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(-) Description

Title :  CRYSTAL STRUCTURE OF MLTF FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH CELL-WALL TETRAPEPTIDE
 
Authors :  T. Dominguez-Gil, I. Acebron, J. A. Hermoso
Date :  23 Jul 15  (Deposition) - 12 Oct 16  (Release) - 22 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Lyase, Lytic Transglycosilase, Cell Wall Recycling (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Dominguez-Gil, M. Lee, I. Acebron-Avalos, K. V. Mahasenan, D. Hesek, D. A. Dik, B. Byun, E. Lastochkin, J. F. Fisher, S. Mobashery, J. A. Hermoso
Activation By Allostery In Cell-Wall Remodeling By A Modula Membrane-Bound Lytic Transglycosylase From Pseudomonas Aeruginosa.
Structure V. 24 1729 2016
PubMed-ID: 27618662  |  Reference-DOI: 10.1016/J.STR.2016.07.019

(-) Compounds

Molecule 1 - MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F
    Chains: A, C
    EC Number: 4.2.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 1402513
    Strain: BWHPSA013
    Synonym: MUREIN LYTIC TRANGLYCOSILASE F
 
Molecule 2 - MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F
    Chains: B, D
    EC Number: 4.2.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 1402513
    Strain: BWHPSA013
    Synonym: MUREIN LYTIC TRANGLYCOSILASE F

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
16X41Ligand/Ion[6-[[(2~{R})-1-AZANYL-1-OXIDANYLIDENE-PROPAN-2-YL]AMINO]-6-OXIDANYLIDENE-5-[[(4~{R})-5-OXIDANYL-5-OXIDANYLIDENE-4-[[(2~{S})-2-[[(2~{R})-2-OXIDANYLPROPANOYL]AMINO]PROPANOYL]AMINO]PENTANOYL]AMINO]HEXYL]AZANIUM
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
16X41Ligand/Ion[6-[[(2~{R})-1-AZANYL-1-OXIDANYLIDENE-PROPAN-2-YL]AMINO]-6-OXIDANYLIDENE-5-[[(4~{R})-5-OXIDANYL-5-OXIDANYLIDENE-4-[[(2~{S})-2-[[(2~{R})-2-OXIDANYLPROPANOYL]AMINO]PROPANOYL]AMINO]PENTANOYL]AMINO]HEXYL]AZANIUM
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
16X4-1Ligand/Ion[6-[[(2~{R})-1-AZANYL-1-OXIDANYLIDENE-PROPAN-2-YL]AMINO]-6-OXIDANYLIDENE-5-[[(4~{R})-5-OXIDANYL-5-OXIDANYLIDENE-4-[[(2~{S})-2-[[(2~{R})-2-OXIDANYLPROPANOYL]AMINO]PROPANOYL]AMINO]PENTANOYL]AMINO]HEXYL]AZANIUM
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
16X4-1Ligand/Ion[6-[[(2~{R})-1-AZANYL-1-OXIDANYLIDENE-PROPAN-2-YL]AMINO]-6-OXIDANYLIDENE-5-[[(4~{R})-5-OXIDANYL-5-OXIDANYLIDENE-4-[[(2~{S})-2-[[(2~{R})-2-OXIDANYLPROPANOYL]AMINO]PROPANOYL]AMINO]PENTANOYL]AMINO]HEXYL]AZANIUM
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
16X4-1Ligand/Ion[6-[[(2~{R})-1-AZANYL-1-OXIDANYLIDENE-PROPAN-2-YL]AMINO]-6-OXIDANYLIDENE-5-[[(4~{R})-5-OXIDANYL-5-OXIDANYLIDENE-4-[[(2~{S})-2-[[(2~{R})-2-OXIDANYLPROPANOYL]AMINO]PROPANOYL]AMINO]PENTANOYL]AMINO]HEXYL]AZANIUM

