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(-) Description

Title :  STRUCTURE OF THE CBS PAIR OF A PUTATIVE D-ARABINOSE 5-PHOSPHATE ISOMERASE FROM KLEBSIELLA PNEUMONIAE SUBSP. PNEUMONIAE.
 
Authors :  M. E. Cuff, L. Volkart, J. Bearden, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
Date :  30 Sep 09  (Deposition) - 22 Dec 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Kpsf-Like Protein, Cbs Domain, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. E. Cuff, L. Volkart, J. Bearden, A. Joachimiak
Structure Of The Cbs Pair Of A Putative D-Arabinose 5-Phosphate Isomerase From Klebsiella Pneumoniae Subsp. Pneumoniae.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE D-ARABINOSE 5-PHOSPHATE ISOMERASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PMCSG19
    Expression System Strain: MODIFIED BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: TARGETED DOMAIN 186-331
    Gene: KPN78578_35760, KPN_03607, YRBH
    Organism Scientific: KLEBSIELLA PNEUMONIAE SUBSP. PNEUMONIAE
    Organism Taxid: 272620
    Strain: MGH 78578

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 20)

Asymmetric/Biological Unit (4, 20)
No.NameCountTypeFull Name
1CMK2Ligand/IonCYTIDINE 5'-MONOPHOSPHATE 3-DEOXY-BETA-D-GULO-OCT-2-ULO-PYRANOSONIC ACID
2GOL3Ligand/IonGLYCEROL
3MSE14Mod. Amino AcidSELENOMETHIONINE
4SO41Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:60 , HOH A:61 , HOH A:63 , HOH A:90 , HOH A:129 , HOH A:161 , ILE A:258 , THR A:260 , GLY A:262 , ASP A:263 , ARG A:265 , ARG A:266 , THR A:284 , ILE A:288 , HIS A:307 , ILE A:308 , CYS A:310 , VAL A:311 , HOH A:360 , HOH A:361 , HOH A:373 , ASN B:242 , LEU B:243 , GLY B:244 , ASP B:261 , HIS B:324 , GOL B:332BINDING SITE FOR RESIDUE CMK A 1
2AC2SOFTWAREHOH A:131 , ASN A:242 , GLY A:244 , ASP A:261 , HIS A:324 , HIS A:326 , GOL A:333 , HOH B:3 , HOH B:114 , ILE B:258 , THR B:260 , GLY B:262 , ASP B:263 , ARG B:265 , ARG B:266 , THR B:284 , GLY B:287 , ILE B:288 , HIS B:307 , ILE B:308 , CYS B:310 , VAL B:311 , HOH B:346 , HOH B:366 , HOH B:374 , HOH B:375 , HOH B:381BINDING SITE FOR RESIDUE CMK B 1
3AC3SOFTWAREHOH A:103 , ARG A:291 , GLY A:316 , ASP A:317BINDING SITE FOR RESIDUE SO4 A 332
4AC4SOFTWARECMK A:1 , HIS A:307 , HOH B:141 , HOH B:179 , HIS B:217 , ASN B:242BINDING SITE FOR RESIDUE GOL B 332
5AC5SOFTWAREASN A:242 , LEU A:243 , ASP A:327 , ARG A:330 , CMK B:1BINDING SITE FOR RESIDUE GOL A 333
6AC6SOFTWAREASN A:301 , HOH A:382 , HOH A:386 , HOH A:391BINDING SITE FOR RESIDUE GOL A 334

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3K2V)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3K2V)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3K2V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3K2V)

(-) Exons   (0, 0)

(no "Exon" information available for 3K2V)

(-) 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:130
 aligned with A6TEL6_KLEP7 | A6TEL6 from UniProtKB/TrEMBL  Length:334

    Alignment length:130
                                   211       221       231       241       251       261       271       281       291       301       311       321       331
         A6TEL6_KLEP7   202 GALGRKLLLRVNDIMHTGDEIPHVGLQATLRDALLEITRKNLGMTAICDDDMNIIGIFTDGDLRRVFDTGVDMRDASIADVMTRGGIRIRPGTLAVDALNLMQSRHITCVLVADGDHLLGVVHMHDLLRA 331
               SCOP domains d3k2va_ A: automated matches                                                                                                       SCOP domains
               CATH domains 3k2vA00 A:202-331 CBS-domain                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh..hhhhh.ee....hhhhhhhhhhhhh..eeeee.....eeeeeehhhhhhhhh........hhhhhhee...ee....hhhhhhhhhhhhh..eeeeee..eeeeeeehhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k2v A 202 GALGRKLLLRVNDImHTGDEIPHVGLQATLRDALLEITRKNLGmTAICDDDmNIIGIFTDGDLRRVFDTGVDmRDASIADVmTRGGIRIRPGTLAVDALNLmQSRHITCVLVADGDHLLGVVHmHDLLRA 331
                                   211    |  221       231       241   |   251 |     261       271  |    281 |     291       301 |     311       321   |   331
                                        216-MSE                      245-MSE 253-MSE              274-MSE  283-MSE             303-MSE               325-MSE  


Chain B from PDB  Type:PROTEIN  Length:128
 aligned with A6TEL6_KLEP7 | A6TEL6 from UniProtKB/TrEMBL  Length:334

    Alignment length:128
                                   212       222       232       242       252       262       272       282       292       302       312       322        
         A6TEL6_KLEP7   203 ALGRKLLLRVNDIMHTGDEIPHVGLQATLRDALLEITRKNLGMTAICDDDMNIIGIFTDGDLRRVFDTGVDMRDASIADVMTRGGIRIRPGTLAVDALNLMQSRHITCVLVADGDHLLGVVHMHDLLR 330
               SCOP domains d3k2vb_ B: automated matches                                                                                                     SCOP domains
               CATH domains 3k2vB00 B:203-330 CBS-domain                                                                                                     CATH domains
           Pfam domains (1) ----------------------------------------------------------------------------CBS-3k2vB01 B:279-330                                Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------CBS-3k2vB02 B:279-330                                Pfam domains (2)
           Pfam domains (3) ----------------------------------------------------------------------------CBS-3k2vB03 B:279-330                                Pfam domains (3)
           Pfam domains (4) ----------------------------------------------------------------------------CBS-3k2vB04 B:279-330                                Pfam domains (4)
         Sec.struct. author hhhhhhhhhhhhh..hhhhh.eee...hhhhhhhhhhhhh..eeeee.....eeeeeehhhhhhhhh........hhhhhhee...ee....hhhhhhhhhhhhh..eeeeee..eeeeeeehhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k2v B 203 ALGRKLLLRVNDImHTGDEIPHVGLQATLRDALLEITRKNLGmTAICDDDmNIIGIFTDGDLRRVFDTGVDmRDASIADVmTRGGIRIRPGTLAVDALNLmQSRHITCVLVADGDHLLGVVHmHDLLR 330
                                   212   |   222       232       242  |    252|      262       272 |     282|      292       302|      312       322  |     
                                       216-MSE                      245-MSE 253-MSE              274-MSE  283-MSE             303-MSE               325-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) (23004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: CBS] (51)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (A6TEL6_KLEP7 | A6TEL6)
molecular function
    GO:0019146    arabinose-5-phosphate isomerase activity    Catalysis of the reaction: D-arabinose 5-phosphate = D-ribulose 5-phosphate + 2 H(+).
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    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.

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