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(-) Description

Title :  CRYSTAL STRUCTURE OF SPACER 6AA-SHORTENED CEPHALOSPORIN ACYLASE MUTANT
 
Authors :  J. Yin, Z. Zhang, G. Wu, X. Huang
Date :  14 Mar 12  (Deposition) - 20 Mar 13  (Release) - 20 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Cephalosporin Acylase, Spacer, Autocleavage, Hydrolase, Glutaryl-7- Aminocephalosporanic-Acid Acylase, N-Terminal Nucleophile (Ntn) Hydrolase Superfamily (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Yin, Z. Zhang, G. Wu, X. Huang
Spacer Shortened Cephalosporin Acylase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - CEPHALOSPORIN ACYLASE
    Chains: A, B
    EC Number: 3.5.1.93
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 31-719
    Gene: CA, CA1
    Mutation: YES
    Organism Scientific: PSEUDOMONAS SP.
    Organism Taxid: 81841
    Strain: C130

 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  (1, 33)

Asymmetric Unit (1, 33)
No.NameCountTypeFull Name
1CD33Ligand/IonCADMIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION

(-) Sites  (33, 33)

Asymmetric Unit (33, 33)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:662BINDING SITE FOR RESIDUE CD A 701
02AC2SOFTWAREASP A:325BINDING SITE FOR RESIDUE CD A 702
03AC3SOFTWAREGLU A:161 , THR A:192BINDING SITE FOR RESIDUE CD A 703
04AC4SOFTWAREASP A:506BINDING SITE FOR RESIDUE CD A 704
05AC5SOFTWAREASP A:74BINDING SITE FOR RESIDUE CD A 705
06AC6SOFTWAREASP A:123 , HOH A:977 , HOH A:1263BINDING SITE FOR RESIDUE CD A 706
07AC7SOFTWAREHIS A:650 , GLU A:679BINDING SITE FOR RESIDUE CD A 707
08AC8SOFTWAREHIS A:465 , HOH A:1471 , HOH A:1472BINDING SITE FOR RESIDUE CD A 708
09AC9SOFTWAREASP A:555BINDING SITE FOR RESIDUE CD A 709
10BC1SOFTWAREASP A:577BINDING SITE FOR RESIDUE CD A 710
11BC2SOFTWAREASP A:328BINDING SITE FOR RESIDUE CD A 711
12BC3SOFTWAREARG A:264 , GLU A:284BINDING SITE FOR RESIDUE CD A 712
13BC4SOFTWAREASP A:425BINDING SITE FOR RESIDUE CD A 713
14BC5SOFTWAREGLU A:674BINDING SITE FOR RESIDUE CD A 714
15BC6SOFTWAREGLU A:316 , ASP A:320 , CD A:716BINDING SITE FOR RESIDUE CD A 715
16BC7SOFTWARESER A:99 , ASP A:101 , GLU A:316 , CD A:715BINDING SITE FOR RESIDUE CD A 716
17BC8SOFTWAREASP A:329BINDING SITE FOR RESIDUE CD A 717
18BC9SOFTWAREGLU A:610BINDING SITE FOR RESIDUE CD A 718
19CC1SOFTWAREASP A:451 , ASP A:452BINDING SITE FOR RESIDUE CD A 719
20CC2SOFTWAREASP B:123BINDING SITE FOR RESIDUE CD B 701
21CC3SOFTWAREASP B:329BINDING SITE FOR RESIDUE CD B 702
22CC4SOFTWAREASP B:74BINDING SITE FOR RESIDUE CD B 703
23CC5SOFTWAREHIS B:650 , GLU B:679BINDING SITE FOR RESIDUE CD B 704
24CC6SOFTWAREHIS B:465 , HOH B:1430 , HOH B:1432BINDING SITE FOR RESIDUE CD B 705
25CC7SOFTWAREASP B:555BINDING SITE FOR RESIDUE CD B 706
26CC8SOFTWAREASP B:577 , HOH B:1286BINDING SITE FOR RESIDUE CD B 707
27CC9SOFTWAREASP B:328BINDING SITE FOR RESIDUE CD B 708
28DC1SOFTWAREASP B:662BINDING SITE FOR RESIDUE CD B 709
29DC2SOFTWAREGLU B:674BINDING SITE FOR RESIDUE CD B 710
30DC3SOFTWAREASP B:425BINDING SITE FOR RESIDUE CD B 711
31DC4SOFTWAREGLU B:316 , ASP B:320 , CD B:713BINDING SITE FOR RESIDUE CD B 712
32DC5SOFTWARESER B:99 , ASP B:101 , GLU B:316 , CD B:712BINDING SITE FOR RESIDUE CD B 713
33DC6SOFTWAREGLU B:610BINDING SITE FOR RESIDUE CD B 714

