2DWU - JenaLib

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Title :   CRYSTAL STRUCTURE OF GLUTAMATE RACEMASE ISOFORM RACE1 FROM BACILLUS ANTHRACIS

Authors :   S. Mehboob, B. D. Santarsiero, M. E. Johnson

Date :   17 Aug 06 (Deposition) - 19 Jun 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

Keywords :   Racemase, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. May, S. Mehboob, D. C. Mulhearn, Z. Wang, H. Yu, G. R. J. Thatcher, B. D. Santarsiero, M. E. Johnson, A. D. Mesecar
Structural And Functional Analysis Of Two Glutamate Racemas Isozymes From Bacillus Anthracis And Implications For Inhibitor Design
J. Mol. Biol. V. 371 1219 2007
PubMed-ID: 17610893 | Reference-DOI: 10.1016/J.JMB.2007.05.093

Molecule 1 - GLUTAMATE RACEMASE
	Chains	:	A, B, C
	EC Number	:	5.1.1.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	RACE-1
	Organism Scientific	:	BACILLUS ANTHRACIS
	Organism Taxid	:	1392

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 10)

No.	Name	Count	Type	Full Name
1	DGL	3	Ligand/Ion	D-GLUTAMIC ACID
2	GOL	4	Ligand/Ion	GLYCEROL
3	K	3	Ligand/Ion	POTASSIUM ION

Biological Unit 1 (2, 5)

No.	Name	Count	Type	Full Name
1	DGL	2	Ligand/Ion	D-GLUTAMIC ACID
2	GOL	3	Ligand/Ion	GLYCEROL
3	K	-1	Ligand/Ion	POTASSIUM ION

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	DGL	2	Ligand/Ion	D-GLUTAMIC ACID
2	GOL	2	Ligand/Ion	GLYCEROL
3	K	-1	Ligand/Ion	POTASSIUM ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TYR B:164 , HOH B:452 , THR C:242 , VAL C:265 , ASP C:266 , HOH C:313	BINDING SITE FOR RESIDUE K C 277
02	AC2	SOFTWARE	THR B:242 , VAL B:265 , ASP B:266 , HOH B:309 , TYR C:164 , HOH C:396	BINDING SITE FOR RESIDUE K B 277
03	AC3	SOFTWARE	TYR A:164 , THR A:242 , VAL A:265 , ASP A:266 , HOH A:320 , HOH A:394	BINDING SITE FOR RESIDUE K A 277
04	AC4	SOFTWARE	ASP C:14 , SER C:15 , PRO C:45 , TYR C:46 , GLY C:47 , CYS C:77 , ASN C:78 , THR C:79 , THR C:121 , CYS C:188 , THR C:189 , HOH C:280 , HOH C:281 , HOH C:282	BINDING SITE FOR RESIDUE DGL C 278
05	AC5	SOFTWARE	ASP B:14 , SER B:15 , PRO B:45 , TYR B:46 , GLY B:47 , CYS B:77 , ASN B:78 , THR B:79 , THR B:121 , CYS B:188 , THR B:189 , HOH B:281 , HOH B:282 , HOH B:283	BINDING SITE FOR RESIDUE DGL B 278
06	AC6	SOFTWARE	ASP A:14 , SER A:15 , PRO A:45 , TYR A:46 , GLY A:47 , CYS A:77 , ASN A:78 , THR A:79 , THR A:121 , CYS A:188 , THR A:189 , HOH A:280 , HOH A:281 , HOH A:282	BINDING SITE FOR RESIDUE DGL A 278
07	AC7	SOFTWARE	VAL C:9 , LYS C:178 , GLU C:179 , ASP C:180 , ARG C:238 , HOH C:300 , HOH C:335 , HOH C:385 , HOH C:415 , HOH C:608 , HOH C:680	BINDING SITE FOR RESIDUE GOL C 279
08	AC8	SOFTWARE	VAL B:9 , SER B:34 , LYS B:178 , GLU B:179 , ASP B:180 , HOH B:317 , HOH B:379 , HOH B:381 , HOH B:401 , HOH B:599	BINDING SITE FOR RESIDUE GOL B 279
09	AC9	SOFTWARE	VAL A:9 , SER A:34 , HIS A:144 , GLU A:179 , ASP A:180 , HOH A:301 , HOH A:324 , HOH A:658	BINDING SITE FOR RESIDUE GOL A 279
10	BC1	SOFTWARE	HIS B:101 , MET B:129 , LYS B:132 , ALA B:133 , GLU B:136 , HOH B:544	BINDING SITE FOR RESIDUE GOL B 280

