ee..........eehhhhheeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gc2 A  -1 NAmRSAQVYRWQIPmDAGVVLRDRRLKTRDGLYVCLRDGEREGWGEISPLPGFSQETWEEAQTALLTWVNDWLQGSEGLPEmPSVAFGASCALAELTGVLPEAADYRAAPLCTGDPDDLVLRLADmPGEKIAKVKVGLYEAVRDGmVVNLLLEAIPDLHLRLDANRAWTPLKAQQFAKYVNPDYRARIAFLEEPCKTRDDSRAFARETGIAIAWDESLREADFTFEAEEGVRAVVIKPTLTGSLDKVREQVAAAHALGLTAVISSSIESSLGLTQLARIAAWLTPGTLPGLDTLHLmQAQQIRPWPGSALPCLKREELERLL 320
                              |      8    |   18        28        38        48        58        68        78 |      88        98       108       118     | 128       138     | 148       158       168       178       188       198       208       218       228       238       248       258       268       278       288      |298       308       318  
                              |          13-MSE                                                             80-MSE                                     124-MSE             144-MSE                                                                                                                                                295-MSE                     
                              1-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 '\|'

Classification and Annotation

SCOP Domains (2, 2)

CATH Domains (2, 2)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (MENC_SALTY | P58486)

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: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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