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(-) Description

Title :  C. BESCII FAMILY 3 PECTATE LYASE DOUBLE MUTANT K108A/E39Q IN COMPLEX WITH TRIGALACTURONIC ACID
 
Authors :  P. M. Alahuhta, V. V. Lunin
Date :  24 Mar 15  (Deposition) - 23 Dec 15  (Release) - 23 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.15
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  (8, 32)

Asymmetric Unit (8, 32)
No.NameCountTypeFull Name
1ADA11Ligand/IonALPHA-D-GALACTOPYRANURONIC ACID
2CA8Ligand/IonCALCIUM ION
3GTR2Ligand/IonBETA-D-GALACTOPYRANURONIC ACID
4IMD1Ligand/IonIMIDAZOLE
5MPD3Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
6MRD5Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
7X0X1Ligand/IonBETA-D-TALOPYRANURONIC ACID
8X1X1Ligand/IonALPHA-D-TALOPYRANURONIC ACID
Biological Unit 1 (6, 13)
No.NameCountTypeFull Name
1ADA4Ligand/IonALPHA-D-GALACTOPYRANURONIC ACID
2CA-1Ligand/IonCALCIUM ION
3GTR1Ligand/IonBETA-D-GALACTOPYRANURONIC ACID
4IMD1Ligand/IonIMIDAZOLE
5MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
6MRD4Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
7X0X-1Ligand/IonBETA-D-TALOPYRANURONIC ACID
8X1X1Ligand/IonALPHA-D-TALOPYRANURONIC ACID
Biological Unit 2 (5, 11)
No.NameCountTypeFull Name
1ADA7Ligand/IonALPHA-D-GALACTOPYRANURONIC ACID
2CA-1Ligand/IonCALCIUM ION
3GTR1Ligand/IonBETA-D-GALACTOPYRANURONIC ACID
4IMD-1Ligand/IonIMIDAZOLE
5MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
6MRD1Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
7X0X1Ligand/IonBETA-D-TALOPYRANURONIC ACID
8X1X-1Ligand/IonALPHA-D-TALOPYRANURONIC ACID

(-) Sites  (28, 28)

