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(-) Description

Title :  STRUCTURE OF THE SALMONELLA ENTERICA N-ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASE
 
Authors :  S. M. Anderson, Z. Wawrzak, E. Gordon, T. Skarina, L. Papazisi, W. F. And A. Savchenko, Center For Structural Genomics Of Infectious Di (Csgid)
Date :  28 Jul 09  (Deposition) - 04 Aug 09  (Release) - 14 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Salmonella, Energy Metabolism, Sugars, Csgid, Carbohydrate Metabolism, Isomerase, Structural Genomics, Center For Structural Genomics Of Infectious Diseases (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  

PubMed: search

(-) Compounds

Molecule 1 - N-ACETYLMANNOSAMINE-6-PHOSPHATE 2-EPIMERASE 2
    Chains: A, B
    EC Number: 5.1.3.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Gene: NANE2, STM3337
    Mutation: YES
    Organism Scientific: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM
    Organism Taxid: 90371
    Strain: LT2
    Synonym: MANNAC-6-P EPIMERASE 2

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 27)

Asymmetric Unit (4, 27)
No.NameCountTypeFull Name
116G1Ligand/IonN-ACETYL-D-GLUCOSAMINE-6-PHOSPHATE
2CL2Ligand/IonCHLORIDE ION
3MSE10Mod. Amino AcidSELENOMETHIONINE
4SO414Ligand/IonSULFATE ION
Biological Unit 1 (3, 13)
No.NameCountTypeFull Name
116G1Ligand/IonN-ACETYL-D-GLUCOSAMINE-6-PHOSPHATE
2CL-1Ligand/IonCHLORIDE ION
3MSE5Mod. Amino AcidSELENOMETHIONINE
4SO47Ligand/IonSULFATE ION
Biological Unit 2 (2, 12)
No.NameCountTypeFull Name
116G-1Ligand/IonN-ACETYL-D-GLUCOSAMINE-6-PHOSPHATE
2CL-1Ligand/IonCHLORIDE ION
3MSE5Mod. Amino AcidSELENOMETHIONINE
4SO47Ligand/IonSULFATE ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:74 , ARG A:83 , MSE A:154 , TYR A:157 , SER A:208 , ARG A:212 , SO4 A:233 , SO4 A:234 , CL A:238 , HOH A:253 , HOH A:286 , HOH A:331 , HOH A:337 , HOH A:395 , HOH A:504 , HOH A:731 , HOH A:875 , HOH A:878BINDING SITE FOR RESIDUE 16G A 230
02AC2SOFTWAREMSE A:154 , GLY A:156 , TYR A:157 , THR A:158 , THR A:159 , HOH A:257 , HOH A:315 , HOH A:460 , HOH A:668 , HOH A:842BINDING SITE FOR RESIDUE SO4 A 231
03AC3SOFTWARESER A:135 , HOH A:299 , HOH A:303 , HOH A:315 , HOH A:336 , HOH A:638 , HOH A:712BINDING SITE FOR RESIDUE SO4 A 232
04AC4SOFTWAREARG B:83 , MSE B:154 , HOH B:278 , HOH B:411 , HOH B:806BINDING SITE FOR RESIDUE SO4 B 230
05AC5SOFTWARELYS A:74 , ARG A:83 , ARG A:144 , ARG A:212 , 16G A:230 , HOH A:254 , HOH A:773 , HOH A:814BINDING SITE FOR RESIDUE SO4 A 233
06AC6SOFTWAREGLY A:185 , ARG A:186 , GLY A:207 , SER A:208 , 16G A:230 , HOH A:244 , HOH A:394 , HOH A:395 , HOH A:415 , HOH A:487 , HOH A:875BINDING SITE FOR RESIDUE SO4 A 234
07AC7SOFTWAREGLY B:185 , ARG B:186 , GLY B:207 , SER B:208 , HOH B:245 , HOH B:454 , HOH B:538 , HOH B:594 , HOH B:600 , HOH B:853BINDING SITE FOR RESIDUE SO4 B 231
08AC8SOFTWARELYS B:74 , ARG B:83 , ARG B:212BINDING SITE FOR RESIDUE SO4 B 232
09AC9SOFTWAREARG B:62 , GLY B:98 , HOH B:391 , HOH B:416 , HOH B:617 , HOH B:726BINDING SITE FOR RESIDUE SO4 B 233
10BC1SOFTWAREHIS B:215 , TRP B:219 , HOH B:445 , HOH B:560 , HOH B:563 , HOH B:851BINDING SITE FOR RESIDUE SO4 B 234
11BC2SOFTWAREARG A:75 , ASP A:76 , HOH A:401 , HOH A:686 , HOH A:795BINDING SITE FOR RESIDUE SO4 A 235
12BC3SOFTWARESER B:155 , GLY B:156 , TYR B:157 , THR B:158 , THR B:159 , HOH B:305 , HOH B:383 , HOH B:838BINDING SITE FOR RESIDUE SO4 B 235
13BC4SOFTWAREARG A:75 , HOH A:587 , HOH A:835BINDING SITE FOR RESIDUE SO4 A 236
14BC5SOFTWAREARG B:121 , HIS B:124 , HOH B:270 , HOH B:873BINDING SITE FOR RESIDUE SO4 B 236
15BC6SOFTWAREARG A:121 , HOH A:250 , HOH A:291 , HOH A:323 , HOH A:417BINDING SITE FOR RESIDUE SO4 A 237
16BC7SOFTWAREGLN A:22 , ARG A:51 , ILE A:72 , LYS A:74 , 16G A:230 , HOH A:367BINDING SITE FOR RESIDUE CL A 238
17BC8SOFTWAREGLN B:22 , ARG B:51 , LYS B:74 , HOH B:344BINDING SITE FOR RESIDUE CL B 237

