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(-) Description

Title :  CRYSTAL STRUCTURE OF PROBABLE SUGAR KINASE PROTEIN FROM RHIZOBIUM ETLI CFN 42 COMPLEXED WITH 1-(4-METHOXYPHENYL)-1-CYCLOPROPANE AND 2-AMINOPERIMIDINE
 
Authors :  V. N. Malashkevich, R. Bhosle, R. Toro, B. Hillerich, A. Gizzi, S. Garfo A. Kar, M. K. Chan, J. Lafluer, H. Patel, B. Matikainen, S. Chamala, S. L A. Celikgil, G. Villegas, B. Evans, J. Love, A. Fiser, K. Khafizov, R. S J. B. Bonanno, S. C. Almo, New York Structural Genomics Research Consortium (Nysgrc)
Date :  18 Apr 13  (Deposition) - 01 May 13  (Release) - 08 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Protein Structure Initiative, New York Structural Genomix Researchconsortium, Nysgrc, Psi-Biology, New York Structural Genomics Research Consortium, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. N. Malashkevich, R. Bhosle, R. Toro, B. Hillerich, A. Gizzi, S. Garforth, A. Kar, M. K. Chan, J. Lafluer, H. Patel, B. Matikainen, S. Chamala, S. Lim, A. Celikgil, G. Villegas, B. Evans, J. Love, A. Fiser, K. Khafizov, R. Seidel, J. B. Bonanno, S. C. Almo
Crystal Structure Of Probable Sugar Kinase Protein From Rhizobium Etli Cfn 42 Complexed With 1-(4-Methoxyphenyl)-1-Cyclopropane And 2-Aminoperimidine
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SUGAR KINASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: BC-PSGX3(BC)
    Expression System Strain: BL21(DE3)CODON+RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: RHE_CH00135
    Organism Scientific: RHIZOBIUM ETLI
    Organism Taxid: 347834
    Strain: CFN 42

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 34)

Asymmetric/Biological Unit (5, 34)
No.NameCountTypeFull Name
11PJ2Ligand/Ion1-(4-METHOXYPHENYL)CYCLOPROPANECARBOXYLIC ACID
21PK8Ligand/Ion1H-PERIMIDIN-2-AMINE
3ADN2Ligand/IonADENOSINE
4K2Ligand/IonPOTASSIUM ION
5MSE20Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:9 , ILE A:11 , ASP A:13 , MSE A:33 , GLY A:56 , GLY A:57 , SER A:58 , ASN A:61 , SER A:113 , MSE A:125 , THR A:127 , GLU A:154 , TYR A:156 , THR A:272 , GLY A:273 , ASP A:276 , PRO A:312 , HOH A:503 , HOH A:519 , HOH A:523 , HOH A:548BINDING SITE FOR RESIDUE ADN A 401
02AC2SOFTWAREILE A:14 , ALA A:38 , ALA A:41 , GLU A:42 , TYR A:45 , ARG A:112 , MSE A:114 , TYR A:128 , HOH A:595 , HOH A:613BINDING SITE FOR RESIDUE 1PJ A 402
03AC3SOFTWAREALA A:81 , ASP A:82 , ASP A:86 , ALA A:262 , ILE A:263 , ARG A:264 , 1PK A:404 , HOH A:691 , HOH A:828BINDING SITE FOR RESIDUE 1PK A 403
04AC4SOFTWAREASP A:86 , 1PK A:403 , HOH A:693 , HOH A:822 , 1PK B:401BINDING SITE FOR RESIDUE 1PK A 404
05AC5SOFTWAREGLU A:42 , 1PK A:406 , HOH A:755 , 1PK B:406BINDING SITE FOR RESIDUE 1PK A 405
06AC6SOFTWAREGLU A:42 , 1PK A:405 , HOH B:851BINDING SITE FOR RESIDUE 1PK A 406
07AC7SOFTWAREASP A:270 , THR A:272 , VAL A:306 , GLN A:309 , GLY A:311BINDING SITE FOR RESIDUE K A 407
08AC8SOFTWARE1PK A:404 , GLU B:42 , 1PK B:402 , 1PJ B:404 , HOH B:809BINDING SITE FOR RESIDUE 1PK B 401
09AC9SOFTWAREASN A:247 , GLU B:42 , 1PK B:401BINDING SITE FOR RESIDUE 1PK B 402
10BC1SOFTWAREASN B:9 , ILE B:11 , ASP B:13 , MSE B:33 , GLY B:56 , GLY B:57 , SER B:58 , ASN B:61 , SER B:113 , MSE B:125 , THR B:127 , GLU B:154 , TYR B:156 , THR B:272 , GLY B:273 , ASP B:276 , PRO B:312 , HOH B:501 , HOH B:511 , HOH B:535 , HOH B:551BINDING SITE FOR RESIDUE ADN B 403
11BC2SOFTWAREHOH A:736 , ILE B:14 , ALA B:38 , ALA B:41 , GLU B:42 , TYR B:45 , PRO B:109 , ARG B:112 , MSE B:114 , TYR B:128 , 1PK B:401 , HOH B:744BINDING SITE FOR RESIDUE 1PJ B 404
12BC3SOFTWAREALA B:81 , ASP B:82 , ASP B:86 , 1PK B:406 , HOH B:834 , HOH B:850BINDING SITE FOR RESIDUE 1PK B 405
13BC4SOFTWARE1PK A:405 , ASP B:86 , 1PK B:405BINDING SITE FOR RESIDUE 1PK B 406
14BC5SOFTWAREASP B:270 , THR B:272 , VAL B:306 , GLN B:309 , GLY B:311BINDING SITE FOR RESIDUE K B 407