Asymmetric Unit (28, 28)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:37 , GLN A:39 , GLU A:84 , ASP A:107 , CA A:202 , ADA A:213 , ADA A:216 , HOH A:399 , HOH A:428binding site for residue CA A 201
02AC2SOFTWAREGLN A:39 , GLU A:84 , CA A:201 , ADA A:213 , ADA A:214 , ADA A:216 , ADA A:217 , HOH A:349binding site for residue CA A 202
03AC3SOFTWAREASP A:64 , GLU A:84 , ASP A:85 , ADA A:214 , ADA A:217 , HOH A:346 , HOH A:483binding site for residue CA A 203
04AC4SOFTWAREASP A:81 , VAL A:82 , GLU A:104 , HOH A:372 , HOH A:392 , HOH A:423 , HOH A:497binding site for residue CA A 204
05AC5SOFTWAREASN A:153 , VAL A:154 , LYS A:155 , ASN A:177 , HOH A:305 , HOH A:330binding site for residue IMD A 205
06AC6SOFTWARELYS A:119 , TYR A:145 , GLU A:147 , PRO A:164 , SER A:186 , TYR A:193 , HOH A:347binding site for residue MPD A 206
07AC7SOFTWARELYS A:141 , ASP A:162 , GLU A:167 , TRP A:169 , PHE A:184 , PRO A:185 , MRD A:208 , HOH A:301 , HOH A:309 , HOH A:322 , HOH A:323 , HOH A:336 , HOH A:363 , HOH A:516 , HOH A:520binding site for residue MPD A 207
08AC8SOFTWARELYS A:141 , ASP A:162 , GLU A:167 , PHE A:184 , PRO A:185 , MPD A:207 , HOH A:301 , HOH A:309 , HOH A:322 , HOH A:323 , HOH A:336 , HOH A:341 , HOH A:363 , HOH A:520binding site for residue MRD A 208
09AC9SOFTWAREVAL A:5 , ILE A:57 , HOH A:357 , HOH A:440 , HOH A:498 , ADA B:209 , ADA B:212 , ADA B:215 , HOH B:336 , HOH B:360 , HOH B:535binding site for residue MRD A 209
10AD1SOFTWARETHR A:0 , ASN A:1 , GLY A:4 , LEU B:6 , ILE B:12 , TYR B:20 , MPD B:205 , HOH B:433binding site for residue MRD A 210
11AD2SOFTWAREILE A:8 , ILE A:12 , TYR A:20 , HOH A:441 , ASN B:1binding site for residue MRD A 211
12AD3SOFTWAREASP A:107 , LYS A:130 , ARG A:133 , LYS A:160 , X1X A:212 , ADA A:213 , ADA A:216 , HOH A:326 , HOH A:387 , HOH A:428 , HOH A:493binding site for residue GTR A 215
13AD4SOFTWAREGLN A:39 , GLU A:84 , ASP A:107 , GLN A:111 , ARG A:133 , ASN A:135 , GLY A:136 , CA A:201 , CA A:202 , X1X A:212 , ADA A:213 , ADA A:214 , GTR A:215 , ADA A:217 , HOH A:326 , HOH A:328 , HOH A:428 , HOH A:445binding site for residue ADA A 216
14AD5SOFTWAREGLN A:39 , GLU A:84 , ASP A:85 , GLN A:111 , ASN A:113 , ASN A:135 , CA A:202 , CA A:203 , ADA A:213 , ADA A:214 , ADA A:216 , HOH A:317 , HOH A:333 , HOH A:343 , HOH A:346 , HOH A:439 , HOH A:483binding site for residue ADA A 217
15AD6SOFTWAREGLN B:37 , GLN B:39 , GLU B:84 , ASP B:107 , CA B:202 , ADA B:208 , ADA B:211 , ADA B:214 , HOH B:352 , HOH B:379 , HOH B:385binding site for residue CA B 201
16AD7SOFTWAREGLN B:39 , GLU B:84 , CA B:201 , ADA B:208 , ADA B:209 , ADA B:211 , ADA B:212 , ADA B:214 , ADA B:215 , HOH B:335binding site for residue CA B 202
17AD8SOFTWAREASP B:64 , GLU B:84 , ASP B:85 , ADA B:209 , ADA B:212 , ADA B:215 , HOH B:354 , HOH B:484binding site for residue CA B 203
18AD9SOFTWAREASP B:81 , VAL B:82 , GLU B:104 , HOH B:393 , HOH B:406 , HOH B:408 , HOH B:495binding site for residue CA B 204
19AE1SOFTWARELEU A:6 , ILE A:25 , MRD A:210 , HOH A:500 , TYR B:20 , HOH B:486binding site for residue MPD B 205
20AE2SOFTWAREASN A:137 , THR A:139 , HOH A:479 , ASN B:122 , ASP B:148 , ASN B:172 , HOH B:313 , HOH B:416binding site for residue MRD B 206
21AE3SOFTWARELYS A:103 , ASP B:107 , LYS B:130 , ARG B:133 , LYS B:160 , ADA B:208 , ADA B:210 , ADA B:211 , GTR B:213 , ADA B:214 , HOH B:310 , HOH B:312 , HOH B:345binding site for residue X0X B 207
22AE4SOFTWARELYS A:103 , HOH A:321 , GLN B:39 , GLU B:84 , ASP B:107 , GLN B:111 , ARG B:133 , ASN B:135 , GLY B:136 , CA B:201 , CA B:202 , X0X B:207 , ADA B:209 , ADA B:210 , ADA B:211 , ADA B:212 , GTR B:213 , ADA B:214 , ADA B:215 , HOH B:312 , HOH B:352 , HOH B:424 , HOH B:443binding site for residue ADA B 208
23AE5SOFTWAREMRD A:209 , GLN B:39 , GLU B:84 , ASP B:85 , GLN B:111 , ASN B:113 , ASN B:135 , CA B:202 , CA B:203 , ADA B:208 , ADA B:211 , ADA B:212 , ADA B:214 , ADA B:215 , HOH B:319 , HOH B:336 , HOH B:354 , HOH B:355 , HOH B:360 , HOH B:387 , HOH B:418 , HOH B:484binding site for residue ADA B 209
24AE6SOFTWARELYS A:103 , ASP B:107 , LYS B:130 , ARG B:133 , LYS B:160 , X0X B:207 , ADA B:208 , ADA B:210 , ADA B:211 , ADA B:214 , HOH B:310 , HOH B:312 , HOH B:345binding site for residue GTR B 213
25AE7SOFTWARELYS A:103 , HOH A:321 , GLN B:39 , GLU B:84 , ASP B:107 , GLN B:111 , ARG B:133 , ASN B:135 , GLY B:136 , CA B:201 , CA B:202 , X0X B:207 , ADA B:208 , ADA B:209 , ADA B:210 , ADA B:211 , ADA B:212 , GTR B:213 , ADA B:215 , HOH B:312 , HOH B:352 , HOH B:424 , HOH B:443binding site for residue ADA B 214
26AE8SOFTWAREMRD A:209 , GLN B:39 , GLU B:84 , ASP B:85 , GLN B:111 , ASN B:113 , ASN B:135 , CA B:202 , CA B:203 , ADA B:208 , ADA B:209 , ADA B:211 , ADA B:212 , ADA B:214 , HOH B:319 , HOH B:336 , HOH B:354 , HOH B:355 , HOH B:360 , HOH B:387 , HOH B:418 , HOH B:484binding site for residue ADA B 215
27AE9SOFTWAREGLN A:39 , GLU A:84 , ASP A:85 , ASP A:107 , GLN 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:215 , ADA A:216 , ADA A:217 , HOH A:314 , HOH A:317 , HOH A:326 , HOH A:328 , HOH A:333 , HOH A:343 , HOH A:346 , HOH A:387 , HOH A:439 , HOH A:445 , HOH A:483 , HOH A:504binding site for Poly-Saccharide residues X1X A 212 through ADA A 214
28AF1SOFTWARETHR A:0 , ASN A:1 , GLY A:4 , ILE A:8 , ILE A:12 , TYR A:20 , GLN A:39 , GLU A:84 , ASP A:85 , LYS A:103 , ASP A:107 , GLN 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 , MRD A:209 , GTR A:215 , ADA A:216 , ADA A:217 , HOH A:314 , HOH A:317 , HOH A:321 , HOH A:326 , HOH A:328 , HOH A:333 , HOH A:343 , HOH A:346 , HOH A:387 , HOH A:439 , HOH A:441 , HOH A:445 , HOH A:483 , HOH A:504 , ASN B:1 , LEU B:6 , ILE B:12 , TYR B:20 , GLN B:39 , GLU B:84 , ASP B:85 , ASP B:107 , GLN 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 , MPD B:205 , X0X B:207 , ADA B:208 , ADA B:209 , ADA B:215 , HOH B:310 , HOH B:312 , HOH B:319 , HOH B:336 , HOH B:345 , HOH B:352 , HOH B:354 , HOH B:355 , HOH B:360 , HOH B:387 , HOH B:391 , HOH B:418 , HOH B:424 , HOH B:433 , HOH B:443 , HOH B:484 , HOH B:485binding site for Poly-Saccharide residues ADA B 210 through ADA B 212

