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(-) Description

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

  12
Asymmetric Unit : AB
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.NameCountTypeFull Name
1CL6Ligand/IonCHLORIDE ION
2GOL6Ligand/IonGLYCEROL
3MSE24Mod. Amino AcidSELENOMETHIONINE
4NH42Ligand/IonAMMONIUM ION
5PO32Ligand/IonPHOSPHITE ION
6PO416Ligand/IonPHOSPHATE ION
Biological Unit 1 (5, 25)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL3Ligand/IonGLYCEROL
3MSE12Mod. Amino AcidSELENOMETHIONINE
4NH41Ligand/IonAMMONIUM ION
5PO31Ligand/IonPHOSPHITE ION
6PO48Ligand/IonPHOSPHATE ION
Biological Unit 2 (5, 25)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL3Ligand/IonGLYCEROL
3MSE12Mod. Amino AcidSELENOMETHIONINE
4NH41Ligand/IonAMMONIUM ION
5PO31Ligand/IonPHOSPHITE ION
6PO48Ligand/IonPHOSPHATE ION

(-) Sites  (32, 32)

Asymmetric Unit (32, 32)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:133 , SER A:177 , SER A:178 , PHE A:179 , ASP A:203 , TYR A:211 , LYS A:215BINDING SITE FOR RESIDUE PO4 A1000
02AC2SOFTWAREGLY A:132 , THR A:135 , MSE A:279 , ASN A:282 , GOL A:1202BINDING SITE FOR RESIDUE PO4 A1001
03AC3SOFTWAREASN A:196 , ASN A:231 , HIS A:233 , TYR A:277 , GLU A:281 , HOH A:2093 , HOH A:2094BINDING SITE FOR RESIDUE PO4 A1002
04AC4SOFTWAREASP A:120 , LYS A:123 , GLU A:168 , HOH A:2056 , HOH A:2084 , HOH A:2169BINDING SITE FOR RESIDUE PO4 A1003
05AC5SOFTWARELYS A:30 , SER A:31 , SER A:88 , PRO A:89 , NH4 A:1501 , HOH A:2001 , HOH A:2003BINDING SITE FOR RESIDUE PO4 A1004
06AC6SOFTWAREASP A:213 , ARG A:238 , GLU A:404 , MSE A:407 , HIS A:445 , HOH A:2160 , HOH A:2166BINDING SITE FOR RESIDUE PO4 A1005
07AC7SOFTWARETYR A:86 , LYS A:107 , SER A:109 , PHE A:114 , ASP A:117 , GLU A:185BINDING SITE FOR RESIDUE PO4 A1006
08AC8SOFTWAREALA 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:2017BINDING SITE FOR RESIDUE PO4 A1007
09AC9SOFTWARESER A:96 , MSE A:97 , PO4 A:1007 , HOH A:2040 , GLY B:74 , HIS B:75 , SER B:96 , PO3 B:1008BINDING SITE FOR RESIDUE PO3 A1008
10BC1SOFTWAREPHE A:182 , TRP A:183 , ILE A:395 , GLU A:397 , GLU A:401 , HOH A:2043BINDING SITE FOR RESIDUE GOL A1200
11BC2SOFTWAREARG A:33 , LYS A:37 , PHE A:62BINDING SITE FOR RESIDUE GOL A1201
12BC3SOFTWAREGLY A:132 , LYS A:133 , SER A:134 , THR A:135 , PO4 A:1001BINDING SITE FOR RESIDUE GOL A1202
13BC4SOFTWAREGLU A:111 , GLY A:155 , ALA A:161 , GLN A:180 , HOH A:2004BINDING SITE FOR RESIDUE CL A1400
14BC5SOFTWAREPHE A:28 , GLU A:51 , LYS A:53BINDING SITE FOR RESIDUE CL A1401
15BC6SOFTWAREGLY A:27 , GLU A:51 , ALA A:52 , HIS A:75 , PO4 A:1007BINDING SITE FOR RESIDUE CL A1402
16BC7SOFTWAREPO4 A:1004BINDING SITE FOR RESIDUE NH4 A1501
17BC8SOFTWARELYS B:133 , SER B:177 , SER B:178 , PHE B:179 , ASP B:203 , TYR B:211 , LYS B:215 , HOH B:2031BINDING SITE FOR RESIDUE PO4 B1000
18BC9SOFTWAREGLY B:132 , THR B:135 , GLN B:278 , MSE B:279 , ASN B:282 , GOL B:1202BINDING SITE FOR RESIDUE PO4 B1001
19CC1SOFTWAREASN B:196 , ASN B:231 , HIS B:233 , TYR B:277 , GLU B:281 , HOH B:2046 , HOH B:2047BINDING SITE FOR RESIDUE PO4 B1002
20CC2SOFTWAREASP B:120 , LYS B:123 , GLU B:168 , HOH B:2024BINDING SITE FOR RESIDUE PO4 B1003
21CC3SOFTWARELYS B:30 , SER B:31 , PRO B:89 , NH4 B:1501 , HOH B:2001 , HOH B:2002BINDING SITE FOR RESIDUE PO4 B1004
22CC4SOFTWAREASP B:213 , ARG B:238 , GLU B:404 , MSE B:407 , HIS B:445 , HOH B:2057 , HOH B:2084BINDING SITE FOR RESIDUE PO4 B1005
23CC5SOFTWARETYR B:86 , LYS B:107 , SER B:109 , PHE B:114 , ASP B:117 , GLU B:185BINDING SITE FOR RESIDUE PO4 B1006
24CC6SOFTWAREALA 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:2020BINDING SITE FOR RESIDUE PO4 B1007
25CC7SOFTWAREGLY 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:2020BINDING SITE FOR RESIDUE PO3 B1008
26CC8SOFTWAREPHE B:182 , TRP B:183 , GLU B:397 , GLU B:401 , HOH B:2022BINDING SITE FOR RESIDUE GOL B1200
27CC9SOFTWAREARG B:33 , LYS B:37 , GLU B:58 , PHE B:62BINDING SITE FOR RESIDUE GOL B1201
28DC1SOFTWAREGLY B:132 , LYS B:133 , SER B:134 , THR B:135 , PO4 B:1001BINDING SITE FOR RESIDUE GOL B1202
29DC2SOFTWAREGLU B:111 , GLY B:155 , PRO B:160 , ALA B:161 , GLN B:180BINDING SITE FOR RESIDUE CL B1400
30DC3SOFTWAREPHE B:28 , GLU B:51BINDING SITE FOR RESIDUE CL B1401
31DC4SOFTWAREGLY B:27 , GLU B:51 , ALA B:52 , HIS B:75 , PO4 B:1007BINDING SITE FOR RESIDUE CL B1402
32DC5SOFTWAREPO4 B:1004BINDING SITE FOR RESIDUE NH4 B1501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4BUC)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asp A:200 -His A:201
2Asp B:200 -His B:201

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4BUC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4BUC)

(-) Exons   (0, 0)

(no "Exon" information available for 4BUC)

(-) 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
   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  (0, 0)

(no "SCOP Domain" information available for 4BUC)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4BUC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4BUC)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (MURD_THEMA | Q9WY76)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0008764    UDP-N-acetylmuramoylalanine-D-glutamate ligase activity    Catalysis of the reaction: D-glutamate + ATP + UDP-N-acetylmuramoyl-L-alanine = ADP + 2 H(+) + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-glutamate.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    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:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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4bub CRYSTAL STRUCTURE OF MURE LIGASE FROM THERMOTOGA MARITIMA IN COMPLEX WITH ADP