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(-) Description

Title :  CRYSTAL STRUCTURE OF THE 70 KDA SOLUBLE LYTIC TRANSGLYCOSYLASE SLT70 FROM ESCHERICHIA COLI AT 1.90 A RESOLUTION IN COMPLEX WITH A 1,6-ANHYDROMUROTRIPEPTIDE
 
Authors :  E. J. Van Asselt, A. -M. W. H. Thunnissen, B. W. Dijkstra
Date :  27 Jun 99  (Deposition) - 31 Aug 99  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha-Superhelix, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. J. Van Asselt, A. M. Thunnissen, B. W. Dijkstra
High Resolution Crystal Structures Of The Escherichia Coli Lytic Transglycosylase Slt70 And Its Complex With A Peptidoglycan Fragment.
J. Mol. Biol. V. 291 877 1999
PubMed-ID: 10452894  |  Reference-DOI: 10.1006/JMBI.1999.3013

(-) Compounds

Molecule 1 - SOLUBLE LYTIC TRANSGLYCOSYLASE SLT70
    Chains: A
    EC Number: 3.2.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: COMPLEXED WITH 1,6-ANHYDROMUROTRIPEPTIDE, DAL-ALA-AH0

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 22)

Asymmetric/Biological Unit (7, 22)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2AH01Ligand/Ion2-(2-ACETYLAMINO-4-HYDROXY-6,8-DIOXA-BICYCLO[3.2.1]OCT-3-YLOXY)-PROPIONIC ACID
3ALA1Mod. Amino AcidALANINE
4DAL1Ligand/IonD-ALANINE
5GOL5Ligand/IonGLYCEROL
6NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
7SO412Ligand/IonSULFATE ION

