4BUC - JenaLib

Title :   CRYSTAL STRUCTURE OF MURD LIGASE FROM THERMOTOGA MARITIMA IN APO FORM

Authors :   S. Favini-Stabile, C. Contreras-Martel, N. Thielens, A. Dessen

Date :   20 Jun 13 (Deposition) - 17 Jul 13 (Release) - 18 Dec 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.17

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

Keywords :   Ligase, Peptidoglycan Synthesis, Adp-Forming Enzyme, Cell Wall, Cell Shape, Cell Cycle, Nucleotide-Binding, Atp-Binding, Cell Division (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Favini-Stabile, C. Contreras-Martel, N. Thielens, A. Dessen
Mreb And Murg As Scaffolds For The Cytoplasmic Steps Of Peptidoglycan Biosynthesis
Environ. Microbiol. V. 15 3218 2013
PubMed-ID: 23826965 | Reference-DOI: 10.1111/1462-2920.12171

Compounds

Molecule 1 - UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE
	Chains	:	A, B
	EC Number	:	6.3.2.9
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET15B
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	2336
	Strain	:	DSM 3109
	Synonym	:	MURD LIGASE, D-GLUTAMIC ACID-ADDING ENZYME, UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE SYNTHETASE

Structural Features

Chains, Units

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

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (6, 56)

Asymmetric Unit (6, 56)

No.	Name	Count	Type	Full Name
1	CL	6	Ligand/Ion	CHLORIDE ION
2	GOL	6	Ligand/Ion	GLYCEROL
3	MSE	24	Mod. Amino Acid	SELENOMETHIONINE
4	NH4	2	Ligand/Ion	AMMONIUM ION
5	PO3	2	Ligand/Ion	PHOSPHITE ION
6	PO4	16	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (5, 25)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	3	Ligand/Ion	GLYCEROL
3	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
4	NH4	1	Ligand/Ion	AMMONIUM ION
5	PO3	1	Ligand/Ion	PHOSPHITE ION
6	PO4	8	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (5, 25)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	3	Ligand/Ion	GLYCEROL
3	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
4	NH4	1	Ligand/Ion	AMMONIUM ION
5	PO3	1	Ligand/Ion	PHOSPHITE ION
6	PO4	8	Ligand/Ion	PHOSPHATE ION

Sites (32, 32)

