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(-) Description

Title :  CRYSTAL STRUCTURE OF D157A MUTANT OF PSEUDOMONAS SP. MIS38 LIPASE
 
Authors :  C. Angkawidjaja, K. Kuwahara, S. Kanaya
Date :  29 Feb 08  (Deposition) - 02 Dec 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.21
Chains :  Asym./Biol. Unit :  A
Keywords :  Family I. 3 Lipase, Beta Roll, Calcium Binding Protein, Rtx Protein, Hydrolase, Calcium Site Mutants (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Kuwahara, C. Angkawidjaja, H. Matsumura, Y. Koga, K. Takano, S. Kanaya
Importance Of The Ca2+-Binding Sites In The N-Catalytic Domain Of A Family I. 3 Lipase For Activity And Stability
Protein Eng. Des. Sel. V. 21 737 2008
PubMed-ID: 18987131  |  Reference-DOI: 10.1093/PROTEIN/GZN057

(-) Compounds

Molecule 1 - LIPASE
    Chains: A
    EC Number: 3.1.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PUC18
    Expression System Strain: DH5
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: PSEUDOMONAS SP.
    Organism Taxid: 91465
    Strain: MIS38
    Synonym: EXTRACELLULAR LIPASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric/Biological Unit (2, 12)
No.NameCountTypeFull Name
1CA10Ligand/IonCALCIUM ION
2ZN2Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:253 , ASP A:275 , ASP A:283 , ASN A:284 , HOH A:687 , HOH A:859BINDING SITE FOR RESIDUE CA A 618
02AC2SOFTWARELYS A:278 , ALA A:281 , ASP A:283 , ASP A:337 , HOH A:680BINDING SITE FOR RESIDUE CA A 619
03AC3SOFTWARESER A:374 , SER A:376 , ASP A:378 , GLY A:391 , ALA A:393 , ASP A:396BINDING SITE FOR RESIDUE CA A 620
04AC4SOFTWAREGLY A:383 , GLY A:385 , ASP A:387 , ASP A:400 , GLY A:402 , ASN A:405BINDING SITE FOR RESIDUE CA A 621
05AC5SOFTWAREARG A:392 , GLY A:394 , ASP A:396 , GLY A:409 , ALA A:411 , ASN A:414BINDING SITE FOR RESIDUE CA A 622
06AC6SOFTWARETHR A:494 , GLY A:496 , ASP A:498 , GLY A:511 , ASP A:513 , ASP A:516BINDING SITE FOR RESIDUE CA A 623
07AC7SOFTWARELEU A:512 , GLY A:514 , ASP A:516 , GLY A:529 , ALA A:531 , ASP A:534BINDING SITE FOR RESIDUE CA A 624
08AC8SOFTWAREGLY A:521 , GLY A:523 , ASP A:525 , SER A:538 , GLY A:540 , ASP A:543BINDING SITE FOR RESIDUE CA A 625
09AC9SOFTWAREGLY A:530 , GLY A:532 , ASP A:534 , PHE A:551 , ASP A:554 , HOH A:676BINDING SITE FOR RESIDUE CA A 626
10BC1SOFTWAREGLY A:541 , THR A:560 , ASN A:562 , ASP A:563 , HOH A:897BINDING SITE FOR RESIDUE CA A 627
11BC2SOFTWAREASP A:128 , HIS A:132BINDING SITE FOR RESIDUE ZN A 628
12BC3SOFTWAREHIS A:517 , GLU A:537BINDING SITE FOR RESIDUE ZN A 629

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ZJ7)

(-) Cis Peptide Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1Ser A:63 -Gln A:64
2Pro A:68 -Gly A:69
3Trp A:72 -Asn A:73
4Ser A:144 -Gly A:145
5Gly A:221 -Gly A:222
6Pro A:458 -Gly A:459
7Gly A:459 -Phe A:460
8Phe A:460 -Leu A:461
9Trp A:462 -Gly A:463
10Lys A:466 -Asp A:467

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ZJ7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ZJ7)

(-) Exons   (0, 0)

(no "Exon" information available for 2ZJ7)

(-) Sequences/Alignments

Asymmetric/Biological 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:616
 aligned with Q9RBY1_9PSED | Q9RBY1 from UniProtKB/TrEMBL  Length:617

