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(-) Description

Title :  C. BESCII FAMILY 3 PECTATE LYASE DOUBLE MUTANT K108A/D107N 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 :  1.25
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  (7, 27)

Asymmetric Unit (7, 27)
No.NameCountTypeFull Name
1ADA8Ligand/IonALPHA-D-GALACTOPYRANURONIC ACID
2CA8Ligand/IonCALCIUM ION
3CL2Ligand/IonCHLORIDE ION
4GTR1Ligand/IonBETA-D-GALACTOPYRANURONIC ACID
5IMD2Ligand/IonIMIDAZOLE
6MPD4Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
7MRD2Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
Biological Unit 1 (4, 8)
No.NameCountTypeFull Name
1ADA3Ligand/IonALPHA-D-GALACTOPYRANURONIC ACID
2CA-1Ligand/IonCALCIUM ION
3CL-1Ligand/IonCHLORIDE ION
4GTR-1Ligand/IonBETA-D-GALACTOPYRANURONIC ACID
5IMD1Ligand/IonIMIDAZOLE
6MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
7MRD2Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
Biological Unit 2 (4, 9)
No.NameCountTypeFull Name
1ADA5Ligand/IonALPHA-D-GALACTOPYRANURONIC ACID
2CA-1Ligand/IonCALCIUM ION
3CL-1Ligand/IonCHLORIDE ION
4GTR1Ligand/IonBETA-D-GALACTOPYRANURONIC ACID
5IMD1Ligand/IonIMIDAZOLE
6MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
7MRD-1Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:37 , GLU A:84 , ASN A:107 , CA A:202 , ADA A:212 , HOH A:401 , HOH A:424binding site for residue CA A 201
02AC2SOFTWAREGLU A:39 , GLU A:84 , CA A:201 , ADA A:212 , ADA A:213 , HOH A:338binding site for residue CA A 202
03AC3SOFTWAREASP A:64 , GLU A:84 , ASP A:85 , ADA A:213 , HOH A:375 , HOH A:388binding site for residue CA A 203
04AC4SOFTWAREASP A:81 , VAL A:82 , GLU A:104 , HOH A:356 , HOH A:359 , HOH A:423 , HOH A:505binding site for residue CA A 204
05AC5SOFTWAREVAL A:154 , LYS A:155 , ASN A:177binding site for residue IMD A 205
06AC6SOFTWARELYS A:119 , TYR A:145 , GLU A:147 , PRO A:164 , SER A:186 , SER A:188 , GLN A:189 , TYR A:193 , HOH A:405 , HOH A:406 , HOH A:413binding site for residue MPD A 206
07AC7SOFTWARETHR A:0 , ASN A:1 , GLY A:4 , HOH A:438 , LEU B:6 , ILE B:12 , TYR B:20binding site for residue MPD A 207
08AC8SOFTWAREILE A:8 , ILE A:12 , TYR A:20 , HOH A:442 , THR B:0 , ASN B:1 , GLY B:4binding site for residue MRD A 208
09AC9SOFTWAREASP A:64 , LYS A:90 , ASN A:113 , ADA A:213 , HOH A:302 , HOH A:331 , HOH A:375 , HOH A:388 , HOH A:498 , HOH A:527 , HOH A:534 , HOH A:557 , HOH A:571binding site for residue MRD A 209
10AD1SOFTWAREASN A:107 , GLY A:129 , LYS A:130 , SER A:156 , HOH A:369binding site for residue CL A 210
11AD2SOFTWAREASN A:1 , LEU A:6 , ILE A:25 , HOH A:485 , TYR B:20 , HOH B:478binding site for residue MPD B 201
12AD3SOFTWAREGLN B:37 , GLU B:84 , ASN B:107 , CA B:203 , ADA B:210 , ADA B:213 , HOH B:360 , HOH B:401 , HOH B:413binding site for residue CA B 202
13AD4SOFTWAREGLU B:39 , GLU B:84 , CA B:202 , ADA B:210 , ADA B:211 , ADA B:213 , ADA B:214 , HOH B:343binding site for residue CA B 203
14AD5SOFTWAREASP B:64 , GLU B:84 , ASP B:85 , ADA B:211 , ADA B:214 , HOH B:349 , HOH B:410binding site for residue CA B 204
15AD6SOFTWAREASP B:81 , VAL B:82 , GLU B:104 , HOH B:376 , HOH B:377 , HOH B:388 , HOH B:502binding site for residue CA B 205
16AD7SOFTWARELYS B:119 , GLU B:147 , TYR B:193 , HOH B:308binding site for residue IMD B 206
17AD8SOFTWARETHR A:139 , HOH A:475 , ASP B:148 , ASN B:172 , HOH B:315 , HOH B:366binding site for residue MPD B 207
18AD9SOFTWAREASN B:107 , GLY B:129 , LYS B:130 , SER B:156 , GTR B:212 , HOH B:344binding site for residue CL B 208
19AE1SOFTWARELYS A:103 , ASN B:107 , LYS B:130 , ARG B:133 , LYS B:160 , CL B:208 , ADA B:209 , ADA B:210 , ADA B:213 , HOH B:306 , HOH B:314 , HOH B:345 , HOH B:379 , HOH B:411binding site for residue GTR B 212
20AE2SOFTWARELYS A:103 , GLU B:39 , GLU B:84 , ASN B:107 , GLN B:111 , ARG B:133 , ASN B:135 , GLY B:136 , CA B:202 , CA B:203 , ADA B:209 , ADA B:210 , ADA B:211 , GTR B:212 , ADA B:214 , HOH B:343 , HOH B:358 , HOH B:402 , HOH B:413 , HOH B:456binding site for residue ADA B 213
21AE3SOFTWAREHOH A:320 , GLU B:39 , GLU B:84 , ASP B:85 , GLN B:111 , ASN B:113 , ASN B:135 , CA B:203 , CA B:204 , ADA B:210 , ADA B:211 , ADA B:213 , HOH B:336 , HOH B:349 , HOH B:354 , HOH B:370 , HOH B:410 , HOH B:447 , HOH B:456binding site for residue ADA B 214
22AE4SOFTWAREGLU A:39 , GLU A:84 , ASP A:85 , ASN 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 , HOH A:302 , HOH A:310 , HOH A:321 , HOH A:336 , HOH A:338 , HOH A:340 , HOH A:341 , HOH A:360 , HOH A:361 , HOH A:372 , HOH A:375 , HOH A:383 , HOH A:385 , HOH A:388 , HOH A:424 , HOH A:434 , HOH A:457 , HOH A:490 , HOH A:492binding site for Poly-Saccharide residues ADA A 211 through ADA A 213
23AE5SOFTWAREGLU A:39 , ASP A:64 , GLU A:84 , ASP A:85 , LYS A:90 , LYS A:103 , ASN A:107 , GLN A:111 , ASN A:113 , GLY A:129 , LYS A:130 , ARG A:133 , ASN A:135 , GLY A:136 , SER A:156 , LYS A:160 , CA A:201 , CA A:202 , CA A:203 , HOH A:302 , HOH A:310 , HOH A:320 , HOH A:321 , HOH A:331 , HOH A:336 , HOH A:338 , HOH A:340 , HOH A:341 , HOH A:360 , HOH A:361 , HOH A:369 , HOH A:372 , HOH A:375 , HOH A:383 , HOH A:385 , HOH A:388 , HOH A:396 , HOH A:424 , HOH A:434 , HOH A:457 , HOH A:490 , HOH A:492 , HOH A:498 , HOH A:527 , HOH A:534 , HOH A:557 , HOH A:571 , GLU B:39 , GLU B:84 , ASP B:85 , ASN 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:202 , CA B:203 , CA B:204 , CL B:208 , ADA B:214 , HOH B:306 , HOH B:314 , HOH B:336 , HOH B:343 , HOH B:345 , HOH B:349 , HOH B:354 , HOH B:358 , HOH B:360 , HOH B:370 , HOH B:379 , HOH B:402 , HOH B:410 , HOH B:411 , HOH B:413 , HOH B:415 , HOH B:447 , HOH B:456binding site for Poly-Saccharide residues ADA B 209 through ADA B 211

