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Zinc coordination sphere in biochemical zinc sites

  • David S. Auld
Chapter

Abstract

Zinc is known to be indispensable to growth and development and transmission of the genetic message. It does this through a remarkable mosaic of zinc binding motifs that orchestrate all aspects of metabolism. There are now nearly 200 three dimensional structures for zinc proteins, representing all six classes of enzymes and covering a wide range of phyla and species. These structures provide standards of reference for the identity and nature of zinc ligands in other proteins for which only the primary structure is known. Three primary types of zinc sites are apparent from examination of these structures: structural,catalytic and cocatalytic. The most common amino acids that supply ligands to these sites are His, Glu, Asp and Cys. In catalytic sites zinc generally forms complexes with water and any three nitrogen, oxygen and sulfur donors with His being the predominant amino acid chosen. Water is always a ligand to such sites. Structural zinc sites have four protein ligands and no bound water molecule. Cys is the preferred ligand in such sites. Cocatalytic sites contain two or three metals in close proximity with two of the metals bridged by a side chain moiety of a single amino acid residue, such as Asp, Glu or His and sometimes a water molecule. Asp and His are the preferred amino acids for these sites. No Cys ligands are found in such sites. The scaffolding of the zinc sites is also important to the function and reactivity of the bound metal. The influence of zinc on quaternary protein structure has led to the identification of a fourth type of zinc binding site, protein interface. In this case zinc sites are formed from ligands supplied from amino acid residues residing in the binding surface of two proteins. The resulting zinc site usually has the coordination properties of a catalytic or structural zinc binding site.

Key words

crystal structure metalloenzyme NMR protein sequence X-ray crystallography XAFS or X-ray absorption fine structure 

Abbreviations

ABC

ATP-binding cassette

AAP

Aeromonas proteolytica aminopeptidase

ADA

adenosine deaminase

ADAM

A disintegrin and metalloprotease domain

ADH

alcohol dehydrogenase

ALA

5-aminolevulinic acid

ALAD

5-aminolevulinic acid dehydratase

Apo2L or TRAIL

apoptosis-inducing ligand 2

BIR

baculovirus inhibitor of apoptosis repeat

BLAP

bovine lens leucine aminopeptidase

CA

carbonic anhydrase

CAM

γ-carbonic anhydrase

CPD A

carboxypeptidase A

CDA

cytidine deaminase

EDTA

ethylenediaminetetraacetic acid

eNOS or NOS-3

endothelial nitric oxide synthase

FPP

farnesyl diphosphate

FTase

farnesyl transferase

H4B

tetrahydrobiopterin

HIV

human immunodeficiency virus

GGPP

geranylgeranyl diphosphate

GSNO

S-nitrosoglutathione

HLA-DR

class II major histocompatibility molecule

huIFN

human interferon

IAP

inhibitor of apoptosis

iNOS or NOS-2

inducible nitric oxide synthase

Im3

E. coli immunity protein

IUB

International Union of Biochemistry

MEROPS

system for classification of peptidase sequences

MetAP-1

methionine aminopeptidase-1

MetAP-2

methionine aminopeptidase-2

MHC

major histocompatibility complex

MMP

matrix metalloproteinase

MPD

2-methyl-2,4-pentanediol

NAD

nicotinamide adenine dinucleotide

NADH

reduced nicotinamide adenine dinucleotide

NADP

nicotinamide adenine dinucleotide phosphate

NGF

nerve growth factor

nNOS, NOS-1

neuronal nitric oxide synthase

PAC

perturbed angular correlation of γ-rays

PAP

purple acid phosphatase

PBG

porphobilinogen

PBGS

porphobilinogen synthase

Peptidase

enzyme acting on peptides

PLBP

periplasmic ligand-bindinprotein

PKC

protein kinase C

PMI

phosphomannose isomerase

PTS

signal transducing protein

PsaA

pneumococcal surface antigen

Proteinase

enzyme acting on proteins

SEA, B etc

staphylococcal enterotoxins type A, B etc

SPEA, C etc

streptococcal pyrogenic exotoxins type A, C etc

SMEZ

streptococcal mitogenic exotoxin

SOD

superoxide dismutase

TCR

T cell receptor

TL

thermolysin

TRAP

tartrate-resistant acid phosphatases

TNF

tumor necrosis factor

TACE

tumor necrosis factor-α-converting enzyme

TSST

toxic shock syndrome toxin

VanX

dipeptidase of vancomycin-resistant pathogenic Enterococci

XAFS

X-ray absorption fine structure.

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Copyright information

© Springer Science+Business Media Dordrecht 2001

Authors and Affiliations

  • David S. Auld
    • 1
  1. 1.Center for Biochemical and Biophysical Sciences and Medicine and Department of PathologyHarvard Medical SchoolBostonUSA

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