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(-) Description

Title :  C. BESCII FAMILY 3 PECTATE LYASE DOUBLE MUTANT K108A/Q111N IN COMPLEX WITH TRIGALACTURONIC ACID
 
Authors :  P. M. Alahuhta, V. V. Lunin
Date :  25 Mar 15  (Deposition) - 23 Dec 15  (Release) - 23 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.48
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Pl3, Parallel Beta-Helix, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Alahuhta, L. E. Taylor, R. Brunecky, D. W. Sammond, W. Michener, M. W. Adams, M. E. Himmel, Y. J. Bomble, V. Lunin
The Catalytic Mechanism And Unique Low Ph Optimum Of Caldicellulosiruptor Bescii Family 3 Pectate Lyase.
Acta Crystallogr. , Sect. D V. 71 1946 2015
PubMed-ID: 26327384  |  Reference-DOI: 10.1107/S1399004715013760

(-) Compounds

Molecule 1 - PECTATE LYASE
    Chains: A, B
    EC Number: 4.2.2.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: ATHE_1854
    Mutation: YES
    Organism Scientific: CALDICELLULOSIRUPTOR BESCII (STRAIN ATCC BAA- 1888 / DSM 6725 / Z-1320)
    Organism Taxid: 521460
    Strain: ATCC BAA-1888 / DSM 6725 / Z-1320

 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  (4, 25)

Asymmetric Unit (4, 25)
No.NameCountTypeFull Name
1ADA10Ligand/IonALPHA-D-GALACTOPYRANURONIC ACID
2CA8Ligand/IonCALCIUM ION
3GTR2Ligand/IonBETA-D-GALACTOPYRANURONIC ACID
4MPD5Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 1 (3, 9)
No.NameCountTypeFull Name
1ADA5Ligand/IonALPHA-D-GALACTOPYRANURONIC ACID
2CA-1Ligand/IonCALCIUM ION
3GTR1Ligand/IonBETA-D-GALACTOPYRANURONIC ACID
4MPD3Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 2 (3, 8)
No.NameCountTypeFull Name
1ADA5Ligand/IonALPHA-D-GALACTOPYRANURONIC ACID
2CA-1Ligand/IonCALCIUM ION
3GTR1Ligand/IonBETA-D-GALACTOPYRANURONIC ACID
4MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:37 , GLU A:84 , ASP A:107 , CA A:202 , ADA A:209 , ADA A:212 , HOH A:378 , HOH A:385 , HOH A:402binding site for residue CA A 201
02AC2SOFTWAREGLU A:39 , GLU A:84 , CA A:201 , ADA A:209 , ADA A:210 , ADA A:212 , ADA A:213 , HOH A:362binding site for residue CA A 202
03AC3SOFTWAREASP A:64 , GLU A:84 , ASP A:85 , ADA A:210 , ADA A:213 , HOH A:342 , HOH A:424binding site for residue CA A 203
04AC4SOFTWAREASP A:81 , VAL A:82 , GLU A:104 , HOH A:341 , HOH A:354 , HOH A:357 , HOH A:476binding site for residue CA A 204
05AC5SOFTWARELYS A:119 , GLU A:147 , SER A:186 , TYR A:193binding site for residue MPD A 205
06AC6SOFTWARETHR A:0 , ASN A:1 , LEU B:6 , ILE B:12 , TYR B:20 , HOH B:429binding site for residue MPD A 206
07AC7SOFTWARELEU A:6 , ILE A:8 , ILE A:12 , TYR A:20 , HOH A:420 , ASN B:1binding site for residue MPD A 207
08AC8SOFTWARELYS A:54 , ASP A:107 , LYS A:130 , ARG A:133 , LYS A:160 , ADA A:208 , ADA A:209 , ADA A:212 , HOH A:305 , HOH A:358 , HOH A:402 , HOH A:437 , HOH A:446binding site for residue GTR A 211
09AC9SOFTWAREGLU A:39 , GLU A:84 , ASP A:107 , ASN A:111 , ARG A:133 , ASN A:135 , GLY A:136 , CA A:201 , CA A:202 , ADA A:208 , ADA A:209 , ADA A:210 , GTR A:211 , ADA A:213 , HOH A:305 , HOH A:362 , HOH A:375 , HOH A:385 , HOH A:411binding site for residue ADA A 212
10AD1SOFTWAREGLU A:39 , GLU A:84 , ASP A:85 , ASN A:113 , ASN A:135 , CA A:202 , CA A:203 , ADA A:209 , ADA A:210 , ADA A:212 , HOH A:310 , HOH A:330 , HOH A:342 , HOH A:362 , HOH A:424binding site for residue ADA A 213
11AD2SOFTWAREGLN B:37 , GLU B:84 , ASP B:107 , CA B:202 , ADA B:208 , ADA B:211 , HOH B:382 , HOH B:389 , HOH B:404binding site for residue CA B 201
12AD3SOFTWAREGLU B:39 , GLU B:84 , CA B:201 , ADA B:208 , ADA B:209 , ADA B:211 , ADA B:212 , HOH B:330binding site for residue CA B 202
13AD4SOFTWAREASP B:64 , GLU B:84 , ASP B:85 , ADA B:209 , ADA B:212 , HOH B:307 , HOH B:415binding site for residue CA B 203
14AD5SOFTWAREASP B:81 , VAL B:82 , GLU B:104 , HOH B:324 , HOH B:359 , HOH B:362 , HOH B:480binding site for residue CA B 204
15AD6SOFTWAREASN A:137 , THR A:139 , HOH A:454 , LYS B:121 , ASP B:148 , ASN B:172 , HOH B:375binding site for residue MPD B 205
16AD7SOFTWAREASP B:81 , CYS B:116 , THR B:117 , LYS B:141 , HOH B:328 , HOH B:453binding site for residue MPD B 206
17AD8SOFTWARELYS A:103 , ASP B:107 , LYS B:130 , ARG B:133 , LYS B:160 , ADA B:207 , ADA B:208 , ADA B:211 , HOH B:304 , HOH B:305 , HOH B:308 , HOH B:382 , HOH B:451binding site for residue GTR B 210
18AD9SOFTWARELYS A:103 , GLU B:39 , GLU B:84 , ASP B:107 , ASN B:111 , ARG B:133 , ASN B:135 , GLY B:136 , CA B:201 , CA B:202 , ADA B:207 , ADA B:208 , ADA B:209 , GTR B:210 , ADA B:212 , HOH B:330 , HOH B:350 , HOH B:371 , HOH B:389 , HOH B:409 , HOH B:430binding site for residue ADA B 211
19AE1SOFTWAREHOH A:389 , GLU B:39 , GLU B:84 , ASP B:85 , ASN B:113 , ASN B:135 , CA B:202 , CA B:203 , ADA B:208 , ADA B:209 , ADA B:211 , HOH B:307 , HOH B:313 , HOH B:315 , HOH B:319 , HOH B:377 , HOH B:415 , HOH B:430 , HOH B:436binding site for residue ADA B 212
20AE2SOFTWAREGLU A:39 , LYS A:54 , GLU A:84 , ASP A:85 , ASP A:107 , ASN A:111 , ASN A:113 , LYS A:130 , ARG A:133 , ASN A:135 , GLY A:136 , LYS A:160 , CA A:201 , CA A:202 , CA A:203 , GTR A:211 , ADA A:212 , ADA A:213 , HOH A:305 , HOH A:310 , HOH A:330 , HOH A:342 , HOH A:355 , HOH A:358 , HOH A:362 , HOH A:375 , HOH A:385 , HOH A:402 , HOH A:411 , HOH A:424 , HOH A:446binding site for Poly-Saccharide residues ADA A 208 through ADA A 210
21AE3SOFTWARELEU A:6 , ILE A:8 , ILE A:12 , TYR A:20 , GLU A:39 , LYS A:54 , GLU A:84 , ASP A:85 , LYS A:103 , ASP A:107 , ASN A:111 , ASN A:113 , LYS A:130 , ARG A:133 , ASN A:135 , GLY A:136 , LYS A:160 , CA A:201 , CA A:202 , CA A:203 , GTR A:211 , ADA A:212 , ADA A:213 , HOH A:305 , HOH A:310 , HOH A:330 , HOH A:342 , HOH A:355 , HOH A:358 , HOH A:362 , HOH A:375 , HOH A:385 , HOH A:389 , HOH A:402 , HOH A:411 , HOH A:420 , HOH A:424 , HOH A:446 , ASN B:1 , GLU B:39 , GLU B:84 , ASP B:85 , ASP B:107 , ASN B:111 , ASN B:113 , LYS B:130 , ARG B:133 , ASN B:135 , GLY B:136 , LYS B:160 , CA B:201 , CA B:202 , CA B:203 , ADA B:211 , ADA B:212 , HOH B:304 , HOH B:305 , HOH B:307 , HOH B:308 , HOH B:313 , HOH B:315 , HOH B:319 , HOH B:330 , HOH B:377 , HOH B:382 , HOH B:393 , HOH B:409 , HOH B:415 , HOH B:422 , HOH B:430 , HOH B:451binding site for Poly-Saccharide residues ADA B 207 through ADA B 209