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3IGS)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ala B:228 -Ser B:229

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3IGS)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3IGS)

(-) Exons   (0, 0)

(no "Exon" information available for 3IGS)

(-) 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:230
 aligned with NANE2_SALTY | Q8ZLQ7 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:230
                             1                                                                                                                                                                                                                                    
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229
          NANE2_SALTY     - -MSLLEQLDKNIAASGGLIVSCQPVPGSPLDKPEIVAAMALAAEQAGAVAVRIEGIDNLRMTRSLVSVPIIGIIKRDLDESPVRITPFLDDVDALAQAGAAIIAVDGTARQRPVAVEALLARIHHHHLLAMADCSSVDDGLACQRLGADIIGTTMSGYTTPDTPEEPDLPLVKALHDAGCRVIAEGRYNSPALAAEAIRYGAWAVTVGSAITRLEHICGWYNDALKKAAS 229
               SCOP domains d3igsa_ A: automated matches                                                                                                                                                                                                           SCOP domains
               CATH domains 3igsA00 A:0-229 Aldolase class I                                                                                                                                                                                                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh.eeee..........hhhhhhhhhhhhhhh...eeeeehhhhhhhhhh.....eeee..............hhhhhhhhhhhh..eeeee........hhhhhhhhhhhh..eeeee..hhhhhhhhhhh...eee...............hhhhhhhhhhh...eeee....hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3igs A   0 AmSLLEQLDKNIAASGGLIVSCQPVPGSPLDKPEIVAAmALAAEQAGAVAVRIEGIDNLRmTRSLVSVPIIGIIKRDLDESPVRITPFLDDVDALAQAGAAIIAVDGTARQRPVAVEALLARIHHHHLLTmADCSSVDDGLACQRLGADIIGTTmSGYTTPDTPEEPDLPLVKALHDAGCRVIAEGRYNSPALAAEAIRYGAWAVTVGSAITRLEHICGWYNDALKKAAS 229
                             |       9        19        29        39        49        59|       69        79        89        99       109       119       129|      139       149    |  159       169       179       189       199       209       219       229
                             |                                   38-MSE                60-MSE                                                               130-MSE                 154-MSE                                                                       
                             1-MSE                                                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:232
 aligned with NANE2_SALTY | Q8ZLQ7 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:232
                               1                                                                                                                                                                                                                                    
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227  
          NANE2_SALTY     - ---MSLLEQLDKNIAASGGLIVSCQPVPGSPLDKPEIVAAMALAAEQAGAVAVRIEGIDNLRMTRSLVSVPIIGIIKRDLDESPVRITPFLDDVDALAQAGAAIIAVDGTARQRPVAVEALLARIHHHHLLAMADCSSVDDGLACQRLGADIIGTTMSGYTTPDTPEEPDLPLVKALHDAGCRVIAEGRYNSPALAAEAIRYGAWAVTVGSAITRLEHICGWYNDALKKAAS 229
               SCOP domains d3igsb_ B: automated matches                                                                                                                                                                                                             SCOP domains
               CATH domains 3igsB00 B:-2-229 Aldolase class I                                                                                                                                                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh.eeee..........hhhhhhhhhhhhhh....eeeeehhhhhhhhh......eeee..............hhhhhhhhhhh...eeeee........hhhhhhhhhhhh..eeeee..hhhhhhhhhhhh..eee...............hhhhhhhhhhh...eeee....hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3igs B  -2 SNAmSLLEQLDKNIAASGGLIVSCQPVPGSPLDKPEIVAAmALAAEQAGAVAVRIEGIDNLRmTRSLVSVPIIGIIKRDLDESPVRITPFLDDVDALAQAGAAIIAVDGTARQRPVAVEALLARIHHHHLLTmADCSSVDDGLACQRLGADIIGTTmSGYTTPDTPEEPDLPLVKALHDAGCRVIAEGRYNSPALAAEAIRYGAWAVTVGSAITRLEHICGWYNDALKKAAS 229
                               |     7        17        27        37|       47        57  |     67        77        87        97       107       117       127  |    137       147      |157       167       177       187       197       207       217       227  
                               1-MSE                               38-MSE                60-MSE                                                               130-MSE                 154-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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3IGS)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (NANE2_SALTY | Q8ZLQ7)
molecular function
    GO:0047465    N-acylglucosamine-6-phosphate 2-epimerase activity    Catalysis of the reaction: N-acyl-D-glucosamine 6-phosphate = N-acyl-D-mannosamine 6-phosphate.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0016857    racemase and epimerase activity, acting on carbohydrates and derivatives    Catalysis of a reaction that alters the configuration of one or more chiral centers in a carbohydrate molecule.
biological process
    GO:0006051    N-acetylmannosamine metabolic process    The chemical reactions and pathways involving N-acetylmannosamine, the acetylated derivative of mannosamine, 2-amino-2-deoxymannose.
    GO:0019262    N-acetylneuraminate catabolic process    The chemical reactions and pathways resulting in the breakdown of N-acetylneuraminate, the anion of 5-(acetylamino)-3,5-dideoxy-D-glycero-D-galacto-non-3-ulosonic acid.
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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