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(-) Description

Title :  C. BESCII FAMILY 3 PECTATE LYASE DOUBLE MUTANT K108A/Q111A 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 :  1.25
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, 30)

Asymmetric Unit (7, 30)
No.NameCountTypeFull Name
1ADA12Ligand/IonALPHA-D-GALACTOPYRANURONIC ACID
2CA9Ligand/IonCALCIUM ION
3GTR2Ligand/IonBETA-D-GALACTOPYRANURONIC ACID
4IMD1Ligand/IonIMIDAZOLE
5MPD4Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
6MRD1Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
7X1X1Ligand/IonALPHA-D-TALOPYRANURONIC ACID
Biological Unit 1 (6, 13)
No.NameCountTypeFull Name
1ADA7Ligand/IonALPHA-D-GALACTOPYRANURONIC ACID
2CA-1Ligand/IonCALCIUM ION
3GTR1Ligand/IonBETA-D-GALACTOPYRANURONIC ACID
4IMD1Ligand/IonIMIDAZOLE
5MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
6MRD1Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
7X1X1Ligand/IonALPHA-D-TALOPYRANURONIC ACID
Biological Unit 2 (3, 8)
No.NameCountTypeFull Name
1ADA5Ligand/IonALPHA-D-GALACTOPYRANURONIC ACID
2CA-1Ligand/IonCALCIUM ION
3GTR1Ligand/IonBETA-D-GALACTOPYRANURONIC ACID
4IMD-1Ligand/IonIMIDAZOLE
5MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
6MRD-1Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
7X1X-1Ligand/IonALPHA-D-TALOPYRANURONIC ACID

(-) Sites  (26, 26)

