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(-) Description

Title :  C. BESCII FAMILY 3 PECTATE LYASE MUTANT E84A
 
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 :  1.50
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, 14)

Asymmetric Unit (4, 14)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2CL1Ligand/IonCHLORIDE ION
3MPD6Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
4MRD3Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
Biological Unit 1 (2, 7)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3MPD5Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
4MRD2Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
4MRD1Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:81 , VAL A:82 , GLU A:104 , HOH A:366 , HOH A:383 , HOH A:403 , HOH A:497binding site for residue CA A 201
02AC2SOFTWAREASP A:64 , ASP A:85 , HOH A:343 , HOH A:345 , HOH A:388 , HOH A:504binding site for residue CA A 202
03AC3SOFTWAREGLU A:39 , ASN A:40 , LYS A:90 , ASN A:113binding site for residue CL A 203
04AC4SOFTWAREASP A:81 , PRO A:115 , CYS A:116 , THR A:117 , LYS A:141 , VAL A:143 , HOH A:408 , HOH A:428 , HOH A:469binding site for residue MPD A 204
05AC5SOFTWARELEU A:6 , ILE A:12 , TYR A:20 , HOH A:418 , THR B:0 , ASN B:1 , GLY B:4binding site for residue MPD A 205
06AC6SOFTWAREASN A:72 , VAL A:73 , VAL A:94 , GLU A:96binding site for residue MPD A 206
07AC7SOFTWAREASN A:1 , TYR A:20 , HOH A:373 , MRD B:204 , HOH B:477binding site for residue MPD A 207
08AC8SOFTWAREHIS A:171 , GLN A:192 , TYR A:193 , HOH A:329 , GLU B:147 , VAL B:165 , TYR B:193binding site for residue MPD A 208
09AC9SOFTWAREASN A:122 , ASP A:148 , ASN A:172 , HOH A:347 , THR B:139 , HOH B:445 , HOH B:479binding site for residue MRD A 209
10AD1SOFTWARELYS A:49 , HOH A:319 , HOH A:331 , GLN B:30binding site for residue MRD A 210
11AD2SOFTWAREASP B:64 , ASP B:85 , HOH B:311 , HOH B:317 , HOH B:402 , HOH B:414binding site for residue CA B 201
12AD3SOFTWAREASP B:81 , VAL B:82 , GLU B:104 , HOH B:353 , HOH B:379 , HOH B:392 , HOH B:465binding site for residue CA B 202
13AD4SOFTWARETHR B:117 , LYS B:119 , TYR B:145 , GLU B:147 , SER B:186 , SER B:188 , GLN B:189 , HOH B:340binding site for residue MPD B 203
14AD5SOFTWARETHR A:0 , ASN A:1 , GLY A:4 , MPD A:207 , LEU B:6 , ILE B:8 , ILE B:12 , TYR B:20 , HOH B:344binding site for residue MRD B 204

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Z05)

(-) 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 4Z05)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Z05)

(-) Exons   (0, 0)

(no "Exon" information available for 4Z05)

(-) 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: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......eeeeeeeeeeeeeeeee..hhh.eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z05 A  -2 VGTNTGGVLVITDTIIVKSGQTYDGKGIKIIAQGMGDGSQSENQKPIFKLEKGANLKNVIIGAPGCDGIHCYGDNVVENVVWEDVGADALTVKSEGVVEVIGGSAKEAADKVFQLNAPCTFKVKNFTATNIGKLVRQNGNTTFKVVIYLEDVTLNNVKSCVAKSDSPVSELWYHNLNVNNCKTLFEFPSQSQIHQY 193
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187      


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....eeeee..eeeeeeeeeeee...eeeeeeeeeeeeeeeeeee.......eeeeeeeeeeeeeeeeeee......eeeeeeeeeeeeeeeee..hhh.eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z05 B  -2 VGTNTGGVLVITDTIIVKSGQTYDGKGIKIIAQGMGDGSQSENQKPIFKLEKGANLKNVIIGAPGCDGIHCYGDNVVENVVWEDVGADALTVKSEGVVEVIGGSAKEAADKVFQLNAPCTFKVKNFTATNIGKLVRQNGNTTFKVVIYLEDVTLNNVKSCVAKSDSPVSELWYHNLNVNNCKTLFEFPSQSQIHQY 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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  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 4Z05)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Z05)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Z05)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)

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

(-) Related Entries Specified in the PDB File

4yz0 4yza 4yzq 4yzx 4z03 4z06