2R8W - JenaLib

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Title :   THE CRYSTAL STRUCTURE OF DIHYDRODIPICOLINATE SYNTHASE (ATU0899) FROM AGROBACTERIUM TUMEFACIENS STR. C58

Authors :   K. Tan, A. Dong, X. Xu, J. Gu, H. Zheng, A. M. Edwards, A. Savchenko, A. Joa Midwest Center For Structural Genomics (Mcsg)

Date :   11 Sep 07 (Deposition) - 25 Sep 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Apc7498, Dihydrodipicolinate Synthase, Agrobacterium Tumefaciens Str. C58, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Tan, A. Dong, X. Xu, J. Gu, H. Zheng, A. M. Edwards, A. Savchenko, A. Joachimiak
The Crystal Structure Of Dihydrodipicolinate Synthase (Atu0899) From Agrobacterium Tumefaciens Str. C58.
To Be Published
PubMed: search

Molecule 1 - AGR_C_1641P
	Atcc	:	33970
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PET DERIVATIVE
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	AGR_C_1641
	Organism Scientific	:	AGROBACTERIUM TUMEFACIENS STR.
	Organism Taxid	:	176299
	Strain	:	C58

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 14)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	CL	2	Ligand/Ion	CHLORIDE ION
3	MSE	10	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:41 , GLY A:76 , SER A:77 , THR A:78 , TYR A:166	BINDING SITE FOR RESIDUE ACT A 333
2	AC2	SOFTWARE	PHE B:41 , SER B:77 , THR B:78 , TYR B:166 , VAL B:242	BINDING SITE FOR RESIDUE ACT B 333
3	AC3	SOFTWARE	ARG A:101 , LEU B:247 , PRO B:248 , VAL B:249 , HOH B:524	BINDING SITE FOR RESIDUE CL A 334
4	AC4	SOFTWARE	ALA A:263 , GLU A:264 , HOH A:433 , LYS B:213	BINDING SITE FOR RESIDUE CL A 335

(no "SS Bond" information available for 2R8W)

Asymmetric/Biological Unit

No.	Residues
1	Arg A:305	-	Pro A:306
2	Arg B:305	-	Pro B:306

(no "SAP(SNP)/Variant" information available for 2R8W)

(no "PROSITE Motif" information available for 2R8W)

(no "Exon" information available for 2R8W)

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:297
 aligned with Q7D0E8_AGRFC | Q7D0E8 from UniProtKB/TrEMBL  Length:302

    Alignment length:297
                             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       
         Q7D0E8_AGRFC     - -MATRFKGLSAFPITPADEAGRVDIEAFSALIARLDAAEVDSVGILGSTGIYMYLTREERRRAIEAAATILRGRRTLMAGIGALRTDEAVALAKDAEAAGADALLLAPVSYTPLTQEEAYHHFAAVAGATALPLAIYNNPTTTRFTFSDELLVRLAYIPNIRAIKMPLPADADYAGELARLRPKLSDDFAIGYSGDWGCTDATLAGGDTWYSVVAGLLPVPALQLMRAAQAGNAEEAKRLDATFQPLWALFKEFGSIRVIYAAANILSLTVSEPPRPILPLTSAERQRVEEALEALS 296
               SCOP domains d2r8wa_ A: automated matches                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 2r8wA00 A:30-326 Aldolase class I                                                                                                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhheeee............hhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhh..eeee........hhhhhhhhhhhhhhhh...eeee.hhhhhh...hhhhhhhhhh...eeeeee......hhhhhhhhhh.......eeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r8w A  30 DmATRFKGLSAFPITPADEAGRVDIEAFSALIARLDAAEVDSVGILGSTGIYmYLTREERRRAIEAAATILRGRRTLmAGIGALRTDEAVALAKDAEAAGADALLLAPVSYTPLTQEEAYHHFAAVAGATALPLAIYNNPTTTRFTFSDELLVRLAYIPNIRAIKmPLPADADYAGELARLRPKLSDDFAIGYSGDWGCTDATLAGGDTWYSVVAGLLPVPALQLmRAAQAGNAEEAKRLDATFQPLWALFKEFGSIRVIYAAANILSLTVSEPPRPILPLTSAERQRVEEALEALS 326
                             |      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       319       
                             |                                                 82-MSE                  107-MSE                                                                                 195-MSE                                                     255-MSE                                                                   
                            31-MSE

Chain B from PDB  Type:PROTEIN  Length:299
 aligned with Q7D0E8_AGRFC | Q7D0E8 from UniProtKB/TrEMBL  Length:302

    Alignment length:299
                               1                                                                                                                                                                                                                                                                                                       
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287         
         Q7D0E8_AGRFC     - ---MATRFKGLSAFPITPADEAGRVDIEAFSALIARLDAAEVDSVGILGSTGIYMYLTREERRRAIEAAATILRGRRTLMAGIGALRTDEAVALAKDAEAAGADALLLAPVSYTPLTQEEAYHHFAAVAGATALPLAIYNNPTTTRFTFSDELLVRLAYIPNIRAIKMPLPADADYAGELARLRPKLSDDFAIGYSGDWGCTDATLAGGDTWYSVVAGLLPVPALQLMRAAQAGNAEEAKRLDATFQPLWALFKEFGSIRVIYAAANILSLTVSEPPRPILPLTSAERQRVEEALEALS 296
               SCOP domains d2r8wb_ B: automated matches                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 2r8wB00 B:28-326 Aldolase class I                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhheeee............hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh..eeee........hhhhhhhhhhhhhhhh...eeee.hhhhh....hhhhhhhhhh...eeeeee......hhhhhhhhhh.......eeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r8w B  28 ETDmATRFKGLSAFPITPADEAGRVDIEAFSALIARLDAAEVDSVGILGSTGIYmYLTREERRRAIEAAATILRGRRTLmAGIGALRTDEAVALAKDAEAAGADALLLAPVSYTPLTQEEAYHHFAAVAGATALPLAIYNNPTTTRFTFSDELLVRLAYIPNIRAIKmPLPADADYAGELARLRPKLSDDFAIGYSGDWGCTDATLAGGDTWYSVVAGLLPVPALQLmRAAQAGNAEEAKRLDATFQPLWALFKEFGSIRVIYAAANILSLTVSEPPRPILPLTSAERQRVEEALEALS 326
                               |    37        47        57        67        77    |   87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317         
                              31-MSE                                             82-MSE                  107-MSE                                                                                 195-MSE                                                     255-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) (23833)

Fold: TIM beta/alpha-barrel (3956)

Superfamily: Aldolase (457)

Family: automated matches (113)

Protein domain: automated matches (113)

Agrobacterium tumefaciens [TaxId: 176299] (2)

1a	d2r8wa_	A:
1b	d2r8wb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Aldolase class I (887)

C58 (Agrobacterium tumefaciens str) (3)

1a	2r8wA00	A:30-326
1b	2r8wB00	B:28-326

(no "Pfam Domain" information available for 2R8W)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (Q7D0E8_AGRFC | Q7D0E8)

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: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.
biological process
	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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Arg A:305 - Pro A:306	[ RasMol ]
		Arg B:305 - Pro B:306	[ RasMol ]

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