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Title :   THE STRUCTURE OF THE BETA-LACTAMASE SUPERFAMILY DOMAIN OF D-ALANYL-D-ALANINE CARBOXYPEPTIDASE FROM BACILLUS SUBTILIS

Authors :   M. E. Cuff, E. Rakowski, K. Buck, A. Joachimiak, Midwest Center For S Genomics (Mcsg)

Date :   01 Apr 10 (Deposition) - 19 May 10 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

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

Keywords :   Penicillin-Binding Protein 5*, Beta-Lactamase, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. E. Cuff, E. Rakowski, K. Buck, A. Joachimiak
The Structure Of The Beta-Lactamase Superfamily Domain Of D-Alanyl-D-Alanine Carboxypeptidase From Bacillus Subtilis.
To Be Published
PubMed: search

Molecule 1 - D-ALANYL-D-ALANINE CARBOXYPEPTIDASE DACB
	Chains	:	A, B
	EC Number	:	3.4.16.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMCSG19
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMIND
	Fragment	:	BETA-LACTAMASE DOMAIN RESIDUES 27-358
	Gene	:	BSU23190, DACB, DACC
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423
	Strain	:	168
	Synonym	:	DD-CARBOXYPEPTIDASE, DD-PEPTIDASE, PENICILLIN-BINDING PROTEIN 5, PBP-5

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 40)

No.	Name	Count	Type	Full Name
1	CIT	4	Ligand/Ion	CITRIC ACID
2	EDO	8	Ligand/Ion	1,2-ETHANEDIOL
3	MSE	28	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (3, 21)

No.	Name	Count	Type	Full Name
1	CIT	3	Ligand/Ion	CITRIC ACID
2	EDO	4	Ligand/Ion	1,2-ETHANEDIOL
3	MSE	14	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (3, 19)

No.	Name	Count	Type	Full Name
1	CIT	1	Ligand/Ion	CITRIC ACID
2	EDO	4	Ligand/Ion	1,2-ETHANEDIOL
3	MSE	14	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	SER B:60 , SER B:92 , SER B:115 , LYS B:205 , THR B:221 , GLY B:222 , TYR B:223 , HOH B:387 , HOH B:406 , HOH B:570 , HOH B:598 , HOH B:627	BINDING SITE FOR RESIDUE CIT B 1
02	AC2	SOFTWARE	SER A:60 , SER A:92 , SER A:115 , LYS A:205 , THR A:221 , GLY A:222 , TYR A:223 , HOH A:659 , HOH A:758	BINDING SITE FOR RESIDUE CIT A 1
03	AC3	SOFTWARE	HOH B:667	BINDING SITE FOR RESIDUE EDO B 359
04	AC4	SOFTWARE	GLU A:162 , HIS A:164 , HOH A:573 , HOH A:661	BINDING SITE FOR RESIDUE EDO A 359
05	AC5	SOFTWARE	ARG B:114 , HOH B:552 , HOH B:593 , HOH B:753	BINDING SITE FOR RESIDUE EDO B 360
06	AC6	SOFTWARE	LYS A:105 , TYR A:109 , ASP A:183 , LYS A:186 , HOH A:527 , HOH A:531	BINDING SITE FOR RESIDUE EDO A 360
07	AC7	SOFTWARE	HIS A:53 , LYS A:148 , ASN A:149 , HOH A:695 , HOH A:721	BINDING SITE FOR RESIDUE EDO A 361
08	AC8	SOFTWARE	ARG A:114 , LYS A:203 , HOH A:473 , HOH A:623 , HOH A:641 , TYR B:136	BINDING SITE FOR RESIDUE CIT A 362
09	AC9	SOFTWARE	LEU A:209 , MSE A:211 , PRO A:214 , HOH A:515 , HOH A:538 , HOH A:559 , HOH A:726	BINDING SITE FOR RESIDUE EDO A 363
10	BC1	SOFTWARE	LYS B:105 , TYR B:109 , ASP B:183 , LYS B:186	BINDING SITE FOR RESIDUE EDO B 361
11	BC2	SOFTWARE	THR B:301 , GLU B:303 , HOH B:656	BINDING SITE FOR RESIDUE EDO B 362
12	BC3	SOFTWARE	LYS A:191 , ILE A:192 , LYS A:203 , THR A:210 , HOH A:538 , HOH A:543 , HOH A:727 , TYR B:136 , GLU B:143 , ARG B:151 , HOH B:427 , HOH B:601	BINDING SITE FOR RESIDUE CIT A 364

