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(-) Description

Title :  CRYSTAL STRUCTURE OF GLUTAMATE 5-KINASE FROM CAMPYLOBACTER JEJUNI
 
Authors :  J. Gorman, L. Shapiro, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  03 Aug 05  (Deposition) - 09 Aug 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Structural Genomics, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Gorman, L. Shapiro
Crystal Structure Of Glutamate 5-Kinase From Campylobacter Jejuni
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLUTAMATE 5-KINASE
    Chains: A, B, C, D
    EC Number: 2.7.2.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: MODIFIED PET
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: PROB
    Organism Scientific: CAMPYLOBACTER JEJUNI
    Organism Taxid: 197
    Synonym: GAMMA-GLUTAMYL KINASE, GK

 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  (2, 20)

Asymmetric Unit (2, 20)
No.NameCountTypeFull Name
1ADP4Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MSE16Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 10)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 10)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:11 , SER A:162 , ASP A:163 , ILE A:164 , GLY A:166 , PHE A:167 , TYR A:168 , LYS A:170 , ASN A:171 , PRO A:172 , SER A:173 , THR A:204 , GLY A:206 , ILE A:207 , LYS A:210 , HOH A:891 , HOH A:1009 , HOH A:1017 , HOH A:1026 , HOH A:1039 , HOH A:1040BINDING SITE FOR RESIDUE ADP A 852
2AC2SOFTWAREHIS B:11 , SER B:162 , ASP B:163 , ILE B:164 , GLY B:166 , PHE B:167 , TYR B:168 , ASN B:171 , SER B:173 , THR B:204 , GLY B:206 , ILE B:207 , LYS B:210 , HOH B:864 , HOH B:868 , HOH B:900 , HOH B:965 , HOH B:968 , HOH B:986BINDING SITE FOR RESIDUE ADP B 853
3AC3SOFTWAREHIS C:11 , SER C:162 , ASP C:163 , ILE C:164 , GLY C:166 , PHE C:167 , TYR C:168 , LYS C:170 , ASN C:171 , SER C:173 , THR C:204 , GLY C:206 , ILE C:207 , LYS C:210 , HOH C:864 , HOH C:926 , HOH C:958 , HOH C:959 , HOH C:997 , HOH C:1001 , HOH C:1016BINDING SITE FOR RESIDUE ADP C 854
4AC4SOFTWAREHIS D:11 , ASP D:141 , SER D:162 , ASP D:163 , ILE D:164 , GLY D:166 , PHE D:167 , TYR D:168 , ASN D:171 , PRO D:172 , SER D:173 , THR D:204 , GLY D:206 , ILE D:207 , LYS D:210 , HOH D:888 , HOH D:895 , HOH D:976 , HOH D:998BINDING SITE FOR RESIDUE ADP D 855

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2AKO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLUTAMATE_5_KINASEPS00902 Glutamate 5-kinase signature.PROB_CAMJE200-217
 
 
 		  4A:202-217
B:202-217
C:202-217
D:202-217
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLUTAMATE_5_KINASEPS00902 Glutamate 5-kinase signature.PROB_CAMJE200-217
 
 
 		  2A:202-217
B:202-217
-
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLUTAMATE_5_KINASEPS00902 Glutamate 5-kinase signature.PROB_CAMJE200-217
 
 
 		  2-
-
C:202-217
D:202-217

(-) Exons   (0, 0)

(no "Exon" information available for 2AKO)

(-) 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:241
 aligned with PROB_CAMJE | Q9PJ29 from UniProtKB/Swiss-Prot  Length:251