Asymmetric Unit (32, 32)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LYS A:133 , SER A:177 , SER A:178 , PHE A:179 , ASP A:203 , TYR A:211 , LYS A:215	BINDING SITE FOR RESIDUE PO4 A1000
02	AC2	SOFTWARE	GLY A:132 , THR A:135 , MSE A:279 , ASN A:282 , GOL A:1202	BINDING SITE FOR RESIDUE PO4 A1001
03	AC3	SOFTWARE	ASN A:196 , ASN A:231 , HIS A:233 , TYR A:277 , GLU A:281 , HOH A:2093 , HOH A:2094	BINDING SITE FOR RESIDUE PO4 A1002
04	AC4	SOFTWARE	ASP A:120 , LYS A:123 , GLU A:168 , HOH A:2056 , HOH A:2084 , HOH A:2169	BINDING SITE FOR RESIDUE PO4 A1003
05	AC5	SOFTWARE	LYS A:30 , SER A:31 , SER A:88 , PRO A:89 , NH4 A:1501 , HOH A:2001 , HOH A:2003	BINDING SITE FOR RESIDUE PO4 A1004
06	AC6	SOFTWARE	ASP A:213 , ARG A:238 , GLU A:404 , MSE A:407 , HIS A:445 , HOH A:2160 , HOH A:2166	BINDING SITE FOR RESIDUE PO4 A1005
07	AC7	SOFTWARE	TYR A:86 , LYS A:107 , SER A:109 , PHE A:114 , ASP A:117 , GLU A:185	BINDING SITE FOR RESIDUE PO4 A1006
08	AC8	SOFTWARE	ALA A:52 , HIS A:75 , ILE A:91 , PO3 A:1008 , CL A:1402 , HOH A:2040 , ALA B:52 , GLY B:73 , GLY B:74 , HOH B:2017	BINDING SITE FOR RESIDUE PO4 A1007
09	AC9	SOFTWARE	SER A:96 , MSE A:97 , PO4 A:1007 , HOH A:2040 , GLY B:74 , HIS B:75 , SER B:96 , PO3 B:1008	BINDING SITE FOR RESIDUE PO3 A1008
10	BC1	SOFTWARE	PHE A:182 , TRP A:183 , ILE A:395 , GLU A:397 , GLU A:401 , HOH A:2043	BINDING SITE FOR RESIDUE GOL A1200
11	BC2	SOFTWARE	ARG A:33 , LYS A:37 , PHE A:62	BINDING SITE FOR RESIDUE GOL A1201
12	BC3	SOFTWARE	GLY A:132 , LYS A:133 , SER A:134 , THR A:135 , PO4 A:1001	BINDING SITE FOR RESIDUE GOL A1202
13	BC4	SOFTWARE	GLU A:111 , GLY A:155 , ALA A:161 , GLN A:180 , HOH A:2004	BINDING SITE FOR RESIDUE CL A1400
14	BC5	SOFTWARE	PHE A:28 , GLU A:51 , LYS A:53	BINDING SITE FOR RESIDUE CL A1401
15	BC6	SOFTWARE	GLY A:27 , GLU A:51 , ALA A:52 , HIS A:75 , PO4 A:1007	BINDING SITE FOR RESIDUE CL A1402
16	BC7	SOFTWARE	PO4 A:1004	BINDING SITE FOR RESIDUE NH4 A1501
17	BC8	SOFTWARE	LYS B:133 , SER B:177 , SER B:178 , PHE B:179 , ASP B:203 , TYR B:211 , LYS B:215 , HOH B:2031	BINDING SITE FOR RESIDUE PO4 B1000
18	BC9	SOFTWARE	GLY B:132 , THR B:135 , GLN B:278 , MSE B:279 , ASN B:282 , GOL B:1202	BINDING SITE FOR RESIDUE PO4 B1001
19	CC1	SOFTWARE	ASN B:196 , ASN B:231 , HIS B:233 , TYR B:277 , GLU B:281 , HOH B:2046 , HOH B:2047	BINDING SITE FOR RESIDUE PO4 B1002
20	CC2	SOFTWARE	ASP B:120 , LYS B:123 , GLU B:168 , HOH B:2024	BINDING SITE FOR RESIDUE PO4 B1003
21	CC3	SOFTWARE	LYS B:30 , SER B:31 , PRO B:89 , NH4 B:1501 , HOH B:2001 , HOH B:2002	BINDING SITE FOR RESIDUE PO4 B1004
22	CC4	SOFTWARE	ASP B:213 , ARG B:238 , GLU B:404 , MSE B:407 , HIS B:445 , HOH B:2057 , HOH B:2084	BINDING SITE FOR RESIDUE PO4 B1005
23	CC5	SOFTWARE	TYR B:86 , LYS B:107 , SER B:109 , PHE B:114 , ASP B:117 , GLU B:185	BINDING SITE FOR RESIDUE PO4 B1006
24	CC6	SOFTWARE	ALA A:52 , GLY A:73 , GLY A:74 , HOH A:2034 , ALA B:52 , HIS B:75 , ILE B:91 , PO3 B:1008 , CL B:1402 , HOH B:2020	BINDING SITE FOR RESIDUE PO4 B1007
25	CC7	SOFTWARE	GLY A:74 , HIS A:75 , SER A:96 , PO3 A:1008 , THR B:95 , SER B:96 , MSE B:97 , PO4 B:1007 , HOH B:2020	BINDING SITE FOR RESIDUE PO3 B1008
26	CC8	SOFTWARE	PHE B:182 , TRP B:183 , GLU B:397 , GLU B:401 , HOH B:2022	BINDING SITE FOR RESIDUE GOL B1200
27	CC9	SOFTWARE	ARG B:33 , LYS B:37 , GLU B:58 , PHE B:62	BINDING SITE FOR RESIDUE GOL B1201
28	DC1	SOFTWARE	GLY B:132 , LYS B:133 , SER B:134 , THR B:135 , PO4 B:1001	BINDING SITE FOR RESIDUE GOL B1202
29	DC2	SOFTWARE	GLU B:111 , GLY B:155 , PRO B:160 , ALA B:161 , GLN B:180	BINDING SITE FOR RESIDUE CL B1400
30	DC3	SOFTWARE	PHE B:28 , GLU B:51	BINDING SITE FOR RESIDUE CL B1401
31	DC4	SOFTWARE	GLY B:27 , GLU B:51 , ALA B:52 , HIS B:75 , PO4 B:1007	BINDING SITE FOR RESIDUE CL B1402
32	DC5	SOFTWARE	PO4 B:1004	BINDING SITE FOR RESIDUE NH4 B1501

