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(-) Description

Title :  C. BESCII FAMILY 3 PECTATE LYASE DOUBLE MUTANT K108A 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 :  1.40
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  (5, 21)

Asymmetric Unit (5, 21)
No.NameCountTypeFull Name
1ADA7Ligand/IonALPHA-D-GALACTOPYRANURONIC ACID
2CA8Ligand/IonCALCIUM ION
3GTR2Ligand/IonBETA-D-GALACTOPYRANURONIC ACID
4MPD3Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
5MRD1Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
Biological Unit 1 (3, 7)
No.NameCountTypeFull Name
1ADA5Ligand/IonALPHA-D-GALACTOPYRANURONIC ACID
2CA-1Ligand/IonCALCIUM ION
3GTR1Ligand/IonBETA-D-GALACTOPYRANURONIC ACID
4MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
5MRD-1Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
Biological Unit 2 (4, 6)
No.NameCountTypeFull Name
1ADA2Ligand/IonALPHA-D-GALACTOPYRANURONIC ACID
2CA-1Ligand/IonCALCIUM ION
3GTR1Ligand/IonBETA-D-GALACTOPYRANURONIC ACID
4MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
5MRD1Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:39 , GLU A:84 , CA A:202 , ADA A:207 , ADA A:208 , ADA A:210 , ADA A:211 , HOH A:364binding site for residue CA A 201
02AC2SOFTWAREGLN A:37 , GLU A:84 , ASP A:107 , CA A:201 , ADA A:207 , ADA A:210 , HOH A:350 , HOH A:370 , HOH A:417binding site for residue CA A 202
03AC3SOFTWAREASP A:64 , GLU A:84 , ASP A:85 , ADA A:208 , ADA A:211 , HOH A:355 , HOH A:426binding site for residue CA A 203
04AC4SOFTWAREASP A:81 , VAL A:82 , GLU A:104 , HOH A:372 , HOH A:379 , HOH A:382 , HOH A:486binding site for residue CA A 204
05AC5SOFTWARELYS A:119 , TYR A:145 , GLU A:147 , PRO A:164 , SER A:186 , TYR A:193binding site for residue MPD A 205
06AC6SOFTWAREASP A:107 , LYS A:130 , ARG A:133 , LYS A:160 , ADA A:206 , ADA A:207 , ADA A:210 , HOH A:303 , HOH A:310 , HOH A:343 , HOH A:350 , HOH A:353 , HOH A:446binding site for residue GTR A 209
07AC7SOFTWAREGLU 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 , ADA A:206 , ADA A:207 , ADA A:208 , GTR A:209 , ADA A:211 , HOH A:310 , HOH A:341 , HOH A:364 , HOH A:370binding site for residue ADA A 210
08AC8SOFTWAREGLU A:39 , GLU A:84 , ASP A:85 , GLN A:111 , ASN A:113 , ASN A:135 , CA A:201 , CA A:203 , ADA A:207 , ADA A:208 , ADA A:210 , HOH A:323 , HOH A:355 , HOH A:364 , HOH A:426 , HOH A:433 , HOH A:448 , HOH A:469 , HOH A:475 , HOH A:485 , HOH A:537binding site for residue ADA A 211
09AC9SOFTWAREGLU B:39 , GLU B:84 , CA B:202 , ADA B:209 , ADA B:210 , HOH B:334binding site for residue CA B 201
10AD1SOFTWAREGLN B:37 , GLU B:84 , ASP B:107 , CA B:201 , ADA B:209 , HOH B:379 , HOH B:400 , HOH B:416binding site for residue CA B 202
11AD2SOFTWAREASP B:64 , GLU B:84 , ASP B:85 , ADA B:210 , HOH B:336 , HOH B:406binding site for residue CA B 203
12AD3SOFTWAREASP B:81 , VAL B:82 , GLU B:104 , HOH B:357 , HOH B:378 , HOH B:384 , HOH B:493binding site for residue CA B 204
13AD4SOFTWARETHR A:0 , ASN A:1 , GLY A:4 , ILE B:12 , TYR B:20 , HOH B:390binding site for residue MPD B 205
14AD5SOFTWAREILE A:25 , ASN B:1 , TYR B:20 , MRD B:207 , HOH B:315 , HOH B:385binding site for residue MPD B 206
15AD6SOFTWAREILE A:8 , ILE A:12 , TYR A:20 , HOH A:447 , ASN B:1 , MPD B:206binding site for residue MRD B 207
16AD7SOFTWAREGLU 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:209 , ADA A:210 , ADA A:211 , HOH A:303 , HOH A:310 , HOH A:323 , HOH A:327 , HOH A:341 , HOH A:343 , HOH A:350 , HOH A:353 , HOH A:355 , HOH A:364 , HOH A:370 , HOH A:426 , HOH A:433 , HOH A:446 , HOH A:448 , HOH A:469 , HOH A:475 , HOH A:537binding site for Poly-Saccharide residues ADA A 206 through ADA A 208
17AD8SOFTWAREILE A:8 , ILE A:12 , TYR A:20 , GLU 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 , ADA A:206 , ADA A:211 , HOH A:303 , HOH A:310 , HOH A:323 , HOH A:341 , HOH A:343 , HOH A:350 , HOH A:353 , HOH A:355 , HOH A:364 , HOH A:366 , HOH A:370 , HOH A:426 , HOH A:433 , HOH A:446 , HOH A:447 , HOH A:448 , HOH A:469 , HOH A:475 , HOH A:537 , ASN B:1 , GLU 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:206 , HOH B:311 , HOH B:312 , HOH B:334 , HOH B:336 , HOH B:347 , HOH B:349 , HOH B:359 , HOH B:371 , HOH B:379 , HOH B:395 , HOH B:400 , HOH B:406 , HOH B:409 , HOH B:429 , HOH B:469binding site for Poly-Saccharide residues GTR B 208 through ADA B 210

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Z03)

(-) 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 4Z03)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Z03)

(-) Exons   (0, 0)

(no "Exon" information available for 4Z03)

(-) 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:195
                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee...eee....eee....eeee...............eee....eeeeeee.......eee...eeeeeeee.......eee...eeeeee..eeeeeeeeeeee...eeeeeeeeeeeeeeeeeee.......eeeeeeeeeeeeeeeeeee......eeeeeeeeee.....ee..hhh.eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z03 A  -1 GTNTGGVLVITDTIIVKSGQTYDGKGIKIIAQGMGDGSQSENQKPIFKLEKGANLKNVIIGAPGCDGIHCYGDNVVENVVWEDVGEDALTVKSEGVVEVIGGSAKEAADAVFQLNAPCTFKVKNFTATNIGKLVRQNGNTTFKVVIYLEDVTLNNVKSCVAKSDSPVSELWYHNLNVNNCKTLFEFPSQSQIHQY 193
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188     


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
                 4z03 B  -2 VGTNTGGVLVITDTIIVKSGQTYDGKGIKIIAQGMGDGSQSENQKPIFKLEKGANLKNVIIGAPGCDGIHCYGDNVVENVVWEDVGEDALTVKSEGVVEVIGGSAKEAADAVFQLNAPCTFKVKNFTATNIGKLVRQNGNTTFKVVIYLEDVTLNNVKSCVAKSDSPVSELWYHNLNVNNCKTLFEFPSQSQIHQY 193
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187
   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 4Z03)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Z03)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Z03)

(-) 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 4yzq 4yzx 4z05 4z06

(-) Related Entries Specified in the PDB File

4yz0 4yza 4yzq 4yzx 4z05 4z06