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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ORN_LYS_ARG DECARBOXYLASE FAMILY PROTEIN SAR0482 FROM METHICILLIN-RESISTANT STAPHYLOCOCCUS AUREUS
 
Authors :  M. Oke, L. G. Carter, K. A. Johnson, H. Liu, S. A. Mcmahon, M. F. White, J. H. Naismith
Date :  25 Jan 10  (Deposition) - 21 Jul 10  (Release) - 11 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Oke, L. G. Carter, K. A. Johnson, H. Liu, S. A. Mcmahon, X. Yan, M. Kerou, N. D. Weikart, N. Kadi, M. A. Sheikh, S. Schmelz, M. Dorward, M. Zawadzki, C. Cozens, H. Falconer, H. Powers, I. M. Overton, C. A. J. Van Niekerk, X. Peng, P. Patel, R. A. Garrett, D. Prangishvili C. H. Botting, P. J. Coote, D. T. F. Dryden, G. J. Barton, U. Schwarz-Linek, G. L. Challis, G. L. Taylor, M. F. White, J. H. Naismith
The Scottish Structural Proteomics Facility: Targets, Methods And Outputs.
J. Struct. Funct. Genomics V. 11 167 2010
PubMed-ID: 20419351  |  Reference-DOI: 10.1007/S10969-010-9090-Y

(-) Compounds

Molecule 1 - ORN/LYS/ARG DECARBOXYLASE FAMILY PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDEST14
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Strain: 252

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric/Biological Unit (3, 10)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
3SM7Ligand/IonSAMARIUM (III) ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:80 , THR A:81 , THR A:82 , HIS A:106 , ASP A:181 , ALA A:183 , HIS A:184 , SER A:208 , HIS A:210 , LYS A:211 , SER A:220 , THR B:243 , SER B:244 , SER B:245BINDING SITE FOR RESIDUE PLP A1211
02AC2SOFTWAREGLU A:417BINDING SITE FOR RESIDUE SM A1445
03AC3SOFTWAREASN A:418 , GLU A:421 , HOH A:2068BINDING SITE FOR RESIDUE SM A1446
04AC4SOFTWAREGLU A:425 , GLU A:428BINDING SITE FOR RESIDUE SM A1447
05AC5SOFTWAREASP A:351 , EDO A:1449 , HOH A:2055 , HOH A:2056BINDING SITE FOR RESIDUE SM A1448
06AC6SOFTWAREASP A:351 , SM A:1448BINDING SITE FOR RESIDUE EDO A1449
07AC7SOFTWARETHR A:243 , SER A:244 , SER A:245 , GLY B:80 , THR B:81 , THR B:82 , HIS B:106 , ASP B:181 , ALA B:183 , HIS B:184 , SER B:208 , HIS B:210 , LYS B:211 , SER B:220BINDING SITE FOR RESIDUE PLP B1211
08AC8SOFTWAREGLU B:119BINDING SITE FOR RESIDUE SM B1445
09AC9SOFTWAREGLU B:124BINDING SITE FOR RESIDUE SM B1446
10BC1SOFTWAREGLU B:301 , HOH B:2040BINDING SITE FOR RESIDUE SM B1447

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2X3L)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Val A:23 -Pro A:24
2Tyr A:154 -Pro A:155
3Tyr A:402 -Pro A:403
4Pro A:403 -Pro A:404
5Val B:23 -Pro B:24
6Tyr B:154 -Pro B:155
7Tyr B:402 -Pro B:403
8Pro B:403 -Pro B:404

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2X3L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2X3L)

(-) Exons   (0, 0)

(no "Exon" information available for 2X3L)

(-) 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:420
                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhh..eee...........hhhhhhhhhh..............hhhhhhhhhhh....eeeeee.hhhhhhhhhhhhh.......eee....hhhhhhhhhhhh..eee.eeee......eeeee...eeeee.........hhhhhhhhhhhh...eeee..............hhhhhh..eeeehhhhhh......eeeeee....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..eeee.....eeeee....hhhhhhhhhhhh.eee.ee....eeee..........hhhhhhhhhhh..............eee....ee.hhh.........eee.............hhhhhhhhhhhhhh..eee.ee..ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2x3l A   5 PILNKLESLNQEEAISLHVPGHKNMTIGHLSQLSMTMDKTEIPGLDDLHHPEEVILKSMKQVEKHSDYDGYFLVNGTTSGILSVIQSFSQKKGDILMARNVHKSVLHALDISQQEGHFIETHQSPLTNHYNKVNLHKLVVLTYPNYYGETFNVEEVIKSLHQLNIPVLIDEAHGAHFGLQGFPDSTLNYQADYVVQSFHKTLPALTMGSVLYIHKNAPYRENIIEYLSYFQTSSPSYLIMASLESAAQFYKTYDSTLFFAKRAQLIECLENKGFEMLQVDDPLKLLIKYEGFTGHDIQNWFMNAHIYLELADDYQALAILPLWHHDDTYLFDSLLRKIEDMILPKKSTQLLTTEGNYKPKWCDLKKAKGKVLARHIVPYPPGIPIIFKGETITENMIELVNEYLETGMIVEGIKNNKILV 443
                                    14        24        34        44        54        64        74        84        94       104       114       124       134    || 151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351      |367       377|      393       403       413       423       433       443
                                                                                                                                                                139|                                                                                                                                                                                                                358|         377|                                                           
                                                                                                                                                                 147                                                                                                                                                                                                                 365          384                                                           