    Alignment length:250
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251
           PROB_CAMJE     2 KRIVVKVGSHVISEENTLSFERLKNLVAFLAKLMEKYEVILVTSAAISAGHTKLDIDRKNLINKQVLAAIGQPFLISVYNELLAKFNKLGGQILLTGKDFDSRKATKHAKNAIDMMINLGILPIINENDATAIEEIVFGDNDSLSAYATHFFDADLLVILSDIDGFYDKNPSEFSDAKRLEKITHIKEEWLQATIKTGSEHGTGGIVTKLKAAKFLLEHNKKMFLASGFDLSVAKTFLLEDKQIGGTLFE 251
               SCOP domains d2akoa1 A:2-251 Glutamate 5-kinase                                                                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeehhhhhh.....hhhhhhhhhhhhhhhhhhheeeeee.hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhhhhhhhh..eeeeee.....hhhhhh..hhhhhhhhhhhh...eeeeee....................ee...hhhhh---------...hhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhh......eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GLUTAMATE_5_KINASE---------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ako A   2 KRIVVKVGSHVISEENTLSFERLKNLVAFLAKLmEKYEVILVTSAAISAGHTKLDIDRKNLINKQVLAAIGQPFLISVYNELLAKFNKLGGQILLTGKDFDSRKATKHAKNAIDmmINLGILPIINENDATAIEEIVFGDNDSLSAYATHFFDADLLVILSDIDGFYDKNPSEFSDAKRLEKITHIKEEWL---------HGTGGIVTKLKAAKFLLEHNKKmFLASGFDLSVAKTFLLEDKQIGGTLFE 251
                                    11        21        31   |    41        51        61        71        81        91       101       111    || 121       131       141       151       161       171       181       191|        -|      211       221  |    231       241       251
                                                            35-MSE                                                                          116-MSE                                                                     192       202                   224-MSE                       
                                                                                                                                             117-MSE                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:241
 aligned with PROB_CAMJE | Q9PJ29 from UniProtKB/Swiss-Prot  Length:251

    Alignment length:250
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251
           PROB_CAMJE     2 KRIVVKVGSHVISEENTLSFERLKNLVAFLAKLMEKYEVILVTSAAISAGHTKLDIDRKNLINKQVLAAIGQPFLISVYNELLAKFNKLGGQILLTGKDFDSRKATKHAKNAIDMMINLGILPIINENDATAIEEIVFGDNDSLSAYATHFFDADLLVILSDIDGFYDKNPSEFSDAKRLEKITHIKEEWLQATIKTGSEHGTGGIVTKLKAAKFLLEHNKKMFLASGFDLSVAKTFLLEDKQIGGTLFE 251
               SCOP domains d2akob_ B: Glutamate 5-kinase                                                                                                                                                                                                                              SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeehhhhhh.....hhhhhhhhhhhhhhhhhhheeeeee.hhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhhhhhhhhh.eeeeee.....hhhhhh..hhhhhhhhhhhh...eeeeee....................ee...hhhhh---------...hhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhh......eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GLUTAMATE_5_KINASE---------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ako B   2 KRIVVKVGSHVISEENTLSFERLKNLVAFLAKLmEKYEVILVTSAAISAGHTKLDIDRKNLINKQVLAAIGQPFLISVYNELLAKFNKLGGQILLTGKDFDSRKATKHAKNAIDmmINLGILPIINENDATAIEEIVFGDNDSLSAYATHFFDADLLVILSDIDGFYDKNPSEFSDAKRLEKITHIKEEWL---------HGTGGIVTKLKAAKFLLEHNKKmFLASGFDLSVAKTFLLEDKQIGGTLFE 251
                                    11        21        31   |    41        51        61        71        81        91       101       111    || 121       131       141       151       161       171       181       191|        -|      211       221  |    231       241       251
                                                            35-MSE                                                                          116-MSE                                                                     192       202                   224-MSE                       
                                                                                                                                             117-MSE                                                                                                                                  


Chain C from PDB  Type:PROTEIN  Length:241
 aligned with PROB_CAMJE | Q9PJ29 from UniProtKB/Swiss-Prot  Length:251