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4E57)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Leu A:132 -Pro A:133
2Trp A:417 -Pro A:418
3Thr A:543 -Pro A:544
4Thr A:630 -Pro A:631
5Leu B:132 -Pro B:133
6Trp B:417 -Pro B:418
7Thr B:543 -Pro B:544
8Thr B:630 -Pro B:631

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4E57)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4E57)

(-) Exons   (0, 0)

(no "Exon" information available for 4E57)

(-) 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:677
 aligned with O86089_9PROT | O86089 from UniProtKB/TrEMBL  Length:720

    Alignment length:683
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715   
         O86089_9PROT    36 QAPIAAYKPRSNEILWDGYGVPHIYGVDAPSAFYGYGWAQARSHGDNILRLYGEARGKGAEYWGPDYEQTTVWLLTNGVPERAQQWYAQQSPDFRANLDAFAAGINAYAQQNPDDISPDVRQVLPVSGADVVAHAHRLMNFLYVASPGRTLGEGDPPDLADQGSNSWAVAPGKTANGNALLLQNPHLSWTTDYFTYYEAHLVTPDFEIYGATQIGLPVIRFAFNQRMGITNTVNGMVGATNYRLTLQDGGYLYDGQVRPFERRQASYRLRQADGTTVDKPLEIRSSVHGPVFERADGTAVAVRVAGLDRPGMLEQYFDMITADSFDDYEAALARMQVPTFNIVYADREGTINYSFNGVAPKRAEGDIAFWQGLVPGDSSRYLWTETHPLDDLPRVTNPPGGFVQNSNDPPWTPTWPVTYTPKDFPSYLAPQTPHSLRAQQSVRLMSENDDLTLERFMALQLSHRAVMADRTLPDLIPAALIDPDPEVQAAARLLAAWDREFTSDSRAALLFEEWARLFAGQNFAGQAGFATPWSLDKPVSTPYGVRDPKAAVDQLRTAIANTKRKYGAIDRPFGDASRMILNDVNVPGAAGYGNLGSFRVFTWSDPDENGVRTPVHGETWVAMIEFSTPVRAYGLMSYGNSRQPGTTHYSDQIERVSRADFRELLLRREQVEAAVQERTPFNF 718
               SCOP domains d4e57a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeee.....eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...............------eeeeeee.hhhh.....eeeeeeeee..hhhh.eeeeeee....eeeeeee.......eee...eeeeee......eeeee..ee..eeee..eee..eeeeeeeeee.....eeeeeeeeee.....eee.....eeeeee......hhhhhhhhhhh..hhhhhhhhhh.......eeeeee....eeeee..........hhhhhhheee..hhhhh.....hhhhh.eee.....eee...............hhhhh..........hhhhhhhhhhhhh....hhhhhhhhhh...hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.........hhhhhhhhhhhhh.........eee...........eee.hhhhhhhhhhhhhhhhhhhhh....hhhhhheeee..eeee....hhhhh....eee..........eeeee.eeeeee.....eeeeee...............hhhhhhh...ee...hhhhhhhhh.eeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e57 A   9 QAPIAAYKPRSNEILWDGYGVPHIYGVDAPSAFYGYGWAQARSHGDNILRLYGEARGKGAEYWGPDYEQTTVWLLTNGVPERAQQWYAQQSPDFRANLDAFAAGINAYAQQNPDDISPEVRQVLPVSGADVVAHAHRLMNFLYVASPGRTLGEGDP------GANSWAVAPGKTANGNALLLQNPHLSWTTDYFTYYEAHLVTPDFEIYGATQIGLPVIRFAFNQRMGITNTVNGMVGATNYRLTLQDGGYLYDGQVRPFERRQASYRLRQADGTTVDKPLEIRSSVHGPVFERADGTAVAVRVAGLDRPGMLEQYFDMITADSFDDYEAALARMQVPTFNIVYADREGTINYSFNGVAPKRAEGDIAFWQGLVPGDSSRYLWTETHPLDDLPRVTNPPGGFVQNSNDPPWTPTWPVTYTPKDFPSYLAPQTPHSLRAQQSVRLMSENDDLTLERFMALQLSHRAVMADRTLPDLIPAALIDPDPEVQAAARLLAAWDREFTSDSRAALLFEEWARLFAGQNFAGQAGFATPWSLDKPVSTPYGVRDPKAAVDQLRTAIANTKRKYGAIDRPFGDASRMILNDVNVPGAAGYGNLGSFRVFTWSDPDENGVRTPVHGETWVAMIEFSTPVRAYGLMSYGNSRQPGTTHYSDQIERVSRADFRELLLRREQVEAAVQERTPFNF 685
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158     |   -  |    172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682   
                                                                                                                                                                                     164    165                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:677
 aligned with O86089_9PROT | O86089 from UniProtKB/TrEMBL  Length:720