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4K8K)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Phe A:107 -Pro A:108
2Phe B:107 -Pro B:108

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4K8K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4K8K)

(-) Exons   (0, 0)

(no "Exon" information available for 4K8K)

(-) 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:331
                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains d4k8ka_ A: automated matches                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee...eeeeeee.hhhhhhhh......eee.hhhhhhhhhhhh...eeee.hhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhh..ee...........eeeeeee.....eeeeeehhhhhhhhhhhhhhhhhhheeeeeee.hhhh..hhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhh....eeeeehhhhhhhhh..hhhhhhhhhhhhh.eeeee.hhh.eeeee..eeeee............hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.........hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k8k A  -2 SmTRFDVLTVGNAIVDIISRCNDQFLIDNQITKAAmNLIDAERAELLYSRmGPALEASGGSAGNTAAGVANLGGKAAYFGNVAADQLGDIFTHDIRAQGVHYQTKPKGAFPPTARSmIFVTEDGERSmNTYLGACVELGPEDVEADVVADAKVTYFEGYLWDPPRAKEAILDCARIAHQHGREmSmTLSDSFCVDRYRGEFLDLmRSGKVDIVFANRQEALSLYQTDDFEEALNRIAADCKIAAVTmSENGAVILKGRERYYVNAIRIREVVDTTGAGDLFASGFLYGYTQGRSLEDCGKLGCLAAGIVIQQIGPRPmTSLSEAAKQAGLI 328
                             |       7        17        27     |  37        47|       57        67        77        87        97       107      |117       127       137       147       157       167       177   | | 187       197    |  207       217       227       237      |247       257       267       277       287       297       307       317       327 
                             |                                33-MSE         48-MSE                                                           114-MSE    125-MSE                                                 181-MSE              202-MSE                                   244-MSE                                                                315-MSE         
                            -1-MSE                                                                                                                                                                                 183-MSE                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:330
                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains d4k8kb_ B: automated matches                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee...eeeeeee.hhhhhhhh......eee.hhhhhhhhhhhh...eeee.hhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhh..ee...........eeeeeee.....eeeeeehhhhhhhhhhhhhhhhhhheeeeeee.hhhh..hhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhh....eeeeehhhhhhhhh..hhhhhhhhhhhhh.eeeee.hhh.eeeee..eeeee............hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.........hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4k8k B  -1 mTRFDVLTVGNAIVDIISRCNDQFLIDNQITKAAmNLIDAERAELLYSRmGPALEASGGSAGNTAAGVANLGGKAAYFGNVAADQLGDIFTHDIRAQGVHYQTKPKGAFPPTARSmIFVTEDGERSmNTYLGACVELGPEDVEADVVADAKVTYFEGYLWDPPRAKEAILDCARIAHQHGREmSmTLSDSFCVDRYRGEFLDLmRSGKVDIVFANRQEALSLYQTDDFEEALNRIAADCKIAAVTmSENGAVILKGRERYYVNAIRIREVVDTTGAGDLFASGFLYGYTQGRSLEDCGKLGCLAAGIVIQQIGPRPmTSLSEAAKQAGLI 328
                            |        8        18        28    |   38        48        58        68        78        88        98       108     | 118      |128       138       148       158       168       178  | |  188       198   |   208       218       228       238     | 248       258       268       278       288       298       308      |318       328
                           -1-MSE                            33-MSE         48-MSE                                                           114-MSE    125-MSE                                                 181-MSE              202-MSE                                   244-MSE                                                                315-MSE         
                                                                                                                                                                                                                  183-MSE
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4K8K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4K8K)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/TrEMBL
        Q2KDX6_RHIEC | Q2KDX6: 4e3a 4jks 4jku 4k8c 4k8p 4k8t 4k93 4k9c 4k9i 4kad 4kah 4kal 4kan 4kbe 4lbg 4lbx 4lc4 4lca

(-) Related Entries Specified in the PDB File

4e3a 4k8c 4k8p 4k8t