    Alignment length:250
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251
           PROB_CAMJE     2 KRIVVKVGSHVISEENTLSFERLKNLVAFLAKLMEKYEVILVTSAAISAGHTKLDIDRKNLINKQVLAAIGQPFLISVYNELLAKFNKLGGQILLTGKDFDSRKATKHAKNAIDMMINLGILPIINENDATAIEEIVFGDNDSLSAYATHFFDADLLVILSDIDGFYDKNPSEFSDAKRLEKITHIKEEWLQATIKTGSEHGTGGIVTKLKAAKFLLEHNKKMFLASGFDLSVAKTFLLEDKQIGGTLFE 251
               SCOP domains d2akoc_ C: Glutamate 5-kinase                                                                                                                                                                                                                              SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeehhhhhee..eehhhhhhhhhhhhhhhhhhheeeeee.hhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhhhhhhhh..eeeeee.....hhhhhh..hhhhhhhhhhhh...eeeeee....ee...........ee.ee...hhhhh---------...hhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhh......eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GLUTAMATE_5_KINASE---------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ako C   2 KRIVVKVGSHVISEENTLSFERLKNLVAFLAKLmEKYEVILVTSAAISAGHTKLDIDRKNLINKQVLAAIGQPFLISVYNELLAKFNKLGGQILLTGKDFDSRKATKHAKNAIDmmINLGILPIINENDATAIEEIVFGDNDSLSAYATHFFDADLLVILSDIDGFYDKNPSEFSDAKRLEKITHIKEEWL---------HGTGGIVTKLKAAKFLLEHNKKmFLASGFDLSVAKTFLLEDKQIGGTLFE 251
                                    11        21        31   |    41        51        61        71        81        91       101       111    || 121       131       141       151       161       171       181       191|        -|      211       221  |    231       241       251
                                                            35-MSE                                                                          116-MSE                                                                     192       202                   224-MSE                       
                                                                                                                                             117-MSE                                                                                                                                  


Chain D from PDB  Type:PROTEIN  Length:241
 aligned with PROB_CAMJE | Q9PJ29 from UniProtKB/Swiss-Prot  Length:251

    Alignment length:250
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251
           PROB_CAMJE     2 KRIVVKVGSHVISEENTLSFERLKNLVAFLAKLMEKYEVILVTSAAISAGHTKLDIDRKNLINKQVLAAIGQPFLISVYNELLAKFNKLGGQILLTGKDFDSRKATKHAKNAIDMMINLGILPIINENDATAIEEIVFGDNDSLSAYATHFFDADLLVILSDIDGFYDKNPSEFSDAKRLEKITHIKEEWLQATIKTGSEHGTGGIVTKLKAAKFLLEHNKKMFLASGFDLSVAKTFLLEDKQIGGTLFE 251
               SCOP domains d2akod_ D: Glutamate 5-kinase                                                                                                                                                                                                                              SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeehhhhhh.....hhhhhhhhhhhhhhhhhhheeeeee.hhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.....hhhhhh..hhhhhhhhhhhh...eeeeee....................ee...hhhhh---------...hhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhh......eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GLUTAMATE_5_KINASE---------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ako D   2 KRIVVKVGSHVISEENTLSFERLKNLVAFLAKLmEKYEVILVTSAAISAGHTKLDIDRKNLINKQVLAAIGQPFLISVYNELLAKFNKLGGQILLTGKDFDSRKATKHAKNAIDmmINLGILPIINENDATAIEEIVFGDNDSLSAYATHFFDADLLVILSDIDGFYDKNPSEFSDAKRLEKITHIKEEWL---------HGTGGIVTKLKAAKFLLEHNKKmFLASGFDLSVAKTFLLEDKQIGGTLFE 251
                                    11        21        31   |    41        51        61        71        81        91       101       111    || 121       131       141       151       161       171       181       191|        -|      211       221  |    231       241       251
                                                            35-MSE                                                                          116-MSE                                                                     192       202                   224-MSE                       
                                                                                                                                             117-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, 4)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (PROB_CAMJE | Q9PJ29)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004349    glutamate 5-kinase activity    Catalysis of the reaction: L-glutamate + ATP = L-glutamyl 5-phosphate + ADP + H(+).
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0055129    L-proline biosynthetic process    The chemical reactions and pathways resulting in the formation of L-proline, an L-enantiomer of a chiral, cyclic, nonessential alpha-amino acid found in peptide linkage in proteins.
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0006561    proline biosynthetic process    The chemical reactions and pathways resulting in the formation of proline (pyrrolidine-2-carboxylic acid), a chiral, cyclic, nonessential alpha-amino acid found in peptide linkage in proteins.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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