    Alignment length:616
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611      
         Q9RBY1_9PSED     2 GVYDYKNFGTADSKALFSDAMAITLYSYHNLDNGFAAGYQHNGFGLGLPATLVTALLGGTDSQGVIPGIPWNPDSEKLALDAVKKAGWTPITASQLGYDGKTDARGTFFGEKAGYTTAQVEILGKYDAQGHLTEIGIAFRGTSGPRENLILDSIGDVINDLLAAFGPKDYAKNYVGEAFGNLLNDVVAFAKANGLSGKDVLVSGHSLGGLAVNSMADLSGGKWGGFFADSNYIAYASPTQSSTDKVLNVGYENDPVFRALDGSTFTGASVGVHDAPKESATDNIVSFNDHYASTAWNLLPFSILNIPTWISHLPTAYGDGMNRIIESKFYDLTSKDSTIIVANLSDPARANTWVQDLNRNAETHKGSTFIIGSDSNDLIQGGSGNDYLEGRAGNDTFRDGGGYNVILGGAGNNTLDLQKSVNTFDFANDGAGNLYVRDANGGISITRDIGSIVTKEPGFLWGLFKDDVTHSVTASGLKVGSNVTQYDASVKGTNGADTLKAHAGGDWLFGLDGNDHLIGGVGNDVFVGGAGNDLMESGGGADTFLFNGAFGQDRVVGFTSNDKLVFLGVQGVLPNDDFRAHASMVGQDTVLKFGGDSVTLVGVALNSLSADGIVIA 617
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HemolysinCabind-2z------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HemolysinCabind-2z------------------------------------------------------------------------ Pfam domains (2)
           Pfam domains (3) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HemolysinCabind-2z------------------------------------------------------------------------ Pfam domains (3)
           Pfam domains (4) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HemolysinCabind-2z------------------------------------------------------------------------ Pfam domains (4)
           Pfam domains (5) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HemolysinCabind-2z------------------------------------------------------------------------ Pfam domains (5)
           Pfam domains (6) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HemolysinCabind-2z------------------------------------------------------------------------ Pfam domains (6)
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.....hhhhhhhhhhh..............hhhhhhhhhhhhh.eee.hhhhhh..........ee.........eeeeeeee.....eeeeeeeee............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhh.eeeeeehhhhhhhhhhhhhh..hhhhh....eeeee..........eeee................hhhhhh............eeeeehhhhh.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.hhhhh....eeeeee.hhhhhh.................eeee......eeee....eeee......eeee....eeee.....eeee...hhhhheeee.....eeee.....eeeee.eeeeeeee.........eeeeeeee..eeee..eee....eee......eee......eee......eee......eee......eee......eeee.....eeeee......eeee..........hhhhheeee..eeeeee..eeeeee..hhhhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zj7 A   2 GVYDYKNFGTADSKALFSDAMAITLYSYHNLDNGFAAGYQHNGFGLGLPATLVTALLGGTDSQGVIPGIPWNPDSEKLALDAVKKAGWTPITASQLGYDGKTDARGTFFGEKAGYTTAQVEILGKYDAQGHLTEIGIAFRGTSGPRENLILDSIGAVINDLLAAFGPKDYAKNYVGEAFGNLLNDVVAFAKANGLSGKDVLVSGHSLGGLAVNSMADLSGGKWGGFFADSNYIAYASPTQSSTDKVLNVGYENDPVFRALDGSTFTGASVGVHDAPKESATDNIVSFNDHYASTAWNLLPFSILNIPTWISHLPTAYGDGMNRIIESKFYDLTSKDSTIIVANLSDPARANTWVQDLNRNAETHKGSTFIIGSDSNDLIQGGSGNDYLEGRAGNDTFRDGGGYNVILGGAGNNTLDLQKSVNTFDFANDGAGNLYVRDANGGISITRDIGSIVTKEPGFLWGLFKDDVTHSVTASGLKVGSNVTQYDASVKGTNGADTLKAHAGGDWLFGLDGNDHLIGGVGNDVFVGGAGNDLMESGGGADTFLFNGAFGQDRVVGFTSNDKLVFLGVQGVLPNDDFRAHASMVGQDTVLKFGGDSVTLVGVALNSLSADGIVIA 617
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611
   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 2ZJ7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2ZJ7)

(-) Pfam Domains  (1, 6)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: HemolysinCabind] (16)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9RBY1_9PSED | Q9RBY1)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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  Cis Peptide Bonds
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    Trp A:72 - Asn A:73   [ RasMol ]  
 

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  2zj7
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  3.1.1.3
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q9RBY1_9PSED | Q9RBY1: 2z8x 2z8z 2zj6 2zvd 3a6z 3a70

(-) Related Entries Specified in the PDB File

2z8x PSEUDOMONAS SP. MIS38 LIPASE PARENT PROTEIN (WILD TYPE)
2z8z S445C MUTANT OF PSEUDOMONAS SP. MIS38 LIPASE
2zj6 D337A MUTANT OF PSEUDOMONAS SP. MIS38 LIPASE