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4YZ0)

(-) 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 4YZ0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4YZ0)

(-) Exons   (0, 0)

(no "Exon" information available for 4YZ0)

(-) 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...eeeeeeee.......eee...eeeeee..eeeeeeeeeeee...eeeeeeeeeeeeeeeeeee.......eeeeeeeeeeeeeeeeeee......eeeeeeeeeeee...ee..hhh.eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4yz0 A  -4 HHVGTNTGGVLVITDTIIVKSGQTYDGKGIKIIAQGMGDGSQSQNQKPIFKLEKGANLKNVIIGAPGCDGIHCYGDNVVENVVWEDVGEDALTVKSEGVVEVIGGSAKEAADAVFQLNAPCTFKVKNFTATNIGKLVRQNGNTTFKVVIYLEDVTLNNVKSCVAKSDSPVSELWYHNLNVNNCKTLFEFPSQSQIHQY 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...eeeeeeee.......eee...eeeeee..eeeeeeeeeeee...eeeeeeeeeeeeeeeeeee.......eeeeeeeeeeeeeeeeeee......eeeeeeeeeeee...ee..hhh.eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yz0 B  -1 GTNTGGVLVITDTIIVKSGQTYDGKGIKIIAQGMGDGSQSQNQKPIFKLEKGANLKNVIIGAPGCDGIHCYGDNVVENVVWEDVGEDALTVKSEGVVEVIGGSAKEAADAVFQLNAPCTFKVKNFTATNIGKLVRQNGNTTFKVVIYLEDVTLNNVKSCVAKSDSPVSELWYHNLNVNNCKTLFEFPSQSQIHQY 193
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188
   Legend:   → Mismatch (orange background)
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  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 4YZ0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4YZ0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4YZ0)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

(-) Related Entries Specified in the PDB File

4yza 4yzq 4yzx 4z03 4z05 4z06