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(-) Description

Title :  CRYSTAL STRUCTURE OF AMIDOHYDROLASE SARO_0799 (TARGET EFI-505250) FROM NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 WITH BOUND CALCIUM
 
Authors :  Y. Patskovsky, R. Toro, R. Bhosle, B. Hillerich, R. D. Seidel, E. Washin A. Scott Glenn, S. Chowdhury, B. Evans, J. Hammonds, W. D. Zencheck, H J. A. Gerlt, F. M. Raushel, S. C. Almo, Enzyme Function Initiative (
Date :  04 Jan 13  (Deposition) - 16 Jan 13  (Release) - 16 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.48
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Hydrolase, Amidohydrolase, Metal Binding Site, Enzyme Function Initiative, Efi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Patskovsky, R. Toro, R. Bhosle, B. Hillerich, R. D. Seidel, E. Washington, A. Scott Glenn, S. Chowdhury, B. Evans, J. Hammonds, W. D. Zencheck, H. J. Imker, J. A. Gerlt, F. M. Raushel, S. C. Almo
Crystal Structure Of Amidohydrolase Sarp_0799 (Target Efi-505250) From Novosphingobium Aromaticivorans
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - METAL-DEPENDENT HYDROLASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: SARO_0799
    Organism Scientific: NOVOSPHINGOBIUM AROMATICIVORANS
    Organism Taxid: 279238
    Strain: DSM 12444

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 25)

Asymmetric Unit (4, 25)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2CL16Ligand/IonCHLORIDE ION
3GOL1Ligand/IonGLYCEROL
4OXD4Ligand/IonOXALIC ACID
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3GOL1Ligand/IonGLYCEROL
4OXD2Ligand/IonOXALIC ACID
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3GOL-1Ligand/IonGLYCEROL
4OXD2Ligand/IonOXALIC ACID

(-) Sites  (25, 25)

Asymmetric Unit (25, 25)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:19 , HIS A:188 , ASP A:314 , HOH A:535 , HOH A:597 , HOH A:1059BINDING SITE FOR RESIDUE CA A 401
02AC2SOFTWARETYR A:51 , ALA A:208 , HOH A:769 , ARG B:265BINDING SITE FOR RESIDUE CL A 402
03AC3SOFTWARETYR A:121 , PRO A:122 , ASP A:123 , HOH A:935BINDING SITE FOR RESIDUE CL A 403
04AC4SOFTWAREGLU A:169 , ARG A:268 , HOH A:1015BINDING SITE FOR RESIDUE CL A 404
05AC5SOFTWARETYR A:232 , PRO A:233 , SER A:234 , HOH A:827 , HOH A:885BINDING SITE FOR RESIDUE CL A 405
06AC6SOFTWAREARG A:265 , HOH A:746 , TYR B:51 , ALA B:208 , OXD B:408BINDING SITE FOR RESIDUE CL A 406
07AC7SOFTWARELEU A:47 , TYR A:51 , PHE A:212 , TYR A:317 , HOH A:597 , HOH A:750 , HOH A:777 , HOH A:1059BINDING SITE FOR RESIDUE OXD A 407
08AC8SOFTWAREGLU B:19 , HIS B:188 , ASP B:314 , HOH B:503 , HOH B:559 , HOH B:1045BINDING SITE FOR RESIDUE CA B 401
09AC9SOFTWAREGLU B:169 , ARG B:268 , HOH B:867BINDING SITE FOR RESIDUE CL B 402
10BC1SOFTWAREARG B:262 , HOH B:836BINDING SITE FOR RESIDUE CL B 403
11BC2SOFTWAREASP B:41 , GLN B:162 , PRO B:193 , ASP B:194 , HOH B:804 , HOH B:978 , HOH B:1047BINDING SITE FOR RESIDUE GOL B 404
12BC3SOFTWAREHOH A:653 , ARG B:58BINDING SITE FOR RESIDUE CL B 405
13BC4SOFTWAREARG B:141 , HOH B:652 , HOH B:1044 , TYR C:121 , PRO C:122 , ASP C:123BINDING SITE FOR RESIDUE CL B 406
14BC5SOFTWARELYS B:274 , THR B:275BINDING SITE FOR RESIDUE CL B 407
15BC6SOFTWARECL A:406 , HOH A:1061 , LEU B:47 , TYR B:51 , HIS B:188 , PHE B:212 , TYR B:317 , HOH B:559 , HOH B:655 , HOH B:709 , HOH B:1045BINDING SITE FOR RESIDUE OXD B 408
16BC7SOFTWAREGLU C:19 , HIS C:188 , ASP C:314 , HOH C:506 , HOH C:567 , HOH C:1049BINDING SITE FOR RESIDUE CA C 401
17BC8SOFTWARETYR C:51 , GLY C:207 , ALA C:208 , OXD C:406 , ARG D:265 , HOH D:835BINDING SITE FOR RESIDUE CL C 402
18BC9SOFTWAREARG C:58 , HOH D:640BINDING SITE FOR RESIDUE CL C 403
19CC1SOFTWAREGLU C:168 , GLU C:169 , ARG C:268BINDING SITE FOR RESIDUE CL C 404
20CC2SOFTWAREARG C:262BINDING SITE FOR RESIDUE CL C 405
21CC3SOFTWARELEU C:47 , TYR C:51 , HIS C:188 , PHE C:212 , TYR C:317 , CL C:402 , HOH C:567 , HOH C:704 , HOH C:791 , HOH C:1049 , HOH D:710BINDING SITE FOR RESIDUE OXD C 406
22CC4SOFTWAREGLU D:19 , HIS D:188 , ASP D:314 , HOH D:511 , HOH D:594 , HOH D:971BINDING SITE FOR RESIDUE CA D 401
23CC5SOFTWAREARG C:265 , TYR D:51 , ALA D:208 , HOH D:816BINDING SITE FOR RESIDUE CL D 402
24CC6SOFTWARETYR D:121 , PRO D:122 , ASP D:123BINDING SITE FOR RESIDUE CL D 403
25CC7SOFTWARELEU D:47 , TYR D:51 , HIS D:188 , PHE D:212 , TYR D:317 , HOH D:594 , HOH D:604 , HOH D:807 , HOH D:971BINDING SITE FOR RESIDUE OXD D 404