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:50 , ALA A:54 , PHE A:66 , GLU A:67 , LEU A:90 , TYR A:94 , GLY A:109 , LEU A:110 , THR A:111 , LEU A:127 , VAL A:155 , LEU A:156 , SER A:159 , SER A:160 , HIS A:161 , VAL A:185 , LEU A:188 , LEU A:201 , ASP A:203 , ASN A:205 , GLU A:206 , MET A:209 , LEU A:229 , TYR A:265 , TYR A:266BINDING SITE FOR RESIDUE 6X4 A 1458

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5AA4)

(-) Cis Peptide Bonds  (17, 17)

Asymmetric Unit
No.Residues
1Glu A:100 -Gly A:101
2Gly A:235 -Gly A:236
3Lys A:253 -Lys A:254
4Ala A:281 -Gln A:282
5Glu A:375 -Pro A:376
6Gln A:458 -Pro A:459
7Gly B:235 -Gly B:236
8Glu B:375 -Pro B:376
9Glu C:42 -Gly C:43
10Glu C:115 -Asp C:116
11Gly C:235 -Gly C:236
12Glu C:375 -Pro C:376
13Glu D:42 -Gly D:43
14Gly D:113 -Arg D:114
15Glu D:174 -Leu D:175
16Gly D:235 -Gly D:236
17Glu D:375 -Pro D:376

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5AA4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5AA4)

(-) Exons   (0, 0)

(no "Exon" information available for 5AA4)

(-) 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:418
                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.......eee..eeehhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhh.....ee.............eee....eee.eeeeee.......hhhhhh...eeee..hhhhhhhhhhhhhh.....eee...hhhhhhhhhhh....eeeeehhhhhhhhhhh..eeeeee....eee..eee....hhhhhhhhhhhhhh...hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.................hhhhhhhh......hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5aa4 A  42 EGVLRVITRNSPATYFQDRNGETGFEYELAKRFAERLGVELKIETADNLDDLYAQLSREGGPALAAAGLTPGREDDASVRYSHTYLDVTPQIIYRNGQQRPTRPEDLVGKRIMVLKGSSHAEQLAELKKQYPELKYEESDAVEVVDLLRMVDVGDIDLTLVDSNELAMNQVYFPNVRVAFDFGEARGLAWALPGGDDDSLMNEVNAFLDQAKKEGLLQRLKDRYYGHVDVLGYVGAYTFAQHLQQRLPRYESHFKQSGKQKDTDWRLLAAIGYQESLWQPGATSKTGVRGLMMLTNRTAQAMGVSNRLDPKQSIQGGSKYFVQIRSELPESIKEPDRSWFALAAYNIGGAHLEDARKMAEKEGLNPNKWLDVKKMLPRLAQKQWYAKTRYGYARGGETVHFVQNVRRYYDILTWVTQP 459
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451        


Chain B from PDB  Type:PROTEIN  Length:417
                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.......eee..eeehhhhhhhhhhhhhhh.eeeeee..hhhhhhhhhhh.....ee.............eee....eee.eeeeee.......hhhhhh....eee..hhhhhhhhhhhhhh.....eee...hhhhhhhhhhh....eeeeehhhhhhhhhhh..eeeeee....eee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.................hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5aa4 B  42 EGVLRVITRNSPATYFQDRNGETGFEYELAKRFAERLGVELKIETADNLDDLYAQLSREGGPALAAAGLTPGREDDASVRYSHTYLDVTPQIIYRNGQQRPTRPEDLVGKRIMVLKGSSHAEQLAELKKQYPELKYEESDAVEVVDLLRMVDVGDIDLTLVDSNELAMNQVYFPNVRVAFDFGEARGLAWALPGGDDDSLMNEVNAFLDQAKKEGLLQRLKDRYYGHVDVLGYVGAYTFTQHLQQRLPRYESHFKQSGKQKDTDWRLLAAIGYQESLWQPGATSKTGVRGLMMLTNRTAQAMGVSNRLDPKQSIQGGSKYFVQIRSELPESIKEPDRSWFALAAYNIGGAHLEDARKMAEKEGLNPNKWLDVKKMLPRLAQKQWYAKTRYGYARGGETVHFVQNVRRYYDILTWVTQ 458
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       