(-) SS Bonds  (0, 0)

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

(-) 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 4YZX)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YZX)

(-) 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
                 4yzx A  -4 HHVGTNTGGVLVITDTIIVKSGQTYDGKGIKIIAQGMGDGSQSENQKPIFKLEKGANLKNVIIGAPGCDGIHCYGDNVVENVVWEDVGEDALTVKSEGVVEVIGGSAKEAANAVFQLNAPCTFKVKNFTATNIGKLVRQNGNTTFKVVIYLEDVTLNNVKSCVAKSDSPVSELWYHNLNVNNCKTLFEFPSQSQIHQY 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......eeeeeeeeeeeeeeeee..hhh.eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yzx B  -1 GTNTGGVLVITDTIIVKSGQTYDGKGIKIIAQGMGDGSQSENQKPIFKLEKGANLKNVIIGAPGCDGIHCYGDNVVENVVWEDVGEDALTVKSEGVVEVIGGSAKEAANAVFQLNAPCTFKVKNFTATNIGKLVRQNGNTTFKVVIYLEDVTLNNVKSCVAKSDSPVSELWYHNLNVNNCKTLFEFPSQSQIHQY 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)
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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 4YZX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 4yz0 4yza 4yzq 4z03 4z05 4z06

(-) Related Entries Specified in the PDB File

4yz0 4yza 4yzq 4z03 4z05 4z06