(no "SS Bond" information available for 3MFD)

(no "Cis Peptide Bond" information available for 3MFD)

(no "SAP(SNP)/Variant" information available for 3MFD)

(no "PROSITE Motif" information available for 3MFD)

(no "Exon" information available for 3MFD)

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
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Chain A from PDB  Type:PROTEIN  Length:326
 aligned with DACB_BACSU | P35150 from UniProtKB/Swiss-Prot  Length:382

    Alignment length: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       327       337       347      
           DACB_BACSU    28 AIDVSAKSAIIIDGASGRVLYAKDEHQKRRIASITKIMTAVLAIESGKMDQTVTVSANAVRTEGSAIYLTEGQKVKLKDLVYGLMLRSGNDAAVAIAEHVGGSLDGFVYMMNQKAEQLGMKNTRFQNPHGLDDHENHYSTAYDMAILTKYAMKLKDYQKISGTKIYKAETMESVWKNKNKLLTMLYPYSTGGKTGYTKLAKRTLVSTASKDGIDLIAVTINDPNDWDDHMKMFNYVFEHYQTYLIAKKGDIPKLKGTFYESKAFIKRDITYLLTEEEKENVKINTTLLKPKKAWEKDASKIPDIVGHMEIMFNDATIAKVPIYYEN 353
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee.....eeeee.......hhhhhhhhhhhhhhhh.....eee.hhhhhhh...........eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhh.hhhhhhhhh..eee......eee..hhhhhh....eeeeeeeee...eeeeeeeeee..eeeeeeee...hhhhhhhhhhhhhhhheeeeeee..ee.hhhh.......eee...eeeeeehhhhh.eeeeeee....hhhhhhhhhh..eeeeeeeee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mfd A  28 AIDVSAKSAIIIDGASGRVLYAKDEHQKRRIASITKImTAVLAIESGKmDQTVTVSANAVRTEGSAIYLTEGQKVKLKDLVYGLmLRSGNDAAVAIAEHVGGSLDGFVYmmNQKAEQLGmKNTRFQNPHGLDDHENHYSTAYDmAILTKYAmKLKDYQKISGTKIYKAETmESVWKNKNKLLTmLYPYSTGGKTGYTKLAKRTLVSTASKDGIDLIAVTINDPNDWDDHmKmFNYVFEHYQTYLIAKKGDIPKLKGTFYESKAFIKRDITYLLTEEEKENVKINTTLLKPKKAWEKDASKIPDIVGHmEImFNDATIAKVPIYYEN 353
                                    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       327       337|      347      
                                                                65-MSE     76-MSE                             112-MSE                  137-MSE   147-MSE                 171-MSE 179-MSE            198-MSE      211-MSE                                       257-MSE                                                                       335-MSE              
                                                                                                                                        138-MSE                                                                                                                  259-MSE                                                                        338-MSE

Chain B from PDB  Type:PROTEIN  Length:306
 aligned with DACB_BACSU | P35150 from UniProtKB/Swiss-Prot  Length:382