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:477 , GLU A:478 , VAL A:485 , SER A:487 , GLN A:496 , GLU A:583 , TYR A:587 , AH0 A:652 , HOH A:1050 , HOH A:1131 , HOH A:2211BINDING SITE FOR RESIDUE NAG A 651
02AC2SOFTWAREARG A:349 , ARG A:448 , ALA A:593 , TYR A:597 , HOH A:1404 , HOH A:2215BINDING SITE FOR RESIDUE SO4 A 701
03AC3SOFTWAREARG A:7 , ARG A:389 , HOH A:1672BINDING SITE FOR RESIDUE SO4 A 702
04AC4SOFTWARESER A:284 , THR A:285 , SER A:286 , HOH A:1486BINDING SITE FOR RESIDUE SO4 A 703
05AC5SOFTWARELEU A:396 , ASP A:397 , ASN A:398 , THR A:399 , LYS A:484 , HOH A:1453 , HOH A:1500 , HOH A:1741BINDING SITE FOR RESIDUE SO4 A 704
06AC6SOFTWARETRP A:113 , SER A:118 , ARG A:616 , HOH A:1111 , HOH A:1139 , HOH A:1244 , HOH A:1263 , HOH A:1633 , HOH A:1837BINDING SITE FOR RESIDUE SO4 A 705
07AC7SOFTWAREALA A:210 , GLN A:245 , HOH A:1349 , HOH A:1799 , HOH A:2114BINDING SITE FOR RESIDUE SO4 A 706
08AC8SOFTWAREPRO A:54 , ALA A:55 , ARG A:85 , HOH A:1063 , HOH A:1175 , HOH A:1693 , HOH A:1836BINDING SITE FOR RESIDUE SO4 A 708
09AC9SOFTWAREMET A:498 , PRO A:499 , GLY A:500 , HOH A:1475 , HOH A:1480 , HOH A:1537 , HOH A:1975BINDING SITE FOR RESIDUE SO4 A 709
10BC1SOFTWAREASN A:247 , GLU A:248 , HOH A:1481BINDING SITE FOR RESIDUE SO4 A 710
11BC2SOFTWAREARG A:302 , PRO A:467 , GLN A:468 , HOH A:1006 , HOH A:1365BINDING SITE FOR RESIDUE SO4 A 711
12BC3SOFTWAREARG A:147 , PRO A:181 , ALA A:182BINDING SITE FOR RESIDUE SO4 A 712
13BC4SOFTWAREARG A:162 , LYS A:166BINDING SITE FOR RESIDUE SO4 A 713
14BC5SOFTWARETYR A:10 , LYS A:14 , TYR A:40 , LEU A:396 , GOL A:907 , HOH A:1122 , HOH A:1252BINDING SITE FOR RESIDUE ACT A 801
15BC6SOFTWAREAH0 A:652 , DAL A:654 , HOH A:2103BINDING SITE FOR RESIDUE ALA A 653
16BC7SOFTWAREARG A:448 , ARG A:476 , AH0 A:652 , ALA A:653 , HOH A:1052 , HOH A:1663BINDING SITE FOR RESIDUE DAL A 654
17BC8SOFTWAREGLN A:477 , NAG A:651 , ALA A:653 , DAL A:654 , HOH A:1733 , HOH A:2024 , HOH A:2211BINDING SITE FOR RESIDUE AH0 A 652
18BC9SOFTWARELEU A:158 , THR A:211 , THR A:214 , GLU A:317 , HOH A:1077 , HOH A:1151BINDING SITE FOR RESIDUE GOL A 901
19CC1SOFTWAREARG A:359 , SER A:510 , PRO A:512 , ASP A:571 , ALA A:572 , TRP A:614 , HOH A:1047 , HOH A:1106 , HOH A:1126BINDING SITE FOR RESIDUE GOL A 902
20CC2SOFTWAREARG A:301 , ASP A:327 , ASP A:571 , HOH A:1014 , HOH A:1026 , HOH A:1047 , HOH A:1572BINDING SITE FOR RESIDUE GOL A 903
21CC3SOFTWAREARG A:545 , ARG A:599 , THR A:607 , MET A:609 , SER A:610 , HOH A:1081 , HOH A:1084 , HOH A:1136 , HOH A:1564 , HOH A:1867BINDING SITE FOR RESIDUE GOL A 904
22CC4SOFTWARETYR A:10 , TYR A:40 , LEU A:41 , ARG A:44 , ACT A:801 , HOH A:1316 , HOH A:1611 , HOH A:2107BINDING SITE FOR RESIDUE GOL A 907

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:106 -A:139

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1QTE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1QTE)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRANSGLYCOSYLASEPS00922 Prokaryotic transglycosylases signature.SLT_ECOLI501-529  1A:474-502

(-) Exons   (0, 0)

(no "Exon" information available for 1QTE)

(-) Sequences/Alignments

Asymmetric/Biological 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:619
 aligned with SLT_ECOLI | P0AGC3 from UniProtKB/Swiss-Prot  Length:645