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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:427
 aligned with MURD_THEMA | Q9WY76 from UniProtKB/Swiss-Prot  Length:430

    Alignment length:433
                                 1                                                                                                                                                                                                                                                                                                                                                                                                                                           
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425   
           MURD_THEMA     - -----MKIGFLGFGKSNRSLLKYLLNHQEAKFFVSEAKTLDGETKKFLEEHSVEYEEGGHTEKLLDCDVVYVSPGIKPDTSMIELLSSRGVKLSTELQFFLDNVDPKKVVGITGTDGKSTATALMYHVLSGRGFKTFLGGNFGTPAVEALEGEYDYYVLEMSSFQLFWSERPYLSNFLVLNISEDHLDWHSSFKEYVDSKLKPAFLQTEGDLFVYNKHIERLRNLEGVRSRKIPFWTDENFATEKELIVRGKKYTLPGNYPYQMRENILAVSVLYMEMFNELESFLELLRDFKPLPHRMEYLGQIDGRHFYNDSKATSTHAVLGALSNFDKVVLIMCGIGKKENYSLFVEKASPKLKHLIMFGEISKELAPFVGKIPHSIVENMEEAFEKAMEVSEKGDVILLSPGGASFDMYENYAKRGEHFREIFKRHGGD 428
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhh.eeeee..hhhhhhhhhhhhh....eeeee.....hhhhhhhhhhh..eee....hhhhhhh.eeee.......hhhhhhhhhh..eeehhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhhhh...eeeee....hhhhhhh....eeeee.hhhhhhh.......eeee............hhhhhhhhhhhhhhhh....eeeee.hhhhh........eeeee.....ee...eeee..eeee.....hhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.........eeeeee..eeeee.....hhhhhhhhhh....eeeeee......hhhhhhhhhh..eeeeeee.hhhhhhhhhh....eee..hhhhhhhhhhhhh....eeeeeee....------.hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4buc A  16 PRGSHmKIGFLGFGKSNRSLLKYLLNHQEAKFFVSEAKTLDGETKKFLEEHSVEYEEGGHTEKLLDCDVVYVSPGIKPDTSmIELLSSRGVKLSTELQFFLDNVDPKKVVGITGTDGKSTATALmYHVLSGRGFKTFLGGNFGTPAVEALEGEYDYYVLEmSSFQLFWSERPYLSNFLVLNISEDHLDWHSSFKEYVDSKLKPAFLQTEGDLFVYNKHIERLRNLEGVRSRKIPFWTDENFATEKELIVRGKKYTLPGNYPYQmRENILAVSVLYmEmFNELESFLELLRDFKPLPHRmEYLGQIDGRHFYNDSKATSTHAVLGALSNFDKVVLImCGIGKKENYSLFVEKASPKLKHLImFGEISKELAPFVGKIPHSIVENmEEAFEKAmEVSEKGDVILLSPGGASF------AKRGEHFREIFKRHGGD 448
                                 |  25        35        45        55        65        75        85        95 |     105       115       125       135    |  145       155       165       175|      185       195       205       215       225       235       245       255       265       275   |   285     | 295       305       315       325       335       345     | 355       365       375|      385       395   |   405 |     415       425      |435       445   
                                 |                                                                          97-MSE                                    140-MSE                             176-MSE                                                                                                279-MSE     291-MSE                314-MSE                              351-MSE                  376-MSE                399-MSE 407-MSE           425    432                
                                21-MSE                                                                                                                                                                                                                                                                         293-MSE