    Alignment length:325
                                    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       327       337       347     
           DACB_BACSU    28 AIDVSAKSAIIIDGASGRVLYAKDEHQKRRIASITKIMTAVLAIESGKMDQTVTVSANAVRTEGSAIYLTEGQKVKLKDLVYGLMLRSGNDAAVAIAEHVGGSLDGFVYMMNQKAEQLGMKNTRFQNPHGLDDHENHYSTAYDMAILTKYAMKLKDYQKISGTKIYKAETMESVWKNKNKLLTMLYPYSTGGKTGYTKLAKRTLVSTASKDGIDLIAVTINDPNDWDDHMKMFNYVFEHYQTYLIAKKGDIPKLKGTFYESKAFIKRDITYLLTEEEKENVKINTTLLKPKKAWEKDASKIPDIVGHMEIMFNDATIAKVPIYYE 352
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Peptidase_S11-3mfdB01 B:28-251                                                                                                                                                                                                  ---------------PBP5_C-3  mfdB03 B:267-352                                                             Pfam domains (1)
           Pfam domains (2) Peptidase_S11-3mfdB02 B:28-251                                                                                                                                                                                                  ---------------PBP5_C-3  mfdB04 B:267-352                                                             Pfam domains (2)
         Sec.struct. author .......eeeeee.....eeeee.......hhhhhhhhhhhhhhhh.....eee.hhhhhh............eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhh.hhhhhhhhh..eee......eee..hhhhhh....eeeeeeeee...eeeeeeeeee..eeeeeeee...hhhhhhhhhhhhhhhheeeeeee.--.hhhhh.......ee....eeeeeehhhhhheeeeee.-----------------.eeeeeee..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mfd B  28 AIDVSAKSAIIIDGASGRVLYAKDEHQKRRIASITKImTAVLAIESGKmDQTVTVSANAVRTEGSAIYLTEGQKVKLKDLVYGLmLRSGNDAAVAIAEHVGGSLDGFVYmmNQKAEQLGmKNTRFQNPHGLDDHENHYSTAYDmAILTKYAmKLKDYQKISGTKIYKAETmESVWKNKNKLLTmLYPYSTGGKTGYTKLAKRTLVSTASKDGIDLIAVTINDPNDWDDHmKmFNYVFEHYQTYLIAK--DIPKLKGTFYESKAFIKRDITYLLTEEEKENVKINTTL-----------------VGHmEImFNDATIAKVPIYYE 352
                                    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      |  -         -    |  337|      347     
                                                                65-MSE     76-MSE                             112-MSE                  137-MSE   147-MSE                 171-MSE 179-MSE            198-MSE      211-MSE                                       257-MSE          274  |                                  314               332  |  |              
                                                                                                                                        138-MSE                                                                                                                  259-MSE           277                                                       335-MSE             
                                                                                                                                                                                                                                                                                                                                                338-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 3MFD)

(no "CATH Domain" information available for 3MFD)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Beta-lactamase (210)

Family: Peptidase_S11 (12)

Bacillus subtilis (1)

1a	Peptidase_S11-3mfdB01	B:28-251
1b	Peptidase_S11-3mfdB02	B:28-251

Clan: no clan defined [family: PBP5_C] (10)

Family: PBP5_C (10)

Bacillus subtilis (1)

2a	PBP5_C-3mfdB03	B:267-352
2b	PBP5_C-3mfdB04	B:267-352

Asymmetric Unit(hide GO term definitions)

Chain A,B (DACB_BACSU | P35150)

molecular function
	GO:0004180	carboxypeptidase activity	Catalysis of the hydrolysis of the terminal or penultimate peptide bond at the C-terminal end of a peptide or polypeptide.
	GO:0004175	endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain.
	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:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	GO:0009002	serine-type D-Ala-D-Ala carboxypeptidase activity	Catalysis of the reaction: (Ac)2-L-Lys-D-alanyl-D-alanine + H2O = (Ac)2-L-Lys-D-alanine + D-alanine.
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: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:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0008360	regulation of cell shape	Any process that modulates the surface configuration of a cell.
	GO:0030435	sporulation resulting in formation of a cellular spore	The process in which a relatively unspecialized cell acquires the specialized features of a cellular spore, a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction.
cellular component
	GO:0005887	integral component of plasma membrane	The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Asymmetric Unit
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	3mfd
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Description

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Ligands, Modified Residues, Ions (3, 40)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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