Asymmetric Unit (26, 26)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:81 , VAL A:82 , GLU A:104 , HOH A:365 , HOH A:376 , HOH A:417 , HOH A:510binding site for residue CA A 201
02AC2SOFTWAREASP A:64 , GLU A:84 , ASP A:85 , ADA A:212 , ADA A:215 , ADA A:218 , HOH A:345 , HOH A:401binding site for residue CA A 202
03AC3SOFTWAREGLU A:39 , GLU A:84 , CA A:204 , ADA A:211 , ADA A:212 , ADA A:214 , ADA A:215 , ADA A:217 , ADA A:218 , HOH A:339binding site for residue CA A 203
04AC4SOFTWAREGLN A:37 , GLU A:84 , ASP A:107 , CA A:203 , ADA A:211 , ADA A:214 , ADA A:217 , HOH A:392 , HOH A:412 , HOH A:426binding site for residue CA A 204
05AC5SOFTWAREX1X A:210 , ADA A:211 , ADA A:213 , ADA A:214 , GTR A:216 , ADA A:217 , HOH A:439 , HOH A:521 , HOH A:526binding site for residue CA A 205
06AC6SOFTWARELYS A:119 , TYR A:145 , GLU A:147 , SER A:186 , GLN A:189 , TYR A:193 , HOH A:338binding site for residue MPD A 206
07AC7SOFTWARETHR A:0 , ASN A:1 , GLY A:4 , LEU B:6 , ILE B:12 , TYR B:20 , HOH B:465binding site for residue MPD A 207
08AC8SOFTWAREILE A:8 , ILE A:12 , TYR A:20 , HOH A:428 , ASN B:1 , GLY B:4binding site for residue MRD A 208
09AC9SOFTWAREVAL A:154 , LYS A:155 , ASN A:177 , HOH A:306binding site for residue IMD A 209
10AD1SOFTWAREASP A:107 , LYS A:130 , ARG A:133 , LYS A:160 , CA A:205 , ADA A:211 , ADA A:213 , ADA A:214 , GTR A:216 , ADA A:217 , HOH A:337 , HOH A:350 , HOH A:394 , HOH A:415 , HOH A:421binding site for residue X1X A 210
11AD2SOFTWAREGLU A:39 , GLU A:84 , ASP A:107 , ARG A:133 , ASN A:135 , GLY A:136 , CA A:203 , CA A:204 , CA A:205 , X1X A:210 , ADA A:212 , ADA A:213 , ADA A:214 , ADA A:215 , GTR A:216 , ADA A:217 , ADA A:218 , HOH A:339 , HOH A:392 , HOH A:434 , HOH A:439 , HOH A:472binding site for residue ADA A 211
12AD3SOFTWAREGLU A:39 , GLU A:84 , ASP A:85 , ASN A:113 , ASN A:135 , CA A:202 , CA A:203 , ADA A:211 , ADA A:214 , ADA A:215 , ADA A:217 , ADA A:218 , HOH A:316 , HOH A:318 , HOH A:339 , HOH A:345 , HOH A:401 , HOH A:456 , HOH A:463 , HOH A:474binding site for residue ADA A 212
13AD4SOFTWARELYS A:54 , ASP A:107 , LYS A:130 , ARG A:133 , LYS A:160 , CA A:205 , X1X A:210 , ADA A:211 , ADA A:213 , ADA A:214 , ADA A:217 , HOH A:325 , HOH A:337 , HOH A:350 , HOH A:415 , HOH A:421 , HOH A:426binding site for residue GTR A 216
14AD5SOFTWAREGLU A:39 , GLU A:84 , ASP A:107 , ARG A:133 , ASN A:135 , GLY A:136 , CA A:203 , CA A:204 , CA A:205 , X1X A:210 , ADA A:211 , ADA A:212 , ADA A:213 , ADA A:214 , ADA A:215 , GTR A:216 , ADA A:218 , HOH A:339 , HOH A:392 , HOH A:434 , HOH A:439 , HOH A:472binding site for residue ADA A 217
15AD6SOFTWAREGLU A:39 , GLU A:84 , ASP A:85 , ASN A:113 , ASN A:135 , CA A:202 , CA A:203 , ADA A:211 , ADA A:212 , ADA A:214 , ADA A:215 , ADA A:217 , HOH A:316 , HOH A:318 , HOH A:339 , HOH A:345 , HOH A:401 , HOH A:456 , HOH A:463 , HOH A:474binding site for residue ADA A 218
16AD7SOFTWAREASN A:1 , LEU A:6 , HOH A:495 , ASN B:1 , TYR B:20 , HOH B:483binding site for residue MPD B 201
17AD8SOFTWAREASP B:81 , VAL B:82 , GLU B:104 , HOH B:381 , HOH B:386 , HOH B:420 , HOH B:514binding site for residue CA B 202
18AD9SOFTWAREASP B:64 , GLU B:84 , ASP B:85 , ADA B:209 , ADA B:212 , HOH B:344 , HOH B:429binding site for residue CA B 203
19AE1SOFTWAREGLU B:39 , GLU B:84 , CA B:205 , ADA B:208 , ADA B:209 , ADA B:211 , ADA B:212 , HOH B:347binding site for residue CA B 204
20AE2SOFTWAREGLN B:37 , GLU B:84 , ASP B:107 , CA B:204 , ADA B:208 , ADA B:211 , HOH B:395 , HOH B:426 , HOH B:434binding site for residue CA B 205
21AE3SOFTWARETHR A:139 , ASN B:122 , ASP B:148 , ASN B:172 , HOH B:322 , HOH B:389binding site for residue MPD B 206
22AE4SOFTWARELYS 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:318 , HOH B:370 , HOH B:388 , HOH B:395 , HOH B:419 , HOH B:437 , HOH B:501binding site for residue GTR B 210
23AE5SOFTWARELYS A:103 , GLU B:39 , GLU B:84 , ASP B:107 , ARG B:133 , ASN B:135 , GLY B:136 , CA B:204 , CA B:205 , ADA B:207 , ADA B:208 , ADA B:209 , GTR B:210 , ADA B:212 , HOH B:347 , HOH B:375 , HOH B:426 , HOH B:491binding site for residue ADA B 211
24AE6SOFTWAREHOH A:329 , GLU B:39 , GLU B:84 , ASP B:85 , ASN B:113 , ASN B:135 , CA B:203 , CA B:204 , ADA B:208 , ADA B:209 , ADA B:211 , HOH B:340 , HOH B:343 , HOH B:344 , HOH B:345 , HOH B:347 , HOH B:409 , HOH B:416 , HOH B:429 , HOH B:491binding site for residue ADA B 212
25AE7SOFTWAREGLU A:39 , LYS A:54 , GLU A:84 , ASP A:85 , ASP A:107 , ASN A:113 , LYS A:130 , ARG A:133 , ASN A:135 , GLY A:136 , LYS A:160 , CA A:202 , CA A:203 , CA A:204 , CA A:205 , X1X A:210 , ADA A:211 , ADA A:212 , GTR A:216 , ADA A:217 , ADA A:218 , HOH A:316 , HOH A:318 , HOH A:325 , HOH A:337 , HOH A:339 , HOH A:345 , HOH A:350 , HOH A:392 , HOH A:394 , HOH A:401 , HOH A:415 , HOH A:421 , HOH A:426 , HOH A:434 , HOH A:439 , HOH A:456 , HOH A:463 , HOH A:472 , HOH A:474binding site for Poly-Saccharide residues ADA A 213 through ADA A 215
26AE8SOFTWARETHR A:0 , ASN A:1 , GLY A:4 , ILE A:8 , ILE A:12 , TYR A:20 , GLU A:39 , GLU A:84 , ASP A:85 , LYS A:103 , ASP A:107 , ASN A:113 , ARG A:133 , ASN A:135 , GLY A:136 , VAL A:154 , LYS A:155 , ASN A:177 , CA A:202 , CA A:203 , CA A:204 , CA A:205 , X1X A:210 , ADA A:211 , ADA A:212 , ADA A:213 , GTR A:216 , ADA A:217 , ADA A:218 , HOH A:306 , HOH A:316 , HOH A:318 , HOH A:329 , HOH A:339 , HOH A:345 , HOH A:392 , HOH A:401 , HOH A:428 , HOH A:434 , HOH A:439 , HOH A:456 , HOH A:463 , HOH A:472 , HOH A:474 , ASN B:1 , GLY B:4 , LEU B:6 , ILE B:12 , TYR B:20 , GLU B:39 , GLU B:84 , ASP B:85 , ASP B:107 , ASN B:113 , LYS B:130 , ARG B:133 , ASN B:135 , GLY B:136 , LYS B:160 , CA B:203 , CA B:204 , CA B:205 , GTR B:210 , ADA B:211 , ADA B:212 , HOH B:318 , HOH B:340 , HOH B:343 , HOH B:344 , HOH B:345 , HOH B:347 , HOH B:370 , HOH B:375 , HOH B:388 , HOH B:395 , HOH B:409 , HOH B:416 , HOH B:419 , HOH B:426 , HOH B:429 , HOH B:437 , HOH B:460 , HOH B:465 , HOH B:491binding site for Poly-Saccharide residues ADA B 207 through ADA B 209

