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(-) Description

Title :  CRYSTAL STRUCTURE OF ENDOGLYCOCERAMIDASE I FROM RHODOCOC-CUS EQUI
 
Authors :  L. Chen
Date :  02 Jul 15  (Deposition) - 02 Sep 15  (Release) - 05 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.11
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Apo, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. B. Han, L. Q. Chen, Z. Li, Y. M. Tan, Y. Feng, G. Y. Yang
Structural Insights Into The Broad Substrate Specificity Of A Novel Endoglycoceramidase I Belonging To A New Subfamily Of Gh5 Glycosidases
J. Biol. Chem. V. 292 4789 2017
PubMed-ID: 28179425  |  Reference-DOI: 10.1074/JBC.M116.763821

(-) Compounds

Molecule 1 - PUTATIVE SECRETED ENDOGLYCOSYLCERAMIDASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'
    Expression System Strain: BL21-GOLD(DE3)PLYSS AG
    Expression System Taxid: 866768
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 27-492
    Gene: REQ_38260
    Organism Scientific: RHODOCOCCUS EQUI
    Organism Taxid: 685727
    Strain: 103S

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 20)

Asymmetric/Biological Unit (2, 20)
No.NameCountTypeFull Name
1EDO19Ligand/Ion1,2-ETHANEDIOL
2NA1Ligand/IonSODIUM ION

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:222 , PRO A:223 , GLU A:267 , PRO A:268 , VAL A:270 , TRP A:272 , ASN A:273 , PRO A:298 , HIS A:299binding site for residue EDO A 601
02AC2SOFTWAREARG A:90 , PHE A:432 , VAL A:433 , SER A:434 , ASP A:435 , ARG A:458 , HOH A:718binding site for residue EDO A 602
03AC3SOFTWAREILE A:41 , THR A:42 , ASP A:53 , ARG A:57 , HIS A:133 , HOH A:703binding site for residue EDO A 603
04AC4SOFTWARETHR A:39 , PRO A:40 , ILE A:41 , ALA A:129 , GLY A:131 , EDO A:606binding site for residue EDO A 604
05AC5SOFTWARETRP A:272 , PRO A:277 , SER A:278 , ASN A:331 , ALA A:334 , ARG A:338binding site for residue EDO A 605
06AC6SOFTWARETHR A:128 , ALA A:129 , PRO A:212 , EDO A:604 , HOH A:706 , HOH A:806binding site for residue EDO A 606
07AC7SOFTWAREALA A:443 , VAL A:444binding site for residue EDO A 607
08AC8SOFTWAREASP A:68 , TYR A:73 , LEU A:74 , GLY A:99 , THR A:100 , SER A:101 , TYR A:116 , HOH A:702binding site for residue EDO A 608
09AC9SOFTWAREPHE A:170 , GLU A:222 , ASN A:273 , GLN A:274binding site for residue EDO A 609
10AD1SOFTWAREARG A:228 , SER A:231 , CYS A:237 , PRO A:238 , ASP A:239 , PHE A:240 , HOH A:743binding site for residue EDO A 610
11AD2SOFTWAREGLU A:114 , ALA A:203 , ARG A:207binding site for residue EDO A 611
12AD3SOFTWAREASP A:68 , ASP A:70 , PRO A:72binding site for residue NA A 612
13AD4SOFTWAREGLN B:108 , ARG B:109 , ARG B:228 , PHE B:240 , THR B:243binding site for residue EDO B 601
14AD5SOFTWAREASP B:103 , SER B:144 , LYS B:145 , ASN B:150 , GLY B:151 , PHE B:152binding site for residue EDO B 602
15AD6SOFTWAREALA B:339 , ASN B:340 , HOH B:703 , HOH B:809binding site for residue EDO B 603
16AD7SOFTWAREHIS B:50 , LEU B:51 , THR B:58 , VAL B:59 , PHE B:367 , HOH B:717 , HOH B:732binding site for residue EDO B 604
17AD8SOFTWAREPRO B:168 , GLY B:169 , PHE B:170 , PRO B:171 , LEU B:172binding site for residue EDO B 605
18AD9SOFTWAREASP B:326 , ARG B:362 , ARG B:366binding site for residue EDO B 606
19AE1SOFTWAREPRO B:268 , ASN B:269 , THR B:271 , TRP B:272 , MET B:276 , PRO B:277 , SER B:278 , HOH B:707 , HOH B:748binding site for residue EDO B 607
20AE2SOFTWAREGLN B:245 , GLN B:249 , ALA B:288 , LEU B:289 , THR B:290 , THR B:291 , HOH B:715binding site for residue EDO B 608
21AE3SOFTWAREGLU B:114 , ALA B:115 , TYR B:116 , LEU B:117 , ARG B:119 , LEU B:120 , THR B:121 , GLY B:122 , ALA B:203 , LEU B:204 , ALA B:205 , GLU B:206 , VAL B:208 , GLU B:209 , HOH B:710binding site for Di-peptide ASP B 118 and ARG B 207

