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(-) Description

Title :  CRYSTAL STRUCTURE OF PROBABLE SUGAR KINASE PROTEIN FROM RHIZOBIUM ETLI CFN 42 COMPLEXED WITH N-(HYDROXYMETHYL)BENZAMIDE
 
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 :  19 Apr 13  (Deposition) - 22 May 13  (Release) - 22 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 N-(Hydroxymethyl)Benzamide
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, 36)

Asymmetric/Biological Unit (5, 36)
No.NameCountTypeFull Name
11Q88Ligand/IonN-(HYDROXYMETHYL)BENZAMIDE
2ADN2Ligand/IonADENOSINE
3DMS4Ligand/IonDIMETHYL SULFOXIDE
4K2Ligand/IonPOTASSIUM ION
5MSE20Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
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:547BINDING SITE FOR RESIDUE ADN A 401
02AC2SOFTWARESER A:188 , PHE A:189 , ASP A:192 , LEU A:218 , SER A:219 , THR A:223 , ASP A:224 , HOH A:612 , HIS B:98 , HOH B:685BINDING SITE FOR RESIDUE 1Q8 A 402
03AC3SOFTWAREILE A:14 , ALA A:41 , GLU A:42 , TYR A:45 , ARG A:112 , DMS A:404 , 1Q8 B:401BINDING SITE FOR RESIDUE DMS A 403
04AC4SOFTWAREARG A:112 , DMS A:403 , 1Q8 B:401BINDING SITE FOR RESIDUE DMS A 404
05AC5SOFTWAREARG A:195 , LEU A:220 , GLN A:222 , ARG A:232 , HOH A:657 , HOH A:665 , HOH A:683 , HOH A:744 , ARG B:93BINDING SITE FOR RESIDUE 1Q8 A 405
06AC6SOFTWAREILE A:36 , ASP A:37 , LEU A:129 , ASP A:159 , HOH A:524 , HOH A:764BINDING SITE FOR RESIDUE 1Q8 A 406
07AC7SOFTWAREGLN A:83 , ASP A:86 , ILE A:87 , HOH A:535 , HOH A:696 , TYR B:45 , ARG B:112 , DMS B:404 , DMS B:405BINDING SITE FOR RESIDUE 1Q8 A 407
08AC8SOFTWAREASP A:270 , THR A:272 , VAL A:306 , GLN A:309 , GLY A:311BINDING SITE FOR RESIDUE K A 408
09AC9SOFTWARETYR A:45 , ARG A:112 , DMS A:403 , DMS A:404 , GLN B:83 , ASP B:86 , ILE B:87 , HOH B:664 , HOH B:687BINDING SITE FOR RESIDUE 1Q8 B 401
10BC1SOFTWAREASN B:9 , ILE B:11 , ASP B:13 , MSE B:33 , GLY B:56 , GLY B:57 , SER B:58 , ASN B:61 , 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 402
11BC2SOFTWAREARG A:1 , HIS A:98 , SER B:188 , PHE B:189 , ASP B:192 , LEU B:218 , SER B:219 , THR B:223 , ASP B:224 , HOH B:590 , HOH B:717BINDING SITE FOR RESIDUE 1Q8 B 403
12BC3SOFTWARE1Q8 A:407 , ILE B:14 , ALA B:41 , GLU B:42 , TYR B:45 , ARG B:112 , DMS B:405BINDING SITE FOR RESIDUE DMS B 404
13BC4SOFTWARE1Q8 A:407 , ALA B:38 , PRO B:109 , ARG B:112 , TYR B:128 , DMS B:404 , HOH B:754BINDING SITE FOR RESIDUE DMS B 405
14BC5SOFTWAREARG A:93 , ARG B:195 , LEU B:220 , GLN B:222 , HOH B:518 , HOH B:591 , HOH B:678BINDING SITE FOR RESIDUE 1Q8 B 406
15BC6SOFTWARELEU B:35 , ILE B:36 , ASP B:37 , LEU B:129 , ASP B:159 , HOH B:521BINDING SITE FOR RESIDUE 1Q8 B 407
16BC7SOFTWAREASP B:270 , THR B:272 , VAL B:306 , GLN B:309 , GLY B:311BINDING SITE FOR RESIDUE K B 408

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4K93)

(-) 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 4K93)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4K93)

(-) Exons   (0, 0)

(no "Exon" information available for 4K93)

(-) 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:330
                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains d4k93a_ 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
                 4k93 A  -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
                            |                                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 d4k93b_ 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
                 4k93 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 4K93)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4K93)

(-) 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 4k8k 4k8p 4k8t 4k9c 4k9i 4kad 4kah 4kal 4kan 4kbe 4lbg 4lbx 4lc4 4lca

(-) Related Entries Specified in the PDB File

4e3a RELATED ID: NYSGRC-014306 RELATED DB: TARGETTRACK
4k9c
4k9i