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Ser A:91 -Pro A:92
2Tyr A:315 -Pro A:316
3Ser B:91 -Pro B:92
4Tyr B:315 -Pro B:316
5Ser C:91 -Pro C:92
6Tyr C:315 -Pro C:316
7Ser D:91 -Pro D:92
8Tyr D:315 -Pro D:316

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4INF)

(-) 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:351
                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeeeeee.hhhhhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhh...eeeeee.........hhhhhhhhhhhhhhhhhhhhhhh...eee.......hhhhhhhhhhhhhhh.....eee..........hhhhhhhhhhhhhhh..eee.........hhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh....eeehhhhhh...hhhhhhhhhhhhhhhh..........hhhhhhhhheeee.....hhhhhhhhhhhhh...ee.........hhhhhhhhhh...hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4inf A   1 MTQDLKTGGEQGYLRIATEEAFATREIIDVYLRMIRDGTADKGMVSLWGFYAQSPSERATQILERLLDLGERRIADMDATGIDKAILALTSPGVQPLHDLDEARTLATRANDTLADACQKYPDRFIGMGTVAPQDPEWSAREIHRGARELGFKGIQINSHTQGRYLDEEFFDPIFRALVEVDQPLYIHPATSPDSMIDPMLEAGLDGAIFGFGVETGMHLLRLITIGIFDKYPSLQIMVGHMGEALPYWLYRLDYMHQAGVRSQRYERMKPLKKTIEGYLKSNVLVTNSGVAWEPAIKFCQQVMGEDRVMYAMDYPYQYVADEVRAMDAMDMSAQTKKKFFQTNAEKWFKL 351
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350 