(-) SS Bonds  (0, 0)

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

(-) 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 4YZA)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YZA)

(-) 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......eeeeeeeeee.....ee..hhh.eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4yza A  -4 HHVGTNTGGVLVITDTIIVKSGQTYDGKGIKIIAQGMGDGSQSENQKPIFKLEKGANLKNVIIGAPGCDGIHCYGDNVVENVVWEDVGEDALTVKSEGVVEVIGGSAKEAADAVFALNAPCTFKVKNFTATNIGKLVRQNGNTTFKVVIYLEDVTLNNVKSCVAKSDSPVSELWYHNLNVNNCKTLFEFPSQSQIHQY 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:196
                                                                                                                                                                                                                                    
               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
                 4yza B  -2 VGTNTGGVLVITDTIIVKSGQTYDGKGIKIIAQGMGDGSQSENQKPIFKLEKGANLKNVIIGAPGCDGIHCYGDNVVENVVWEDVGEDALTVKSEGVVEVIGGSAKEAADAVFALNAPCTFKVKNFTATNIGKLVRQNGNTTFKVVIYLEDVTLNNVKSCVAKSDSPVSELWYHNLNVNNCKTLFEFPSQSQIHQY 193
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187
   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 4YZA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 4yzq 4yzx 4z03 4z05 4z06

(-) Related Entries Specified in the PDB File

4yz0 4yzq 4yzx 4z03 4z05 4z06