Chain B from PDB  Type:PROTEIN  Length:423
                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhh..eee...........hhhhhhhhhh..............hhhhhhhhhhh....eeeeee.hhhhhhhhhhhhh.......eee....hhhhhhhhhhhh..eee.eeee......eeeee...eeeee.........hhhhhhhhhhhh...eeee..............hhhhhh..eeeehhhhhh......eeeeee....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..eeee.....eeeee....hhhhhhhhhhh..eee.ee....eeee..........hhhhhhhhhhhh.............eee.....eeee.hhh.........eee.............hhhhhhhhhhhhhh..eee.ee..eeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2x3l B   5 PILNKLESLNQEEAISLHVPGHKNMTIGHLSQLSMTMDKTEIPGLDDLHHPEEVILKSMKQVEKHSDYDGYFLVNGTTSGILSVIQSFSQKKGDILMARNVHKSVLHALDISQQEGHFIETHQSPLTNHYNKVNLHKLVVLTYPNYYGETFNVEEVIKSLHQLNIPVLIDEAHGAHFGLQGFPDSTLNYQADYVVQSFHKTLPALTMGSVLYIHKNAPYRENIIEYLSYFQTSSPSYLIMASLESAAQFYKTYDSTLFFAKRAQLIECLENKGFEMLQVDDPLKLLIKYEGFTGHDIQNWFMNAHIYLELADDYQALAILPLWHHDDTYLFDSLLRKIEDMILPKKSVQLLTTEGNYKPKYVTWCDLKKAKGKVLARHIVPYPPGIPIIFKGETITENMIELVNEYLETGMIVEGIKNNKILV 443
                                    14        24        34        44        54        64        74        84        94       104       114       124       134    || 151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       367       377|      390       400       410       420       430       440   
                                                                                                                                                                139|                                                                                                                                                                                                                 359|        377|                                                              
                                                                                                                                                                 147                                                                                                                                                                                                                  366         381
   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 2X3L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2X3L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2X3L)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2X3L)

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 Related Entries

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

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(-) Related Entries Specified in the PDB File

2x3f CRYSTAL STRUCTURE OF THE METHICILLIN-RESISTANT STAPHYLOCOCCUS AUREUS SAR2676, A PANTOTHENATE SYNTHETASE.
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2x3m CRYSTAL STRUCTURE OF HYPOTHETICAL PROTEIN ORF239 FROM PYROBACULUM SPHERICAL VIRUS
2x3n CRYSTAL STRUCTURE OF PQSL, A PROBABLE FAD-DEPENDENT MONOOXYGENASE FROM PSEUDOMONAS AERUGINOSA
2x3o CRYSTAL STRUCTURE OF THE HYPOTHETICAL PROTEIN PA0856 FROM PSEUDOMONAS AERUGINOSA
2x4g CRYSTAL STRUCTURE OF PA4631, A NUCLEOSIDE-DIPHOSPHATE- SUGAR EPIMERASE FROM PSEUDOMONAS AERUGINOSA
2x4h CRYSTAL STRUCTURE OF THE HYPOTHETICAL PROTEIN SSO2273 FROM SULFOLOBUS SOLFATARICUS
2x4j CRYSTAL STRUCTURE OF ORF137 FROM PYROBACULUM SPHERICAL VIRUS
2x4k CRYSTAL STRUCTURE OF SAR1376, A PUTATIVE 4- OXALOCROTONATE TAUTOMERASE FROM THE METHICILLIN-RESISTANT STAPHYLOCOCCUS AUREUS (MRSA)
2x4l CRYSTAL STRUCTURE OF DESE, A FERRIC-SIDEROPHORE RECEPTOR PROTEIN FROM STREPTOMYCES COELICOLOR