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:232 -A:237
2A:302 -A:321
3B:232 -B:237
4B:302 -B:321

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Ala A:71 -Pro A:72
2Phe A:170 -Pro A:171
3Phe A:233 -Pro A:234
4Pro A:283 -Pro A:284
5Trp A:373 -His A:374
6Phe B:170 -Pro B:171
7Phe B:233 -Pro B:234
8Pro B:283 -Pro B:284

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5CCU)

(-) 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:449
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee..eee.....ee..eeeee..............hhhhhhhhhhh...eeeeeehhhhhh......hhhhhhhhhhhhhhhhh...eeeeee.....hhhhh....hhhhh.............hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh....eeeee......hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh....eee..hhhhhhh..................eee..ee.hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh...ee.ee......hhhhhhhhhhhhh.eeee.............hhhhhhhh..eeeee.eeeeeeee......eeeeeee......eeee..........eeeee.eee.......eeeeee.....eeeeee.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ccu A  37 PATPITTLQADGTHLVDGYGRTVLLHGVNNVDKDAPYLPAGETLTPQDIDILVRHGFNTVRLGTSFDALMPQRGQIDEAYLDRLTGVVDALTARGMHVLLDNHQDGLSKAWGGNGFPEWAIESRPREWEPNPGFPLYYLMPSLNAGWDEVWGNTHGALDHLGTALGALAERVEGKPGVMGIELLNEPWPGSRFLSCFPNGCPDFDRTYQAAMQKLTDAVRAQNPTIPVYWEPNVTWNQMMPSNLFAPPVTPALTTADVVFAPHDYCIPSQLAIYLGLPQALRGLCVPQQDLTWSNIDAITERANVPTVITEFGDGDPTVLKNTLARADERFIGWQYWHFGAGNATDPFLGEVGRQLVRTYPQATAGEPGRMIFDADNGDFAYRFTPRAATRPTEIFVSDLHYPDGYAVQVDGGQVTSAPGARIVTVVADGSGPVTVKINRPGSAGAEVP 485
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476         


Chain B from PDB  Type:PROTEIN  Length:436
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee..eee.....ee..eeeee...hhhhh.....hhhhhhhhhhh...eeeeeehhhhhh......hhhhhhhhhhhhhhhhh...eeeeee.....hhhhh....hhhhh.............hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.....eeeee......hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh......eee..hhhhhhh..................eee..ee.hhhhhh....hhhhhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhh.eeee.............hhhhhhhh..eeeee.eeeeeeee......eeeeeee......eeee..........eeeee.eee.......eeeeee.....eeeeee.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ccu B  38 ATPITTLQADGTHLVDGYGRTVLLHGVNNVDKDAPYLPGETLTPQDIDILVRHGFNTVRLGTSFDALMPQRGQIDEAYLDRLTGVVDALTARGMHVLLDNHQDGLSKAWGGNGFPEWAIESRPREWEPNPGFPLYYLMPSLNAGWDEVWGNTHGALDHLGTALGALAERVEGKPGVMGIELLNEPWPGSRFLSCFPNGCPDFDRTYQAAMQKLTDAVRAQNPTIPVYWEPNVTWNQMMPSNLFAPPVTPALTTADVVFAPHDYCIPSQLARGLCVPQQDLTWSNIDAITERANVPTVITEFGDPTVLKNTLARADERFIGWQYWHFGAGNATDPFLGEVGRQLVRTYPQATAGEPGRMIFDADNGDFAYRFTPRAATRPTEIFVSDLHYPDGYAVQVDGGQVTSAPGARIVTVVADGSGPVTVKINRPGSAGAEVP 485
                                    47        57        67       |78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       316|      327       337       347 ||    359       369       379       389       399       409       419       429       439       449       459       469       479      
                                                                75|                                                                                                                                                                                                                                   307||                            349|                                                                                                                                     
                                                                 77                                                                                                                                                                                                                                    316|                             352                                                                                                                                     
                                                                                                                                                                                                                                                                                                        318
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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 5CCU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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