    Alignment length:683
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715   
         O86089_9PROT    36 QAPIAAYKPRSNEILWDGYGVPHIYGVDAPSAFYGYGWAQARSHGDNILRLYGEARGKGAEYWGPDYEQTTVWLLTNGVPERAQQWYAQQSPDFRANLDAFAAGINAYAQQNPDDISPDVRQVLPVSGADVVAHAHRLMNFLYVASPGRTLGEGDPPDLADQGSNSWAVAPGKTANGNALLLQNPHLSWTTDYFTYYEAHLVTPDFEIYGATQIGLPVIRFAFNQRMGITNTVNGMVGATNYRLTLQDGGYLYDGQVRPFERRQASYRLRQADGTTVDKPLEIRSSVHGPVFERADGTAVAVRVAGLDRPGMLEQYFDMITADSFDDYEAALARMQVPTFNIVYADREGTINYSFNGVAPKRAEGDIAFWQGLVPGDSSRYLWTETHPLDDLPRVTNPPGGFVQNSNDPPWTPTWPVTYTPKDFPSYLAPQTPHSLRAQQSVRLMSENDDLTLERFMALQLSHRAVMADRTLPDLIPAALIDPDPEVQAAARLLAAWDREFTSDSRAALLFEEWARLFAGQNFAGQAGFATPWSLDKPVSTPYGVRDPKAAVDQLRTAIANTKRKYGAIDRPFGDASRMILNDVNVPGAAGYGNLGSFRVFTWSDPDENGVRTPVHGETWVAMIEFSTPVRAYGLMSYGNSRQPGTTHYSDQIERVSRADFRELLLRREQVEAAVQERTPFNF 718
               SCOP domains d4e57b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeee.....eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...............------eeeeeee.hhhh.....eeeeeeeee..hhhh.eeeeeee....eeeeeee.......eee...eeeeee......eeeee..ee..eeee..eee..eeeeeeeeee.....eeeeeeeeee.....eee.....eeeeee......hhhhhhhhhhh..hhhhhhhhhh.......eeeeee....eeeee..........hhhhhhheee..hhhhh.....hhhhh.eee.....eee...............hhhhh..........hhhhhhhhhhhhh....hhhhhhhhhh...hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.........hhhhhhhhhhhhh.........eee...........eee.hhhhhhhhhhhhhhhhhhhhh....hhhhhheeee..eeee....hhhhh....eee..........eeeee.eeeeee.....eeeeee...............hhhhhhh...ee...hhhhhhhhh.eeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e57 B   9 QAPIAAYKPRSNEILWDGYGVPHIYGVDAPSAFYGYGWAQARSHGDNILRLYGEARGKGAEYWGPDYEQTTVWLLTNGVPERAQQWYAQQSPDFRANLDAFAAGINAYAQQNPDDISPEVRQVLPVSGADVVAHAHRLMNFLYVASPGRTLGEGDP------GANSWAVAPGKTANGNALLLQNPHLSWTTDYFTYYEAHLVTPDFEIYGATQIGLPVIRFAFNQRMGITNTVNGMVGATNYRLTLQDGGYLYDGQVRPFERRQASYRLRQADGTTVDKPLEIRSSVHGPVFERADGTAVAVRVAGLDRPGMLEQYFDMITADSFDDYEAALARMQVPTFNIVYADREGTINYSFNGVAPKRAEGDIAFWQGLVPGDSSRYLWTETHPLDDLPRVTNPPGGFVQNSNDPPWTPTWPVTYTPKDFPSYLAPQTPHSLRAQQSVRLMSENDDLTLERFMALQLSHRAVMADRTLPDLIPAALIDPDPEVQAAARLLAAWDREFTSDSRAALLFEEWARLFAGQNFAGQAGFATPWSLDKPVSTPYGVRDPKAAVDQLRTAIANTKRKYGAIDRPFGDASRMILNDVNVPGAAGYGNLGSFRVFTWSDPDENGVRTPVHGETWVAMIEFSTPVRAYGLMSYGNSRQPGTTHYSDQIERVSRADFRELLLRREQVEAAVQERTPFNF 685
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158     |   -  |    172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682   
                                                                                                                                                                                     164    165
   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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4E57)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4E57)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (O86089_9PROT | O86089)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016811    hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides    Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a linear amide.
biological process
    GO:0017000    antibiotic biosynthetic process    The chemical reactions and pathways resulting in the formation of an antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.

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  4e57
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  O86089_9PROT | O86089
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  3.5.1.93
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 Related Entries

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

UniProtKB/Swiss-Prot
        O86089_9PROT | O86089: 1gk0 1gk1
UniProtKB/TrEMBL
        O86089_9PROT | O86089: 1ghd 4e55 4e56

(-) Related Entries Specified in the PDB File

4e55 4e56