Chain C from PDB  Type:PROTEIN  Length:413
                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.......eee..eeehhhhhhhhhhhhh...eeeeee..hhhhhhhhhh......ee.............eee....eee..eeeee................eeee..hhhhhhhhhhhh.......eee...hhhhhhhhhhhh...eeeehhhhhhhhhhhh..eeeeee....eee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.................hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5aa4 C  42 EGVLRVITRNSPATYFQDRNGETGFEYELAKRFAERLGVELKIETADNLDDLYAQLSREGGPALAAAGLTPGREDDASVRYSHTYLDVTPQIIYRNGQQRPTRPEDLVGKRIMVLKGSSHAEQLAELKKQYPELKYEESDAVEVVDLLRMVDVGDIDLTLVDSNELAMNQVYFPNVRVAFDFGEARGLAWALPGGDDDSLMNEVNAFLDQAKKEGLLQRLKDRYYGHGYVGAYTFAQHLQQRLPRYESHFKQSGKQKDTDWRLLAAIGYQESLWQPGATSKTGVRGLMMLTNRTAQAMGVSNRLDPKQSIQGGSKYFVQIRSELPESIKEPDRSWFALAAYNIGGAHLEDARKMAEKEGLNPNKWLDVKKMLPRLAQKQWYAKTRYGYARGGETVHFVQNVRRYYDILTWVTQ 458
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261      |275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455   
                                                                                                                                                                                                                                                            268|                                                                                                                                                                                         
                                                                                                                                                                                                                                                             273                                                                                                                                                                                         


Chain D from PDB  Type:PROTEIN  Length:417
                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.......eee..eeehhhhhhhhhhhhhhh.eeeeee..hhhhhhhhhh......ee.............eee....eee.eeeeee.......hhhhhh....eee..hhhhhhhhhhhh.......eee...hhhhhhhhhhhh....eeeehhhhhhhhhhh..eeeeee....eee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.................hhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5aa4 D  42 EGVLRVITRNSPATYFQDRNGETGFEYELAKRFAERLGVELKIETADNLDDLYAQLSREGGPALAAAGLTPGREDDASVRYSHTYLDVTPQIIYRNGQQRPTRPEDLVGKRIMVLKGSSHAEQLAELKKQYPELKYEESDAVEVVDLLRMVDVGDIDLTLVDSNELAMNQVYFPNVRVAFDFGEARGLAWALPGGDDDSLMNEVNAFLDQAKKEGLLQRLKDRYYGHVDVLGYVGAYTFTQHLQQRLPRYESHFKQSGKQKDTDWRLLAAIGYQESLWQPGATSKTGVRGLMMLTNRTAQAMGVSNRLDPKQSIQGGSKYFVQIRSELPESIKEPDRSWFALAAYNIGGAHLEDARKMAEKEGLNPNKWLDVKKMLPRLAQKQWYAKTRYGYARGGETVHFVQNVRRYYDILTWVTQ 458
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451
   Legend:   → Mismatch (orange background)
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  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 5AA4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5AA4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5AA4)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5AA4)

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 Related Entries

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(-) Related Entries Specified in the PDB File

5aa1 CRYSTAL STRUCTURE OF MLTF FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH NAG-ANHNAM-PENTAPEPTIDE
5aa2 CRYSTAL STRUCTURE OF MLTF FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH NAM-PENTAPEPTIDE.
5aa3 CRYSTAL STRUCTURE OF MLTF FROM PSEUDOMONAS AERUGINOSA IN THE PRESENCE OF TETRASACCHARIDE AND TETRAPEPTIDE