Chain B from PDB  Type:PROTEIN  Length:427
 aligned with MURD_THEMA | Q9WY76 from UniProtKB/Swiss-Prot  Length:430

    Alignment length:433
                                 1                                                                                                                                                                                                                                                                                                                                                                                                                                           
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425   
           MURD_THEMA     - -----MKIGFLGFGKSNRSLLKYLLNHQEAKFFVSEAKTLDGETKKFLEEHSVEYEEGGHTEKLLDCDVVYVSPGIKPDTSMIELLSSRGVKLSTELQFFLDNVDPKKVVGITGTDGKSTATALMYHVLSGRGFKTFLGGNFGTPAVEALEGEYDYYVLEMSSFQLFWSERPYLSNFLVLNISEDHLDWHSSFKEYVDSKLKPAFLQTEGDLFVYNKHIERLRNLEGVRSRKIPFWTDENFATEKELIVRGKKYTLPGNYPYQMRENILAVSVLYMEMFNELESFLELLRDFKPLPHRMEYLGQIDGRHFYNDSKATSTHAVLGALSNFDKVVLIMCGIGKKENYSLFVEKASPKLKHLIMFGEISKELAPFVGKIPHSIVENMEEAFEKAMEVSEKGDVILLSPGGASFDMYENYAKRGEHFREIFKRHGGD 428
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhh.eeeee..hhhhhhhhhhhhh....eeeee.....hhhhhhhhhhh..eee....hhhhhhh.eeee.......hhhhhhhhhh..eeehhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhhhh...eeeee....hhhhhhh....eeeee.hhhhhhhh......eeee............hhhhhhhhhhhhhhhh....eeeee.hhhhh........eeeee.....ee...eeee..eeee.....hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh........eeeeee..eeeee.....hhhhhhhhhh....eeeeee......hhhhhhhhhh..eeeeeee.hhhhhhhhhh....eee..hhhhhhhhhhhhh....eeeeeee....------.hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4buc B  16 PRGSHmKIGFLGFGKSNRSLLKYLLNHQEAKFFVSEAKTLDGETKKFLEEHSVEYEEGGHTEKLLDCDVVYVSPGIKPDTSmIELLSSRGVKLSTELQFFLDNVDPKKVVGITGTDGKSTATALmYHVLSGRGFKTFLGGNFGTPAVEALEGEYDYYVLEmSSFQLFWSERPYLSNFLVLNISEDHLDWHSSFKEYVDSKLKPAFLQTEGDLFVYNKHIERLRNLEGVRSRKIPFWTDENFATEKELIVRGKKYTLPGNYPYQmRENILAVSVLYmEmFNELESFLELLRDFKPLPHRmEYLGQIDGRHFYNDSKATSTHAVLGALSNFDKVVLImCGIGKKENYSLFVEKASPKLKHLImFGEISKELAPFVGKIPHSIVENmEEAFEKAmEVSEKGDVILLSPGGASF------AKRGEHFREIFKRHGGD 448
                                 |  25        35        45        55        65        75        85        95 |     105       115       125       135    |  145       155       165       175|      185       195       205       215       225       235       245       255       265       275   |   285     | 295       305       315       325       335       345     | 355       365       375|      385       395   |   405 |     415       425      |435       445   
                                21-MSE                                                                      97-MSE                                    140-MSE                             176-MSE                                                                                                279-MSE     291-MSE                314-MSE                              351-MSE                  376-MSE                399-MSE 407-MSE           425    432                
                                                                                                                                                                                                                                                                                                               293-MSE

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SCOP Domains (0, 0)

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Gene Ontology (11, 11)

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