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

Asymmetric Unit

No.	Residues
1	Cys A:44	-	Pro A:45
2	Leu A:267	-	Pro A:268
3	Cys B:44	-	Pro B:45
4	Leu B:267	-	Pro B:268
5	Cys C:44	-	Pro C:45
6	Leu C:267	-	Pro C:268

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

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

(no "Exon" information available for 2DWU)

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:265
 aligned with Q81UL8_BACAN | Q81UL8 from UniProtKB/TrEMBL  Length:276

    Alignment length:265
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264     
         Q81UL8_BACAN     5 HKHSVIGVLDSGVGGLTVASEIIRQLPKESICYIGDNERCPYGPRSVEEVQSFVFEMVEFLKQFPLKALVVACNTAAAATLAALQEALSIPVIGVIHPGARAAIKVTKKGKIGVIGTVGTIQSNMYEKALHELDTYLKVHSHACPTLATVVENRLEDTAYVTQQVKQALLPLTKEDIDTLILGCTHYPLLESYIKKELGEDVTIISSAEETAIELSTILQHKGILADNLNPKHRFFTTGSVSSFEHIAERWLGYQISVDCVDLPV 269
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2dwuA01 A:5-98,A:212-269  [code=3.40.50.1860, no name defined]                                2dwuA02 A:99-211  [code=3.40.50.1860, no name defined]                                                           2dwuA01 A:5-98,A:212-269                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee....hhhhhhhhhhhh....eeeee.hhhh.....hhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhh...eeehhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhh..hhhhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhh...........eeee..hhhhhhhhhhhhhh....eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dwu A   5 HKHSVIGVLDSGVGGLTVASEIIRQLPKESICYIGDNERCPYGPRSVEEVQSFVFEMVEFLKQFPLKALVVACNTAAAATLAALQEALSIPVIGVIHPGARAAIKVTKKGKIGVIGTVGTIQSNMYEKALHELDTYLKVHSHACPTLATVVENRLEDTAYVTQQVKQALLPLTKEDIDTLILGCTHYPLLESYIKKELGEDVTIISSAEETAIELSTILQHKGILADNLNPKHRFFTTGSVSSFEHIAERWLGYQISVDCVDLPV 269
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264

Chain B from PDB  Type:PROTEIN  Length:266
 aligned with Q81UL8_BACAN | Q81UL8 from UniProtKB/TrEMBL  Length:276

    Alignment length:266
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264      
         Q81UL8_BACAN     5 HKHSVIGVLDSGVGGLTVASEIIRQLPKESICYIGDNERCPYGPRSVEEVQSFVFEMVEFLKQFPLKALVVACNTAAAATLAALQEALSIPVIGVIHPGARAAIKVTKKGKIGVIGTVGTIQSNMYEKALHELDTYLKVHSHACPTLATVVENRLEDTAYVTQQVKQALLPLTKEDIDTLILGCTHYPLLESYIKKELGEDVTIISSAEETAIELSTILQHKGILADNLNPKHRFFTTGSVSSFEHIAERWLGYQISVDCVDLPVK 270
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2dwuB01 B:5-98,B:212-270  [code=3.40.50.1860, no name defined]                                2dwuB02 B:99-211  [code=3.40.50.1860, no name defined]                                                           2dwuB01 B:5-98,B:212-270                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee....hhhhhhhhhhhh....eeeee.hhhh.....hhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhh...eeehhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhh..hhhhhhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhh..........eeee..hhhhhhhhhhhhhh....eee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dwu B   5 HKHSVIGVLDSGVGGLTVASEIIRQLPKESICYIGDNERCPYGPRSVEEVQSFVFEMVEFLKQFPLKALVVACNTAAAATLAALQEALSIPVIGVIHPGARAAIKVTKKGKIGVIGTVGTIQSNMYEKALHELDTYLKVHSHACPTLATVVENRLEDTAYVTQQVKQALLPLTKEDIDTLILGCTHYPLLESYIKKELGEDVTIISSAEETAIELSTILQHKGILADNLNPKHRFFTTGSVSSFEHIAERWLGYQISVDCVDLPVK 270
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264