    Alignment length:619
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   645 
                                    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       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       | 
            SLT_ECOLI    28 DSLDEQRSRYAQIKQAWDNRQMDVVEQMMPGLKDYPLYPYLEYRQITDDLMNQPAVTVTNFVRANPTLPPARTLQSRFVNELARREDWRGLLAFSPEKPGTTEAQCNYYYAKWNTGQSEEAWQGAKELWLTGKSQPNACDKLFSVWRASGKQDPLAYLERIRLAMKAGNTGLVTVLAGQMPADYQTIASAIISLANNPNTVLTFARTTGATDFTRQMAAVAFASVARQDAENARLMIPSLAQAQQLNEDQIQELRDIVAWRLMGNDVTDEQAKWRDDAIMRSQSTSLIERRVRMALGTGDRRGLNTWLARLPMEAKEKDEWRYWQADLLLERGREAEAKEILHQLMQQRGFYPMVAAQRIGEEYELKIDKAPQNVDSALTQGPEMARVRELMYWNLDNTARSEWANLVKSKSKTEQAQLARYAFNNQWWDLSVQATIAGKLWDHLEERFPLAYNDLFKRYTSGKEIPQSYAMAIARQESAWNPKVKSPVGASGLMQIMPGTATHTVKMFSIPGYSSPGQLLDPETNINIGTSYLQYVYQQFGNNRIFSSAAYNAGPGRVRTWLGNSAGRIDAVAFVESIPFSETRGYVKNVLAYDAYYRYFMGDKPTLMSATEWGRRY-   -
               SCOP domains d1qtea1 A:1-450 70 KDa soluble lytic transglycosylase (SLT70), superhelical domain                                                                                                                                                                                                                                                                                                                                                                                d1qtea2 A:451-618 70 kDa soluble lytic transglycosylase, SLT70                                                                                                          - SCOP domains
               CATH domains 1qteA01 A:1-363 70-kda Soluble Lytic Transglycosylase, domain 1                                                                                                                                                                                                                                                                                                            ------------1qteA02 A:376-445  [code=1.10.1240.20, no name defined]               1qteA03 A:446-618  [code=1.10.530.10, no name defined]                                                                                                                       - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SLT-1qteA01 A:455-575                                                                                                    -------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.....hhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh......hhhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhh.....................hhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhh....hhhhhh...hhhhhhhhhh....hhhhhhhhhhhhhh.................hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TRANSGLYCOSYLASE             --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qte A   1 DSLDEQRSRYAQIKQAWDNRQMDVVEQMMPGLKDYPLYPYLEYRQITDDLMNQPAVTVTNFVRANPTLPPARTLQSRFVNELARREDWRGLLAFSPEKPGTTEAQCNYYYAKWNTGQSEEAWQGAKELWLTGKSQPNACDKLFSVWRASGKQDPLAYLERIRLAMKAGNTGLVTVLAGQMPADYQTIASAIISLANNPNTVLTFARTTGATDFTRQMAAVAFASVARQDAENARLMIPSLAQAQQLNEDQIQELRDIVAWRLMGNDVTDEQAKWRDDAIMRSQSTSLIERRVRMALGTGDRRGLNTWLARLPMEAKEKDEWRYWQADLLLERGREAEAKEILHQLMQQRGFYPMVAAQRIGEEYELKIDKAPQNVDSALTQGPEMARVRELMYWNLDNTARSEWANLVKSKSKTEQAQLARYAFNNQWWDLSVQATIAGKLWDHLEERFPLAYNDLFKRYTSGKEIPQSYAMAIARQESAWNPKVKSPVGASGLMQIMPGTATHTVKMFSIPGYSSPGQLLDPETNINIGTSYLQYVYQQFGNNRIFSSAAYNAGPGRVRTWLGNSAGRIDAVAFVESIPFSETRGYVKNVLAYDAYYRYFMGDKPTLMSATEWGRRYA 653
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       ||
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   618|
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    653
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Lysozyme (266)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SLT_ECOLI | P0AGC3)
molecular function
    GO:0016837    carbon-oxygen lyase activity, acting on polysaccharides    Catalysis of the cleavage of a carbon-oxygen bond by the elimination of an alcohol from a polysaccharide.
    GO:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0008933    lytic transglycosylase activity    Catalysis of the specific cleavage of the beta-(1->4) glycosidic linkage between N-acetylmuramyl and N-acetylglucosaminyl residues in peptidoglycan, with the concomitant formation of 1,6-anhydro-N-acetylmuramyl residues.
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:0009253    peptidoglycan catabolic process    The chemical reactions and pathways resulting in the breakdown of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.
    GO:0000270    peptidoglycan metabolic process    The chemical reactions and pathways involving peptidoglycans, any of a class of glycoconjugates found only in bacterial cell walls and consisting of strands of glycosaminoglycan cross-linked by oligopeptides to form a huge and rigid network.
cellular component
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0030288    outer membrane-bounded periplasmic space    The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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        SLT_ECOLI | P0AGC3: 1qsa 1sly

(-) Related Entries Specified in the PDB File

1sly CONTAINS THE SAME PROTEIN COMPLEX WITH BULGECIN A