Chain B from PDB  Type:PROTEIN  Length:349
                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeee.hhhhhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhh...eeeeee.........hhhhhhhhhhhhhhhhhhhhhhh...eee.......hhhhhhhhhhhhhhh.....eee..........hhhhhhhhhhhhhhh..eee.........hhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh....eeehhhhhh...hhhhhhhhhhhhhhh...........hhhhhhhhheeee.....hhhhhhhhhhhhh...ee.........hhhhhhhhhh...hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4inf B   3 QDLKTGGEQGYLRIATEEAFATREIIDVYLRMIRDGTADKGMVSLWGFYAQSPSERATQILERLLDLGERRIADMDATGIDKAILALTSPGVQPLHDLDEARTLATRANDTLADACQKYPDRFIGMGTVAPQDPEWSAREIHRGARELGFKGIQINSHTQGRYLDEEFFDPIFRALVEVDQPLYIHPATSPDSMIDPMLEAGLDGAIFGFGVETGMHLLRLITIGIFDKYPSLQIMVGHMGEALPYWLYRLDYMHQAGVRSQRYERMKPLKKTIEGYLKSNVLVTNSGVAWEPAIKFCQQVMGEDRVMYAMDYPYQYVADEVRAMDAMDMSAQTKKKFFQTNAEKWFKL 351
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342         


Chain C from PDB  Type:PROTEIN  Length:348
                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............eeeeeee.hhhhhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhh...eeeeee.........hhhhhhhhhhhhhhhhhhhhhhh...eee.......hhhhhhhhhhhhhhh.....eee..........hhhhhhhhhhhhhhh..eee.........hhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh....eeehhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhheeee.....hhhhhhhhhhhhh...ee.........hhhhhhhhhh...hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4inf C   4 DLKTGGEQGYLRIATEEAFATREIIDVYLRMIRDGTADKGMVSLWGFYAQSPSERATQILERLLDLGERRIADMDATGIDKAILALTSPGVQPLHDLDEARTLATRANDTLADACQKYPDRFIGMGTVAPQDPEWSAREIHRGARELGFKGIQINSHTQGRYLDEEFFDPIFRALVEVDQPLYIHPATSPDSMIDPMLEAGLDGAIFGFGVETGMHLLRLITIGIFDKYPSLQIMVGHMGEALPYWLYRLDYMHQAGVRSQRYERMKPLKKTIEGYLKSNVLVTNSGVAWEPAIKFCQQVMGEDRVMYAMDYPYQYVADEVRAMDAMDMSAQTKKKFFQTNAEKWFKL 351
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343        


Chain D from PDB  Type:PROTEIN  Length:348
                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............eeeeeee.hhhhhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhh....eeeeee.........hhhhhhhhhhhhhhhhhhhhhhh...eee.......hhhhhhhhhhhhhhh.....eee..........hhhhhhhhhhhhhhh..eee.........hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh....eeehhhhhh...hhhhhhhhhhhhhhh...........hhhhhhhhheeee.....hhhhhhhhhhhhh...ee.........hhhhhhhhhh...hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4inf D   4 DLKTGGEQGYLRIATEEAFATREIIDVYLRMIRDGTADKGMVSLWGFYAQSPSERATQILERLLDLGERRIADMDATGIDKAILALTSPGVQPLHDLDEARTLATRANDTLADACQKYPDRFIGMGTVAPQDPEWSAREIHRGARELGFKGIQINSHTQGRYLDEEFFDPIFRALVEVDQPLYIHPATSPDSMIDPMLEAGLDGAIFGFGVETGMHLLRLITIGIFDKYPSLQIMVGHMGEALPYWLYRLDYMHQAGVRSQRYERMKPLKKTIEGYLKSNVLVTNSGVAWEPAIKFCQQVMGEDRVMYAMDYPYQYVADEVRAMDAMDMSAQTKKKFFQTNAEKWFKL 351
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343
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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 4INF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

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  4inf
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  Q2GA79_NOVAD | Q2GA79
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 Related Entries

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

UniProtKB/TrEMBL
        Q2GA79_NOVAD | Q2GA79: 4qrn 4qs5 4qs6 4qtg

(-) Related Entries Specified in the PDB File

4ing THE STRUCTURE OF THE SAME PROTEIN WITH 4-HYDROXY-3-METHOXY- 5-NITROBENZOIC ACID RELATED ID: EFI-505250 RELATED DB: TARGETTRACK