Chain C from PDB  Type:PROTEIN  Length:266
 aligned with Q81UL8_BACAN | Q81UL8 from UniProtKB/TrEMBL  Length:276

    Alignment length:266
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264      
         Q81UL8_BACAN     5 HKHSVIGVLDSGVGGLTVASEIIRQLPKESICYIGDNERCPYGPRSVEEVQSFVFEMVEFLKQFPLKALVVACNTAAAATLAALQEALSIPVIGVIHPGARAAIKVTKKGKIGVIGTVGTIQSNMYEKALHELDTYLKVHSHACPTLATVVENRLEDTAYVTQQVKQALLPLTKEDIDTLILGCTHYPLLESYIKKELGEDVTIISSAEETAIELSTILQHKGILADNLNPKHRFFTTGSVSSFEHIAERWLGYQISVDCVDLPVK 270
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2dwuC01 C:5-98,C:212-270  [code=3.40.50.1860, no name defined]                                2dwuC02 C:99-211  [code=3.40.50.1860, no name defined]                                                           2dwuC01 C:5-98,C:212-270                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee....hhhhhhhhhhhh....eeeee.hhhh.....hhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhh...eeehhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhh..hhhhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhh...........eeee..hhhhhhhhhhhhhh....eee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dwu C   5 HKHSVIGVLDSGVGGLTVASEIIRQLPKESICYIGDNERCPYGPRSVEEVQSFVFEMVEFLKQFPLKALVVACNTAAAATLAALQEALSIPVIGVIHPGARAAIKVTKKGKIGVIGTVGTIQSNMYEKALHELDTYLKVHSHACPTLATVVENRLEDTAYVTQQVKQALLPLTKEDIDTLILGCTHYPLLESYIKKELGEDVTIISSAEETAIELSTILQHKGILADNLNPKHRFFTTGSVSSFEHIAERWLGYQISVDCVDLPVK 270
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264

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 2DWU)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.1860, no name defined] (18)

Bacillus anthracis. Organism_taxid: 1392. (2)

1a	2dwuA02	A:99-211
1b	2dwuB02	B:99-211
1c	2dwuA01	A:5-98,A:212-269
1d	2dwuB01	B:5-98,B:212-270
1e	2dwuC01	C:5-98,C:212-270
1f	2dwuC02	C:99-211

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (Q81UL8_BACAN | Q81UL8)

molecular function
	GO:0008881	glutamate racemase activity	Catalysis of the reaction: L-glutamate = D-glutamate.
	GO:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
	GO:0036361	racemase activity, acting on amino acids and derivatives	Catalysis of the interconversion of the two enantiomers of a chiral amino acid or amino acid derivative.
	GO:0016855	racemase and epimerase activity, acting on amino acids and derivatives	Catalysis of a reaction that alters the configuration of one or more chiral centers in an amino acid.
biological process
	GO:0071555	cell wall organization	A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
	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.
	GO:0006807	nitrogen compound metabolic process	The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.
	GO:0009252	peptidoglycan biosynthetic process	The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.
	GO:0008360	regulation of cell shape	Any process that modulates the surface configuration of a cell.

Asymmetric Unit
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	Cis Peptide Bonds
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		Cys B:44 - Pro B:45	[ RasMol ]
		Cys C:44 - Pro C:45	[ RasMol ]
		Leu A:267 - Pro A:268	[ RasMol ]
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		Leu C:267 - Pro C:268	[ RasMol ]

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	2dwu
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Description

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Ligands, Modified Residues, Ions (3, 10)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

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