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:60 -Pro A:61
2Ala B:60 -Pro B:61

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YZQ)

(-) 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:198
                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeee...eee....eeeeeeeeeee...............eee....eeeeeee.......eee...eeee..ee.......eee...eeeeee..eeeeeeeeeeee...eeeeeeeeeeeeeeeeeee.......eeeeeeeeeeeeeeeeeee......eeeeeeeeeeeeeeeee..hhh.eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4yzq A  -4 HHVGTNTGGVLVITDTIIVKSGQTYDGKGIKIIAQGMGDGSQSENQKPIFKLEKGANLKNVIIGAPGCDGIHCYGDNVVENVVWEDVGEDALTVKSEGVVEVIGGSAKEAADAVFNLNAPCTFKVKNFTATNIGKLVRQNGNTTFKVVIYLEDVTLNNVKSCVAKSDSPVSELWYHNLNVNNCKTLFEFPSQSQIHQY 193
                                     5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185        


Chain B from PDB  Type:PROTEIN  Length:195
                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee...eee....eeeeeeeeeee...............eee....eeeeeee.......eee...eeee..ee.......eee...eeeeee..eeeeeeeeeeee...eeeeeeeeeeeeeeeeeee.......eeeeeeeeeeeeeeeeeee......eeeeeeeeeeee...ee..hhh.eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yzq B  -1 GTNTGGVLVITDTIIVKSGQTYDGKGIKIIAQGMGDGSQSENQKPIFKLEKGANLKNVIIGAPGCDGIHCYGDNVVENVVWEDVGEDALTVKSEGVVEVIGGSAKEAADAVFNLNAPCTFKVKNFTATNIGKLVRQNGNTTFKVVIYLEDVTLNNVKSCVAKSDSPVSELWYHNLNVNNCKTLFEFPSQSQIHQY 193
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188
   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 4YZQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)

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  4.2.2.2
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 Related Entries

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        B9MKT4_CALBD | B9MKT4: 3t9g 4ew9 4yz0 4yza 4yzx 4z03 4z05 4z06

(-) Related Entries Specified in the PDB File

4yz0 4yza 4yzx 4z03 4z05 4z06